Artemisia includes several keystone shrub species that dominate the North American sagebrush steppe. Their growth, survival, and establishment are negatively affected by exotic invasive grasses such as Taeniatherum caput-medusae. While the outcomes of symbiotic relationships between Artemisia spp. and arbuscular mycorrhizal fungi (AMF) are ambiguous, the benefits of ameliorated nutrient and drought stress may be cryptic and better revealed under competition. We evaluated the effects of a commercial AMF inoculum on ameliorating biotic (competition with T. caput-medusae) and abiotic (drought) stress of Artemisia tridentata ssp. wyomingensis, Artemisia arbuscula, and Artemisia nova when grown in sterile and microbially active field soil. Stress amelioration was measured as an increase in biomass production and nutrient acquisition. Mycorrhizal colonization of roots was lower in Artemisia plants grown in competition, while T. caput-medusae colonization was higher in plants with greater moisture. Both types of stress negatively affected plant biomass. Commercial AMF inoculation did not increase biomass. Colonization from field soil increased average phosphorous concentration under drought for A. tridentata ssp. wyomingensis by 36% and A. nova by 125%. While commercial inoculum and live soil led to AMF colonization of T. caput-medusae, only the commercial inoculum increased average phosphorus uptake by 71%.The genus  Artemisia species (a keystone plant species) have to endure competition with exotic annual grasses such as Bromus tectorum (cheatgrass), Ventenata dubia (ventenata), and Taeniatherum caput-medusae (medusahead) [Ecosystem deterioration is one of the most important problems in many areas around the world . An apprusahead) . These ausahead) ,6. Anothusahead) ,8,9,10.To survive in harsh environments, plant species have different resource acquisition strategies to be more or less competitive . Yet, moB. tectorum and T. caput-medusae have shown ambiguous results to AMF [T. caput-medusae since inoculation could potentially affect the dynamics of competition. Enhancing the competitive ability of perennial native shrubs using AMF during the establishment phase could be a key step for restoration programs . Howevers to AMF ,25. Furts to AMF ,27. ThusArtemisia tridentata ssp. wyomingensis Beetle and Young (Wyoming big sagebrush), Artemisia arbuscula Nutt (low sagebrush), and Artemisia nova A. Nelson (black sagebrush). A. tridentata ssp. wyomingensis is a known mycorrhizal plant that has been extensively studied for restoration, although mycorrhizal responsiveness is ambiguous, while A. arbuscula and A. nova have been much less studied [Important native plant species from sagebrush steppe include  studied ,29,30,31A. tridentata ssp. wyomingensis, A. arbuscula, and A. nova) during the establishment phase while facing biotic (intraspecific competition from T. caput-medusae) and abiotic (drought) stress. We hypothesized that: (1) a commercial AMF inoculum ameliorates stress in Artemisia spp. imposed by competition from T. caput-medusae and drought, and (2) T. caput-medusae is not more competitive under mycorrhizal conditions.We evaluated the effect of a commercial AMF inoculum on the competitive ability of three sagebrush shrubs , soil type (live field soil or autoclaved field soil), moisture levels (40% and 80% field capacity), competition (presence/absence of T. caput-medusae), and inoculum type . Sham inoculum is the autoclaved substrate (field soil or AMF inoculum) in which we reincorporated a microbial wash to have a media with the soil organisms except for AMF and was included as a control to compare the mycorrhizal effects only [A competition experiment with cts only . For theA. tridentata ssp. wyomingensis, A. nova, and A. arbuscula were obtained from commercial vendors during the summer of 2017, and seeds of T. caput-medusae were collected from the Crooked River National Grasslands during the fall of 2018. Field soil was obtained from the same area where T. caput-medusae was collected, a disturbed sagebrush grassland ecosystem. Coordinates where the soil was sampled are 44°27′50″ N–121°0′57″ W. The collected soil had a loam texture  and a Munsell color 10YR 4/3 (dry) and 10YR 2/2 (wet). The mycorrhizal inoculum was AM120 standard . Label contents of inoculum are 100% Rhizophagus intraradices. Seeds of A. tridentata ssp. wyomingensis, A. arbuscula and A. nova. After germination, only one seedling was left per pot. Moisture treatments began after the 2-week period. Soil moisture treatments (40% and 80% field capacity) were determined using the gravimetric method [Containers were plastic Poly-tainer™ cans of 2.41 L , 15.2 cm (6 in) diameter and 17 cm (7 in) depth. Containers were steam sterilized at 80 °C for 2 h to remove possible contaminants. We added 2 kg of soil to each pot (autoclaved or field), then a layer of 100 g of either mycorrhizal inoculum or sham inoculum, followed by another layer of 100 g of soil. Seeds were sown and kept under constant moisture for two weeks to ensure germination. Multiple seeds were sown in each pot for c method  based onArtemisia species with 15 individuals of T. caput medusae for a density of 600 plants m−2 [T. caput-medusae were sown in each pot, and only fifteen were left. For each combination, we had 5 replicates, giving a total of 240 pots in the study. Competition was simulated by growing each of the ants m−2 . Twenty To account for the microbial communities from the field soil and possibly from the inoculum substrate, we made a microbial wash that was added to sterilized soil to create a sham inoculum with all microbial communities except for AMF from both soil and inoculum . MicrobiAll plants were grown for 6 months (26 weeks). Moisture treatments began after 2 weeks of emergence of germinated seeds to allow establishment of at least one individual in each pot. After the growing period, all plants were manually harvested. Shoots were cut and stored in paper bags. Roots were carefully extracted from the soil, washed, and a subsample was stored in 20 mL vials containing a mixture of 50% ethanol and 5% acetic acid for root colonization measurements. w/v) KOH for 20 min, then rinsed with warm water, followed by an incubation period of 10 min in 1% HCL, incubated then in trypan blue stain  for 20 min, rinsed with warm water, and incubated in de-stain  overnight at room temperature [Roots for colonization were cleared and stained: roots were incubated at 90 °C in 5% , root colonization, and plant nutrient content . Plant nutrient analysis was conducted at the Soil Health Laboratory at Oregon State University. N was analyzed by dry combustion with a direct measure of total nitrogen by Elemental Macro Cube analyzer . Soil nutrients P and K were extracted using a Mehlich 3 solution and quantified on Agilent 5110 ICP-OES. Mycorrhizal effects were subsampled from a fraction of the root system, the rest was used to estimate dry weight. Because of the small root size for all T. caput-medusae) as main effects and block as a random effect. Before analysis, variables that did not meet the normality and equal variance were log10 (x + 1) transformed in order to fulfill assumptions of the model. Data was analyzed using R (2021) with a separate factorial ANOVA for each plant species using soil type (autoclaved or field soil), moisture level (high or low), inoculum , and competition , AMF inoculation , and presence/absence of competition  but not by moisture level . In general, drought and competition resulted in lower colonization, and inoculum addition resulted in a significant colonization increase in autoclaved soils. Colonization was present in inoculated plants . Inoculated plants grown in field soils with both competition and drought had a significant increase in colonization compared to sham-inoculated plants from field soils with competition and drought stress (p = 0.002). Still, this level of colonization was significantly less compared to sham-inoculated plants grown in field soils, under drought, and without competition (p < 0.001). For A. arbuscula, the combination of drought and competition in inoculated plants grown in field soils resulted in a significant decrease in colonization (p = 0.04) (p = 0.007). The species A. nova did not respond with colonization increases with the addition of the inoculum (p > 0.05). The presence of colonization was higher in field soils (p < 0.001). The addition of competition to autoclaved inoculated soils with drought resulted in zero % of colonization for A. tridentata ssp. wyomingensis and A. nova. The species ure only . However = 0.04) . Interesld soils . HoweverT. caput-medusae did not statistically differ when grown as competition with different Artemisia species . Colonization of this species was driven by differences in soil , moisture , and inoculum application . Colonization was greater in high moisture treatments compared to low moisture (p < 0.05). When T. caput-medusae was grown with A. tridentata ssp. wyomingensis and A. arbuscula, inoculation of field soils did not result in significant changes of colonization. However, colonization was greater in low moisture treatments when grown in inoculated field soils with A. nova.Colonization of moisture . InoculaA. tridentata ssp. wyomingensis , A. arbuscula , and A. nova . All 3 Artemisia species produced more biomass when grown alone, compared to plants grown with competition , A. arbuscula , and A. nova  and with shoot/root production for A. tridentata ssp. wyomingensis  and A. arbuscula . Drought treatments resulted in a decrease of biomass production in all three species (p > 0.05), when compared to non-inoculated treatments. Inoculation decreased shoot growth of A. arbuscula and root growth of A. nova when grown without competition in high moisture levels  as field soils produced more biomass without competition. From the three species, A. arbuscula produced the greatest shoot and root biomass when grown in competition at high moisture levels regardless of inoculation  and A. nova  and to root biomass for A. tridentata ssp. wyomingensis . With the exception of sham-inoculated autoclaved soil, treatments with higher shoot and total biomass production were also the treatments with highest colonization for both A. tridentata ssp. wyomingensis and A. nova. ANOVA revealed that colonization was related to total and shoot biomass production for T. caput-medusae total biomass responded to the different Artemisia species , soil type , moisture level , and inoculum . Shoot biomass responded to soil type , moisture level , and inoculum type . Root production varied by associated Artemisia species , soil type , moisture , and inoculum type . Total, shoot, and root biomass production were greater in T. caput medusae grown in autoclaved soils, while field soils always had lower biomass production , with moisture level being more significant  than soil type  and inoculum . N content was greater in low moisture treatments, regardless of soil or inoculum type . N content of A. nova did not significantly change among any soil, moisture, or inoculation treatments (p > 0.05). P content in A. tridentata ssp. wyomingensis significantly varied by moisture level  and soil type . P content was greater when grown at low moisture in field soils with both sham and AMF inoculums (0.49% and 0.49%) compared to all other treatments (A. arbuscula had no significant differences in P content for any treatments or interactions (p > 0.05). A. nova had a greater P content when grown with low moisture and field soils with sham inoculum . K content in A. tridentata ssp. wyomingensis statistically responded to moisture level only , as it was greater when grown in low moisture, field soils with sham and AMF inoculums (2.77% and 2.52%) (A. arbuscula and A. nova had no significant differences among treatments (p > 0.05). Nutrient acquisition for the lum type . A. arbueatments . A. arbud 2.52%) . K conteT. caput-medusae grown as competition for the three Artemisia species is shown in T. caput-medusae when grown with A. tridentata ssp. wyomingensis responded to the interaction of moisture level and inoculum , as it was greater when grown at low moisture, in autoclaved soil, and with commercial inoculum (0.70%). N content of T. caput-medusae associated with A. arbuscula responded to a greater extent to the interaction of moisture and soil  as it was greater in field soils with high moisture. When grown with A. nova, N concentration responded to inoculum  and the interaction of soil and moisture  as it was greater when inoculated with commercial AMF, at high moisture, and in both soil types (0.82% and 0.70).Nutrient content measured in T. caput-medusae grown with A. tridentata ssp. wyomingensis significantly varied by moisture level  and the interaction of moisture and soil . P content was greater at high moisture levels in field soil with sham and AMF inoculums (0.12% and 0.10%) and in low moisture, autoclaved soils with AMF inoculum , soil type , and the interaction of moisture and soil , as P concentration increased when grown in both high and low moisture, field and autoclaved soils, and inoculated with commercial AMF. Finally, when grown associated with A. nova, P content of T. caput-medusae reported no significant differences in any treatments (p > 0.05). P concentration of inoculum . P conceT. caput-medusae grown with A. tridentata and A. nova varied by moisture  and soil type . K was greater in high moisture, autoclaved soils, and inoculum (0.59% and 0.73%) , soil type , inoculum , and the interaction of moisture and soil .K content in d 0.73%) . K conteArtemisia species, and that such inoculum would not make T. caput-medusae more competitive. Based on our results, we cannot support either hypothesis as we did not find evidence that by using a commercial AMF inoculum we can effectively ameliorate biotic (intraspecific competition) or abiotic (drought) stress in the tested Artemisia species. We also found evidence of nutrient increases for T. caput-medusae with the addition of the commercial inoculum. We tested the hypothesis that by using a commercial AMF inoculum we would ameliorate biotic and abiotic stress in three Artemisia species was affected by competition and drought rather than AMF inoculation. Drought is a widely recognized factor that affects plant growth [Artemisia species were outcompeted by the faster shoot and root growth from T. caput-medusae, which reduced moisture access to the roots and likely created a nutrient depleted environment for the Artemisia seedlings to grow even though they were colonized by AMF. Biomass production of the t growth ,39. Plant growth . Some plt growth . Competit growth . A high-t growth ,40. TherArtemisia tridentata ssp. wyomingensis, and A. nova received N, P, and K gains from AMF colonization from live field soils subjected to drought without competition. This corresponds with the stress-gradient hypothesis, suggesting that mutualism is promoted under certain levels of stress [Artemisia plants were subjected to both types of stress, the AMF symbiosis did not provide any measurable effect. However, further research is required to validate this hypothesis.Furthermore, the mycorrhizal symbiosis represents a considerable carbon cost for the host, which might be too much for a newly emerged seedling under a competitive environment ,41. Whenf stress . In thisf stress ,15,16,45Rhizophagus intraradices, and the field soil was obtained from a disturbed site. Furthermore, other studies suggest that each AMF inoculum type has a different response even in the same plant species [A. tridentata ssp. wyomingensis, A. arbuscula, and A. nova direct mycorrhizal benefits might depend on differential AMF communities that were not present in the inoculum or in the soil.These results are in contrast to some studies suggesting that mycorrhizal inoculation provided growth benefits  as well  species . For sloT. caput-medusae responds as a facultative mycorrhizal plant. T. caput medusae biomass was greater in soils without AMF, and the re-addition of the soil microbial community provided no measurable effect. Other studies also ruled out the effect of the soil microbial and bacterial communities as possible drivers of T. caput-medusae invasiveness [T. caput-medusae found similar results when colonized from field soils, having a lower biomass production compared to autoclaved soils [T. caput-medusae. However, why might a facultative mycorrhizal plant exhibit greater AMF colonization than an obligate AMF species? Facultative mycorrhizal species are able to associate with several AMF species and maintain low levels of colonization which might increase during stress periods to obtain benefits and become established even in degraded soils [Bromus tectorum) are known for their response to stressors such as drought and competition by allocating less resources to biomass and more to reproduction [T. caput-medusae can effectively compete and become established. Further studies are required to understand this response such as a continuous evaluation of T. caput-medusae on the field AMF densities over time. Finally, we cannot discard the possibility of a particular species or strain of AMF present in our field site that could be driving such growth depression in T. caput-medusae and further studies on fungal communities are required to test such hypotheses.Our findings suggest that siveness . Previoued soils . We expeed soils . Some inoduction . So, eveArtemisia species, but we found evidence of mycorrhizal benefits from live field soils in three Artemisia species without competition and from commercial AMF inoculum on T. caput-medusae. Furthermore, stressful conditions such as competition and drought mediated AMF colonization and growth responses on the Artemisia plant species. The effect of AMF promoting plant growth with and without stress has been previously studied mostly on crops species but not so much on rangeland plant species. Even though plant biomass did not reflect direct benefits (biomass increases) associated with nutrient acquisition in stressful conditions, a constant increase in non-mobile nutrients may be associated to long term plant establishment or fertility, which eventually might result in a more competitive plant. Proper maintenance of P supply has an important role in plant hydraulic connectivity and water uptake and hence resistance to stress.We were unable to accept our original hypotheses that a commercial AMF inoculum would reduce stress on the T. caput-medusae. We found evidence that T. caput-medusae received N, P, and K increases when inoculated with the commercial AMF. This finding implies that AMF inoculation (at least an inoculum composed of Rhizophagus intraradices) might not be recommended in rangelands in which T. caput-medusae is present. However, this response needs to be further evaluated, particularly under field conditions.Inoculation using external AMF sources has been a debated topic as their effects on invasive species are not completely clear. Our research provides valuable information for restoration in rangelands that face invasion with invasive species such as


In vitro activities of delafloxacin and ciprofloxacin were evaluated against Burkholderia pseudomallei mutants expressing or lacking defined resistance-nodulation-cell division (RND) efflux pumps using CLSI methodology at pHs of 5.8 and 7.2. Delafloxacin MIC values were as much as 8-fold lower at pH 5.8 than those at pH 7.2, while ciprofloxacin MICs increased as much as 8-fold. The data from this study suggest that compared to ciprofloxacin, delafloxacin may have improved efflux avoidance, notably at acidic pH. In contrast to ciprofloxacin, delafloxacin may thus retain its therapeutic potential, even in BpeEF-OprC efflux-pump-expressing B. pseudomallei strains that compromise the use of fluoroquinolones, such as ciprofloxacin.IMPORTANCE Resistance-nodulation-cell division (RND) efflux pumps play a major role in intrinsic and acquired antibiotic resistance in Burkholderia pseudomallei, and these pumps are its only known multidrug resistance determinants. Fluoroquinolones have performed poorly in clinical settings and are currently not recommended for treatment of B. pseudomallei infections. While the reasons for the poor clinical performance of this pathogen remain unclear, efflux may be partially responsible since fluoroquinolones like ciprofloxacin are prone to efflux by RND pumps, notably BpeEF-OprC. In vitro efficacy testing using a panel of efflux-proficient and efflux-deficient strains allows identification of fluoroquinolones that compared to ciprofloxacin are less prone to efflux. Burkholderia pseudomallei is an aerobic, non-spore-forming, nonfermenting Gram-negative opportunistic pathogen  superfamily (B. pseudomallei isolates and is responsible for the organism’s intrinsic aminoglycoside and macrolide resistance (B. pseudomallei 1026b, but can be upregulated in BpeR mutants (–B. pseudomallei (folM mutations, resistance to sulfamethoxazole has been observed (bpeAB-oprB and bpeEF-oprC in B. pseudomallei by fluoroquinolone pump substrates, such as ciprofloxacin (pathogen . It is tpathogen , 3. Intrthe cell –6. The cerfamily . Sequencerfamily . AmrAB-Osistance . AmrR resistance . The Bpe mutants . The Bpe mutants . More re mutants –13. The domallei , but it domallei , and wheobserved . To our floxacin , 11.B. pseudomallei, which can survive within host cell organelles, such as lysosomes, where the pH is acidic (Delafloxacin differs from the other fluoroquinolones, such as ciprofloxacin, in the absence of a protonatable substituent, which confers to the molecule a weak acid character. This property further increases delafloxacin’s potency in acidic environments and may result in improved efficacy against s acidic . In a pos acidic .B. pseudomallei isolates as well as provide further evidence of differentiation from the other fluoroquinolones, delafloxacin and ciprofloxacin were tested against a panel of B. pseudomallei RND efflux mutants using the standard CLSI MIC methodology with pH adjustments to pHs 5.8 and 7.2 (Escherichia coli ATCC 25922, was tested in parallel with the mutant strains and the delafloxacin and ciprofloxacin MIC results were within CLSI quality control ranges (B. pseudomallei 1026b (To confirm delafloxacin activity against resistant  and 7.2 . The conl ranges . The effei 1026b , and theei 1026b .Burkholderiathailandensis (As demonstrated in previously published studies , delafloandensis , 6, the in vitro efficacy of delafloxacin is superior to that of ciprofloxacin. The data from this study suggests that compared to ciprofloxacin, delafloxacin may have improved efflux avoidance, notably at acidic pH. In contrast to ciprofloxacin, delafloxacin may thus retain its therapeutic potential, even in BpeEF-OprC-expressing B. pseudomallei strains that compromise use of other fluoroquinolones. Further evaluation of delafloxacin in animal models of melioidosis is warranted.In conclusion, as evidenced by MICs obtained at pHs 5.8 and pH 7.2, the


Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai–Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.The  Scrophularia L.  comprises 200–300 species worldwide, is a taxonomically challenging and complicated lineage with great morphological diversity and high levels of reticulation evolution [Scrophularia was formally divided into two morphologically distinct sections in Stiefelhagen’s (1910) [Scrophularia sect. Scrophularia is characterized by perennial herbs with reticulate leaf veins, and Scrophularia sect. Caninae is characterized by perennial subshrubs and xerophytes without reticulate leaf veins. The latter primarily distributed in Central Asia and Northwest China [Scrophularia [Scrophularia reported to date was based on nuclear ribosomal ITS and two plastid DNA loci  comprising 147 species [S. sect. Caninae) were only weakly supported, and incongruences between cytoplasmic and nuclear data were discovered [The figwort genus volution ,2,3,4,5.volution ,7. Scrops 1910)  widely a10  widelphularia ,13,14,15S. incisa complex (S. sect. Caninae) is a group of subshrubby plants that are primarily (but not exclusively) distributed in the deserts and steppes of Northwest China. It consists of three closely related species: S. incisa Weinm., S. kiriloviana Schischk and S. dentata Royle ex Benth [S. incisa displays a belt-like pattern of distribution, primarily in the northern Chinese provinces of Qinghai and Gansu as well as in Inner Mongolia, spreading to Central Asia in the west and to Siberia in the east [S. dentata occurs in western and southern Tibet, northwest India and Pakistan; S. kiriloviana is found in Xinjiang Province and Central Asia [Scrophularia based on nrITS and cpDNA placed this species complex as a monophyletic group embedded within the S. sect. Caninae clade [S. incisa complex based on plastid DNA  indicated that the evolutionary relationships among the major clades of the S. incisa complex were poorly resolved with insufficient genetic informative sites [S. incisa complex.ex Benth ,17. Theyex Benth ,19. Of tthe east ; S. dentral Asia , with prae clade . Populatve sites . TherefoS. incisa complex were reported, specifically aiming to: (1) characterize the entire plastid genomes of the S. incisa complex and comparative analyses with other plastomes of the genus using publicly available data; (2) gain insights into the Scrophularia plastid genome’s evolutionary pattern and resolve phylogenetic relationships within the S. incisa complex; (3) examine variations in simple sequence repeats (SSRs), repeat sequences and mutational hotspot regions for future studies of species identification and phylogeographic studies of Scrophularia.Plastid genomes with a relatively small size, and a conserved structure and gene content have greatly facilitated the study of comparative genomics and species evolution ,23,24. CS. incisa complex, including three individuals of S. kiriloviana from Xinjiang, two individuals of S. incisa from Qinghai and one individual of S. dentata from Tibet, together with a closely related species S. integrifolia from Tajikistan, were collected (S. buergeriana (KP718626), S. dentata (MF861202), S. henryi (NC036943) and S. takeimensis (KP718628) were downloaded from NCBI for comparative analyses with S. incisa complex.Leaves of six individuals of major clades of ollected , Table 1Scrophularia individual, raw reads of the paired-end sequencing data were trimmed to get rid of adapters and the reads with the Phred value of base calling quality score less than 20 using CLC Genomics Workbench v10.1.1 ). Second, the left reads with high quality were assembled into contigs applying the CLC assembler, under all optimally controlled parameters as: minimum contig length of 200 bp, mismatch cost = 2, deletion and insertion costs = 3, length fraction = 0.9 and similarity fraction = 0.8. Third, because of both organellar and nuclear DNA contained in the sequencing data, all contigs were aligned and directed according to the reference plastome of S. buergeriana (KP718626) to obtain the correct ones by BLAST (http://blast.ncbi.nlm.nih.gov/ (accessed on 23 June 2008)). Finally, the filtered clean contigs were ordered and realigned with the reference chloroplast genome and complete chloroplast sequences of Scrophularia were generated in GENEIOUS v11.01 (http://www.geneious.com (accessed on 26 September 2017)) [The de novo assembly and reference-guided combined method was implemented to assemble these raw reads into complete plastid genomes . First, na KP7186 to obtaiS. buergeriana (KP718626). Additionally, all the determined tRNA genes were further confirmed by the predicted corresponding structures in tRNAscan-SE v1.21 [http://vmbioinfo.toulouse.inra.fr/emboss (accessed on 15 July 2007)) and CODONW v1.4.2 (http://codonw. sourceforge.net/ (accessed on 12 May 2005)).Complete plastomes were annotated in the GENEIOUS v11.01 and DOGMA  database software ,32,33,34SE v1.21 . The plaSE v1.21 . FinallySE v1.21 ,38, as wScrophularia species mentioned above and the S. incisa complex plastid genomes were performed with mVISTA tool (genome.lbl.gov/vista/index.shtml (accessed on 1 July 2004)) in reference to the annotation of S. buergeriana [taE) and nucleotide diversity (iP) values of protein-coding and non-coding regions that were extracted following criterion of the aligned length larger than 200 bp and no less than one mutation site.Chloroplast genome comparative analyses across these rgeriana . For thergeriana  to evaluScrophularia were searched by running MICROSATELLITE (MISA) perl script [The program REPuter  was operl script , accordil script ,44.In genetics, the ratio (ω) of non-synonymous (Ka) and synonymous (Ks) substitution rates is usually employed to ascertain whether the selection pressure acting on the protein-coding gene exists or not ,46,47. IScrophularia, two of Verbascum, five of Buddleja and six individuals from four genera of tribe Myoporeae as the outgroup taxa based on previous studies [Altogether 26 chloroplast genomes representing 7 genera of Scrophulariaceae  were dir studies ,51,52. T studies . The max studies ,54, with studies . Bayesia studies ,57, withS. incisa complex and one individual of S. integrifolia were sequenced using the Illumina HiSeq 2500 system with totals from 14,276,152 to 20,707,954 clean reads produced. Seven complete plastid genomes from four species of S. sect. Caninae with no gaps were obtained by means of de novo and reference-guided assembly. Integrating previously published chloroplast genomes of S. dentata (MF861202), S. buergeriana Miq. (KP718626), S. henryi Hemsl. (NC036943) and S. takeimensis Nakai (KP718628), the nucleotide sequences of the eight S. sect. Caninae chloroplast genomes were determined to be 152,088–152,688 bp, and the three S. sect. Scrophularia species ranged limitedly from 152,425 bp to 153,631 bp  genes and 4 ribosomal RNA (rRNA) genes, thereinto 115 unique and 17 duplicated genes  had two introns. The region ycf1 gene appeared as a pseudogene  values ranged from 55.423 (S. dentata Tibet ZG4) to 56.141 (S. kiriloviana Xinjiang AK1)  . The mosang AK1) . Except ly 37.9% , which fScrophularia species [Scrophularia cp genomes were highly conserved throughout evolution in various aspects of genome features concerning gene content, arrangement and GC content, as well as codon usage.Altogether, our newly obtained results generally correspond with other previously reported  species ,65, and Scrophularia chloroplast genomes  for these loci in the coding regions ranged from 0.00158 (ycf2) to 0.02438 (rps15); rps15, ndhG, ycf1, ccsA, ndhF and rps11 with a high Pi value (>0.01) were considered as divergence hotspots. The Pi values of non-coding regions ranged from 0.00112 to 0.04866; in addition, 11 of the most divergent and variable regions with Pi values greater than 0.015 included trnH–psbA, rpl32–trnL, ndhF–rpl32, trnL–rps16, ycf3–trnS, petA–psbJ, ndhE–ndhG, ndhC–ndhV, ccsA–ndhD, ycf4–cemA and rps4–trnT. The hotspot and variable regions could be profitable in the development of genetic markers for the species phylogenetic identification analysis of Scrophularia.In conformity to most studies ,67, IRs Scrophularia cp genomes with REPuter program [S. incisa (Qinghai XH7) comprised the maximum number of repeats (52), whereas S. dentata possessed the least (38)  and S. takesimensis exhibited the most distinct repeats (8), while S. henryi and S. buergeriana contained the fewest number (2), respectively  a. The pephularia . Accordiectively .Scrophularia plastomes through MISA analysis identification. The amount of SSRs per single plastome ranged between 40 (S. integrifolia Tajikistan H8) and 53 (S. incisa Qinghai XH7), with 11 SSRs shared among all plastomes  to 2.65591 (S. incisa Gansu DJ1), and the highest Ka/Ks value was 3.2702 (S. buergeriana) among these 11 Scrophularia individuals (S. incisa (Gansu DJ1), and other genes had higher synonymous than non-synonymous changes, suggesting high evolutionary constraints in the Scrophularia genome species. The Ka/Ks of most genes were less than 1, indicating that they may be subjected to purification options, i.e., mutations were detrimental and eliminated in the population (rpl22 gene of S. takesimensis (KP718628) , the rps15 gene of all the individuals expect S. buergeriana (KP718626) and S. henryi (MF861203), and the ycf15 gene of all the individuals   and synonymous (Ks) substitution rates together with the Ka/Ks (ω) value to detect the selective pressure on the 80 cp genes of eleven ividuals . In factpulation . Among t > 0.05) .Buddleja was sister to Verbascum and Scrophularia, and S. sect. Caninae was resolved as a robust monophyletic clade. Within S. sect. Caninae, S. integrifolia (Tajikistan H8) was sister to the clade of the S. incisa complex, and within the complex S. kiriloviana, AK1 was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana  and S. incisa  were clustered into sister clades  was 1.01824, but it was less than 1 in other individuals, so we thought that this group of data does not indicate that the gene has received positive selection.SSRs are often used as molecular markers for population genetic studies. We identified 40 to 53 chloroplast SSRs  in the eS. incisa complex were reconstructed in the framework of Scrophulariaceae based on the complete chloroplast genomes. The phylogenomic analysis of Scrophulariaceae, based on current species coverage of 26 cp genomes representing four tribes, provided full support for the monophyly of the three groups of tribe Scrophularieae, tribe Buddlejeae and tribe Myoporeae + Leucophylleae  from the west of the Tianshan Mountains in Tajikistan was at the basal position, followed by an S. kiriloviana individual (Xinjiang AK1) from the eastern foothills of the Pamirs Plateau in Southwest Xinjiang, which was consistent with our previous phylogeographic study of the S. incisa complex based on psbA-trnH, trnL-trnF and trnQ-rps16 markers [S. incisa complex, a topology of (S. dentata + (S. incisa + S. kiriloviana)) was strongly supported. This result solves the polytomy of the S. incisa complex in the previous study [S. kiriloviana from Xinjiang does not form a single monophyletic cluster, maybe due to introgression and/or incomplete lineage sorting between S. kiriloviana AK1 and neighboring S. integrifolia, the S. incisa complex is subdivided into three distinct gene pools and all the S. kiriloviana individuals show dominant red genetic clusters from the Xinjiang gene pool based on previous nSSR population data [S. incisa complex. In combination with our previous ancestral distribution reconstruction analysis and species distribution range of S. sect. Caninae [S. incisa complex with subsequent diversification on the Qinghai–Tibet Plateau (QTP), the Tianshan Mountains, the Mongolian Plateau and surrounding regions. This pattern has been explored across various genera, such as Solms-laubachia, Incarvillea and Myricaria [Our present study contributes a phylogenetic framework to the chloroplast genome evolution of Scrophulariaceae, especially for the  Caninae . Within  markers ,21. Withus study ,21. In aion data ,21. Ther Caninae ,9,17,21,yricaria ,89,90,91S. incisa complex by comparing the complete chloroplast genome sequences of the main representatives covering all the lineages within the S. incisa complex. This analysis revealed that their chloroplast genomes are highly conserved in terms of length, genomic structure, gene number and arrangement. Close relationships between these three taxa were inferred and confirmed depending on high chloroplast genome similarities and the topology of phylogenetic trees in which S. incisa, S. kiriloviana and S. dentata form a strong supported distinct cluster within the S. sect. Caninae clade of genus Scrophularia. Recognition of highly variable regions and distinct microsatellite loci patterns in the chloroplast genomes of the S. incisa complex and three other species of Scrophularia could potentially be used in the future for identification and discrimination of these taxa. These analyses of chloroplast genomes consequently contributed to our understanding of the plastid phylogeny of the S. incisa complex and provide valued implications for the evolutionary history and conservation of these medicinal plants, as well as the genus Scrophularia in general.The present study was designed to improve the phylogenetic resolution within the desert and steppe subshrubs


Background and Objectives: Periodontitis is a chronic multifactorial inflammatory infectious disease marked by continuous degradation of teeth and surrounding parts. One of the most important periodontal pathogens is P. intermedia, and with its interpain A proteinase, it leads to an increase in lethal infection. Materials and Methods: The current study was designed to create a multi-epitope vaccine using an immunoinformatics method that targets the interpain A of P. intermedia. For the development of vaccines, P. intermedia peptides InpA were found appropriate. To create a multi-epitope vaccination design, interpain A, B, and T-cell epitopes were found and assessed depending on the essential variables. The vaccine construct was evaluated based on its stability, antigenicity, and allergenicity. Results: The vaccine construct reached a more significant population and was able to bind to both the binding epitopes of major histocompatibility complex (MHC)-I and MHC-II. Through the C3 receptor complex route, P. intermedia InpA promotes an immunological subunit. Utilizing InpA-C3 and vaccination epitopes as the receptor and ligand, the molecular docking and dynamics were performed using the ClusPro 2.0 server. Conclusion: The developed vaccine had shown good antigenicity, solubility, and stability. Molecular docking indicated the vaccine’s 3D structure interacts strongly with the complement C3. The current study describes the design for vaccine, and steady interaction with the C3 immunological receptor to induce a good memory and an adaptive immune response against Interpain A of P. intermedia.  Prevotella intermedia, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans have significant effects on the microbiota, disrupting tissue homeostasis [With the advances in technology and science, significant progress has been made in understanding microorganisms and disease processes. The knowledge of the disease process has undergone a paradigm shift from early models that assumed the quantity of plaque to current concepts of host-microbial interactions . Periodoeostasis ,5. P. intermedia have evolved defenses against complement killing to become successful pathogens [A localized chronic inflammation and subsequent loss of the tooth’s supporting structures result from the intricate interplay of the bacterial virulence factors and defense mechanisms of the host ,7. Many athogens . The funathogens .Prevotella intermedia, an oral Gram-negative anaerobe, helps in converting hemoglobin to an iron (III) protoporphyrin IX pigment. The bacterium produces InpA (interpain A), a 90-kDa cysteine protease, a homolog of streptopain from Streptococcus pyogenes (SpeB). Under situations of low redox potential and higher pH in the infected gingival crevice and diseased periodontal pocket, where the host closely regulates the availability of haeme, InpA greatly contributes to the acquisition of haeme [Prevotella intermedia’s cysteine protease Interpain A (InpA) collaborates with P. gingivalis’ HmuY hameophore, demonstrating further post-translational interaction. Notably, gingipains work in concert with karilysin or Interpain A to suppress complement, indicating that these complementary proteases may still prevent complement activation after being released and diffused across the biofilm that is defending the entire microbial community [of haeme . Haem alommunity .Computational immunology, often known as immunoinformatics, is a subfield of bioinformatics that uses bioinformatics methods to comprehend and analyze immunological data . UtiliziP. intermedia (Interpain A) has a significant role in host immune modulation and providing the required nutrition to the microbiome, the current study aimed to design a vaccine that targets Interpain A using an immunoinformatics approach.Since P. intermedia with the help of positive assays for linear epitopes [P. intermedia. The antigenic peptides prediction tool (http://imed.med.ucm.es/Tools/antigenic.pl) (accessed on 12 March 2022) and the AllerTop v2.0 servers (http://ddg-pharmfac.net/AllergenFP/) (accessed on 12 March 2022) were used to screen 3BBA for average antigenic propensity and allergenicity [Immune epitope database analysis was used to identify the protein structure of the epitope of epitopes . The nethttp://tools.iedb.org/mhci/), (accessed on 14 March 2022). The percentile rank and IC50 value of peptide-MHC-II interactions were determined using the NN Align technique and the IEDB MHC-II epitope prediction tool. The origin species was a person. Further analysis was conducted on the Human Leukocyte Antigen–DR isotype (HLA-DR), HLA-DP, and HLA-DQ loci. Since these results represent a greater affinity, IC50 values of 10 nM and a percentile rank of 1.5 were utilized for prediction. We assessed the antigenic properties of anticipated HTL epitopes. Finally, the allergenicity, toxicity, and antigenicity of the 3BBA epitopes from Cytotoxic T lymphocytes (CTL), Helper T cell (HTL), and B cell lymphoma (BCL) were considered. For the creation of multi-epitope vaccines, the predicted 3BBA epitopes were utilized [Using NetCTL1.2  , lymphocutilized . Expression and distribution of HLA alleles expressed diverse presentations between regions and ethnicity, which may impact the creation of multi-epitope-based vaccines . The popAdjuvant, CTL, HTL, and BCL epitopes were combined to form appropriate links to allow the epitopes, in vivo, adequate room to function. Human-defensin-2 (PDB ID: 1FD 3) served as an adjuvant along with a B-cell epitope utilizing an EAAAK linker to boost the immunogenicity of the vaccine candidate ,20. The Through the use of the Swiss model, the iterative threading modeling method was used to predict and validate the three-dimensional structure of the vaccine construct. http://www.pymol.org) (accessed on 15 March 2022), and the ideal complex was selected to assess which complex had a lesser energy score [Utilizing 2a73 complement C3 and the vaccine receptor and ligand, molecular docking with ClusPro 2.0 program was used in order to assess the co-action of the vaccine and with the host immune receptor. So, using three sequential steps—rigid body docking, clustering of lowest energy structures, and structural refinement—complexes were created. The docked structure was examined using PyMol  simulation. Desmond software  used MD to imitate vaccine-C3. Desmond  ran a 100-nanosecond simulation of molecular dynamics. The receptor-ligand complex was reduced and optimized by Maestro’s Protein Preparation Wizard. Using System Builder, all systems were created. An orthorhombic solvent model is TIP3P. (Points from TIIP3) The simulation made use of OPLS 2005. NaCl at 0.15 M simulated physiological conditions. The ensemble of 300 K and 1 atm NPT was used throughout the simulation. Simulation models were lax. The simulation’s stability was evaluated by comparing the root-mean-square deviation (RMSD) over time for the protein and ligand.P. intermedia, 3BBA was chosen based on its antigenic propensity  and center energy (the energy between receptor and ligand) of −661.2 kJ mol−1  plot demonstrates that stability was obtained at 40 ns. Following that, fluctuations in protein RMSD values remained within 1.5 throughout the simulation time. The RMSD values of ligands range from 2.0 angstrom to 100 ns.P. intermedia is a bacterium that is closely associated with various periodontal diseases and other infections [P. intermedia has frequently been found in subgingival plaque in human patients with necrotizing gingivitis, pregnancy gingivitis, and adult periodontitis [P. intermedia is challenging to eliminate because it quickly develops antibiotic resistance [P. intermedia [The primary goal of the periodontal vaccine is to depreciate disease progression and eventually eradicate periodontal disease . P. intefections ,23. P. idontitis . Additiosistance . An in-dsistance . Numeroutermedia . Howevertermedia .Interpain A, a cysteine protease from the cysteine-histidine-dyad class, was investigated in its zymogenic and mature self-processed forms. The latter is made up of a bivalved portion with two subdomains. Complement is an important component of the innate immune defense system, with the primary purpose of recognizing and killing bacteria ,29.P. intermedia [P. intermedia, most likely due to a reaction to endotoxin. Yet, kinetic tests demonstrated that opsonization occurred substantially faster when the classical pathway was intact [P. intermedia through many sensory chemicals. However, it appears that P. intermedia can bind to C3 and, to some extent, overwhelm complement defenses, allowing chronic infections to develop in the oral cavity [P. gingivalis gingipains [Heat inactivation of the complement system greatly reduces the opsonic activity in vitro, indicating that complement is required for host defense against termedia ,31. Mores intact . Surpriss intact . As a rel cavity . Furtherngipains . When apngipains .P. intermedia 3BBA epitope peptide depicted higher antigenicity, immunogenicity, non-allergenic and non-toxic nature, and increased MHC-I and II binding than other epitopes. The present study results show that the current vaccine design is non-allergic, non-antigenic, non-toxic, and does exhibit good immunogenicity. Moreover, molecular docking and dynamics results exhibit excellent and stable binding throughout the stimulation period. This is due to the increased affinity of the vaccine for the C3 receptors. Further studies with DNA cloning are required to make this vaccine a reality. Epitopes induce cytotoxic T- and B-cell lymphocytes to destroy pathogenic microbes through cytokine action . CytokinP. intermedia is a common bacterium that is associated with periodontal infections. It also contributes to the sustainability of the microbiome by providing essential substrates such as albumin and haem. Future well-designed studies are required to evaluate the efficacy of this vaccine design. Furthermore, it will be interesting to observe the overall effect of the elimination of P. intermedia on the microbiome.The current study provides the first vaccine design for Interpain A using an Immunoinformatic approach.


Astragalus sinicus Linne 1767 is a traditional winter-growing green manure, that plays an important role in upgrading soil fertility and maintaining crop yield and quality for rice fields. This study reports the complete chloroplast genome of A. sinicus. The chloroplast genome contained 110 complete genes, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30 tRNA genes with 123,830 bp in length and a 34.66% GC content with IR loss. The evolutionary history, referred to as the maximum-likelihood (ML), showed that A. sinicus and Astragalus bhotanensis were most closely related. The chloroplast genome analysis of A. sinicus will serve as a reference for future studies on species evolution, plant conservation, and molecular phylogeny in Astragalus. Astragalus sinicus Linne 1767, also known as Chinese Milk Vetch, is native to China and nowadays grows throughout southern China, Japan, and Korea  under the voucher number KQnum20210807003. Genomic DNA was extracted from fresh seedling leaves using the modified CTAB method  as a reference sequence. Gene annotation was performed using CPGAVAS v2  were collected for sequencing. A specimen was deposited at the College of Bioscience and Engineering, Jiangxi Agricultural University (A. sinicus (GenBank accession number: OM287552) remains a cyclic form with IR loss, consistent with other Fabaceae species (Liu et al. The complete chloroplast genome of A. sinicus phylogenetic position, the chloroplast genome sequences of 10 Astragalus species and Oxytropis bicoloras were downloaded from NCBI to construct the phylogenetic tree, with O. bicoloras being an outgroup. Multiple sequence alignment of the full-length chloroplast genome sequences was performed using MAFFT v.7.313 (Katoh and Standley A. sinicus clustered with A. bhotanensis, Astragalus galactites, Astragalus laxmannii, Astragalus strictus, and Astragalus nuttallianus with high support values, in line with previous reports (Ding et al. A. sinicus displayed the closest phylogenetic relationships with A. bhotanensis. The A. sinicus complete chloroplast genome provides useful information for the taxonomy, evolution, and molecular biology study of genus Astragalus, and might also facilitate the genetic research and breeding of A. sinicus.To further investigate the


The development of next generation sequencing (NGS) methods has created the need for detailed analysis and control of each protocol step. NGS library preparation protocols may include steps with incorporation of various service sequences, such as sequencing adapters, primers, sample-, cell-, and molecule-specific barcodes. Despite a fairly high level of current knowledge, during the protocol development process researches often have to deal with various kinds of unexpected experiment outcomes, which result either from lack of information, lack of knowledge, or defects in reagent manufacturing. Detection and analysis of service sequences, their distribution and linkage may provide important information for protocol optimization. Here we introduce FastContext, a tool designed to analyze NGS read structure, based on sequence features found in reads, and their relative position in the read. The algorithm is able to create human readable read structures with user-specified patterns, to calculate counts and percentage of every read structure. Despite the simplicity of the algorithm, FastContext may be useful in read structure analysis and, as a result, can help better understand molecular processes that take place at different stages of NGS library preparation. The project is open-source software, distributed under GNU GPL v3, entirely written in the programming language Python, and based on well-maintained packages and commonly used data formats. Thus, it is cross-platform, may be patched or upgraded by the user if necessary. The FastContext package is available at the Python Package Index (https://pypi.org/project/FastContext), the source code is available at GitHub (https://github.com/regnveig/FastContext). Since the advent of next generation sequencing (NGS) methods20 years ago, those methods have been actively evolvingand are currently applied to various areas of biology. Due tothe increasing capacity of sequencers, it is now possible toobtain billions of short molecule sequences in a single NGSrun. In order to utilize such a high throughoutput of modernsequencers, there is a practice of sample pooling. This methodrequires incorporation of sample-specific service sequences(barcodes), which allow to distinguish individual samples inraw sequencing data.Other types of service sequences could be incorporated intothe target molecules, such as sequencing adapters and primers,biotin-labeled oligonucleotides for target molecules enrichment, molecule- and cell-specific barcodes,which are designed to identify a molecule  and/or a cell of origin .There are many strategies in molecular genetics that areused for service sequences incorporation: direct ligationof DNA or RNA molecules, template-switching activity ofreverse transcriptases, and incorporation of synthetic DNAtransposons. During the whole process of new NGS methodsdevelopment it is crutial to control each protocol step. In lightof that, detection and analysis of service sequences distributionmay provide important information for protocol optimization.Here we introduce the FastContext tool, which is designedto analyze and compute statistics on NGS read structures. FastContextallows to search for user-specified sequences in NGSreads, gather data on their linkage, frequency of occurence,and present statistics in a user-friendly manner.The script is completely written in the programming languagePython (version 3.8). It is packaged as a part of the PythonPackage Index (https://pypi.org/project/FastContext) andcan be installed via pip. Therefore, it works out of the box onevery operating system.We used the following Python libraries:1. bioPython, version 1.79 : FastQ filesparsing and sequences manipulation;2. python-Levenshtein (Available at: https://github.com/ztane/python-Levenshtein), version 0.12.2: calculating sequencesLevenshtein distance;3. pandas, version 1.2.5 : tables creation;4. tqdm, version 4.61.2 : visualization.All libraries listed above, except python-Levenshtein, arewidely used and well maintained.FastContext supports multi-processingWe developed an algorithm which parses raw sequencingdataset, searches each read or read pair for user specified patterns,and then generates a human-readable representation ofthe search results, which we call “read structure”. Algorithmscheme is represented in the Fig.1.InputInput files are provided in FastQ format (Full specification of FastQ format is available at http://maq.sourceforge.net/fastq.shtml). The user can provideone (in the single-end mode) or two (in the paired-end mode)FastQ files. Files may be uncompressed or compressed withgzip or bz2 algorithms.OutputOutput results are provided as an HTML page (further:“summaryfile”), containing run options and tables with readstructures, their counts, and percentages . The sequencestrand  is displayed after acolon .The user can manually set minimal rate value (rate floor)to be displayed. Also, the user can save the read structurefor each read or read pair, with the read name, the sequence,and Phred qualities, as a gzip-compressed JavaScript ObjectNotation (JSON) object (further: “detailed statistics file”)Full specification of JSON format could be found at JSON official website:https://www.json.org..PatternsPattern names and sequences are provided as a plain JSONobject, e. g.:{ foo": "CTGTCTCTTATACAC", "bar": "CCGAAAACACG","baz": "TCGTCGGG"}.It should be noted that pattern sequences are searched inthe order they are provided by the user, forward strand (thesequence itself) first, reverse strand (a reverse complement ofthe sequence) after. Therefore, the patterns order matters insearch and should be carefully considered before running theprogram. FastContext expects patterns to be sorted from longto short, which is the best option for overlapping or nestedsequences, and otherwise gives you a warning.K-mersFastContext performs the search based on full match, anda pattern sequence with one single sequencing error will beskipped as an unrecognized sequence . Thisis especially important for long patterns, which are underrepresenteddue to higher cumulative frequency of sequencingerrors. In addition, oligonucleotide synthesis errors and someenzymatic steps of NGS library preparation, such as A-tailing,may produce molecules one base pair shorter or longer thanexpected. In order to simplify identification of such extendedor truncated sequences, we have implemented the ability tomark short unrecognized sequences (K-mers) of certain length. If a K-mer identified in the read is onebase longer or shorter than a pattern sequence, we can supposethis K-mer is the pattern sequence, and test the hypothesis ina more detailed analysis of reads.Levenshtein distances analysisAdditional features implemeted to account for sequencingerrors include analysis of Levenshtein distances betweendifferent pattern sequences , and betweenpattern sequences and read sequence. Pattern analysis is shownin the summary file, data on every single read can be found inthe detailed statistics file.Analysis of distances between pattern sequences can preventpattern match or nesting, when sequences are confusedwith each other because of a few sequencing errors. Also,FastContext warns the user about palindromes and sequencesthat can become palindromic because of sequencing errors.This kind of sequence may affect statistics of forward-reverseorientation.Analysis of distances between pattern and read sequencescan show similarity of an unrecognized sequence and a patternsequence, so the user could suggest the real read structure evenif FastContext fails to do that. All these data may be found in adetailed statistics file, with Levenshtein read analysis enabled(disabled by default).System requirements and performanceBy design, FastContext stores FASTQ reads in random accessmemory (RAM), therefore, the only system limitation is theRAM size. Tests we have performed show that 8 Gb RAM isenough for processing 10,000 reads, which is a high enoughsample size for practical application of the tool.There are two stages that determine the time taken forcompleting a task. Reading data from a physical storage depends on the storage characteristics. Readanalysis is parallelized and depends on the core number. Weestimated FastContext performance characteristics on thelaboratory computing server with 16 cores and 50 Gb RAM.The dependence of processing speed on process count matchesthe expected values. 10,000 of paired-end reads are processingfor 2 seconds with 4 cores used, saving JSON increases thattime to 6 seconds. With Levenshtein statistics, the same dataare processing for 11 seconds, and 80 seconds are requiredto save JSON.Code accessFastContext source code is available at GitHub (https://github.com/regnveig/FastContext) and is distributed under GNUGeneral Public License v3.Despite the simplicity of the algorithm, FastContext may beuseful in read structure analysis. It has an appealing combinationof cutadapt  and FastQC featuresRecently, A. Bravo et al. (2021) presented a tool named2FAST2Q, which has features similar to FastContext, includingextracting and counting feature occurrences in FastQfiles. Unlike FastContext, 2FAST2Q can search for frequentunknown sequences , canhandle sequence mismatches, takes into account base Phredqualities, and therefore provides more accurate statistics onfeature counts. The qualitative difference of FastContext is thatthe tool can collect statistics on relative position of featuresin the read and features linkage.There remains the problem of sequencing errors. The possibilityof errors is directly dependent on sequence length.FastContext performs the search based on full match, there fore, under equal conditions, pattern sequences of greaterlength have a lower chance to be found, which may impactresulting statistics.Similarity based on Levenshtein distance is a crude approximationto probability of presence of a particular sequence.It fails to take account of in vitro processes during librarypreparation and sequencing. This problem may be solved infuture versions. As for now, the user can find Phred qualityscores for each read in a detailed statistics file, and estimateanalysis quality manually.Another possible feature that can be discussed is wildcards.This feature may be implemented in future versions.From all of the above, we can conclude that FastContext iseffective as a tool for NGS data analysis, and could be a veryuseful source of information in the development of new molecularbiology methods.The authors declare no conflict of interest.Aldridge S., Teichmann S. Single cell transcriptomics comes of age.Nat. Commun. 2020;11(1):4307. DOI 10.1038/s41467-020-18158-5.Andrews S. FastQC: A quality control tool for high throughput sequencedata. 2010. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.Bravo A., Typas A., Veening J. 2FAST2Q: A general-purpose sequencesearch and counting program for FASTQ files [preprint]. BioRxiv.2021. DOI 10.1101/2021.12.17.473121.Cock P., Antao T., Chang J., Chapman B., Cox C., Dalke A., Friedberg I.,Hamelryck T., Kauff F., Wilczynski B., de Hoon M. Biopython:freely available Python tools for computational molecular biologyand bioinformatics. Bioinformatics. 2009;25(11):1422-1423. DOI10.1093/bioinformatics/btp163.Costa-Luis C., Larroque S., Altendorf K., Mary H., Korobov M.,Yorav-Raphael N., Ivanov I., Bargull M., Rodrigues N., Chen G.,Newey C., Zugnoni M., Pagel M., Dektyarev M., Rothberg A.,Lee A., Panteleit D., Dill F., Kemenade H., McCracken J., NordlundM., Nechaev N., Desh O. tqdm: A fast, Extensible ProgressBar for Python and CLI. Zenodo. 2022. DOI 10.5281/zenodo.595120.Gridina M., Mozheiko E., Valeev E., Nazarenko L., Lopatkina M., MarkovaZ., Yablonskaya M., Voinova V., Shilova N., Lebedev I., FishmanV. A cookbook for DNase Hi-C. Epigenetics Chromatin. 2021;14(1):15. DOI 10.1186/s13072-021-00389-5.Martin M. Cutadapt removes adapter sequences from high-throughputsequencing reads. EMBnet J. 2011;17(1):10-12. DOI 10.14806/ej.17.1.200.Smirnov A., Fishman V., Yunusova A., Korablev A., Serova I., SkryabinB., Rozhdestvensky T., Battulin N. DNA barcoding reveals thatinjected transgenes are predominantly processed by homologousrecombination in mouse zygote. Nucleic Acids Res. 2020;48(2):719-735. DOI 10.1093/nar/gkz1085.The Pandas Development Team. pandas-dev/pandas: Pandas. Zenodo.2020. DOI 10.5281/zenodo.3509134.


Aliarcobacter, A. faecis and A. lanthieri, isolated from human or livestock feces, are closely related to Aliarcobacter zoonotic pathogens . In this study, comparative genomics analysis was carried out to examine the virulence-related, including virulence, antibiotic, and toxin (VAT) factors in the reference strains of A. faecis and A. lanthieri that may enable them to become potentially opportunistic zoonotic pathogens.Emerging pathogenic bacteria are an increasing threat to public health. Two recently described species of the genus flaA, flaB, flgG, flhA, flhB, fliI, fliP, motA and cheY1) as motility and export apparatus, as well as genes encoding the Twin-arginine translocation (Tat) , type II (pulE and pulF) and III  secretory pathways, allowing them to secrete proteins into the periplasm and host cells. Invasion and immune evasion genes  are found in both species, while adherence genes (cadF and cj1349) are only found in A. lanthieri. Acid (clpB), heat (clpA and clpB), osmotic (mviN), and low-iron (irgA and fur2) stress resistance genes were observed in both species, although urease genes were not found in them. In addition, arcB, gyrA and gyrB were found in both species, mutations of which may mediate the resistance to quaternary ammonium compounds (QACs). Furthermore, 11 VAT genes including six virulence , two antibiotic resistance [tet(O) and tet(W)] and three cytolethal distending toxin  genes were validated with the PCR assays. A. lanthieri tested positive for all 11 VAT genes. By contrast, A. faecis showed positive for ten genes except for cdtB because no PCR assay for this gene was available for this species.Our results showed that the genomes of the reference strains of both species have flagella genes (A. faecis and A. lanthieri reference strains through comparative genomics analysis and PCR assays highlighted the potential zoonotic pathogenicity of these two species. However, it is necessary to extend this study to include more clinical and environmental strains to explore inter-species and strain-level genetic variations in virulence-related genes and assess their potential to be opportunistic pathogens for animals and humans.The identification of the virulence, antibiotic-resistance, and toxin genes in the genomes of The online version contains supplementary material available at 10.1186/s12864-022-08663-w. Aliarcobacter (formerly Arcobacter) belongs to the family Campylobacteraceae in Epsilonproteobacteria  and three cytolethal distending toxin  genes were tested. However, six virulence , two antibiotic resistance [tet(O) and tet(W)] and two cytolethal distending toxin (cdtA and cdtC) genes were tested for A. faecis. No ctdB-based PCR assay was available for A. faecis.The detection of VAT genes was carried out using our previously developed species- and gene-specific primer pairs, mono- and multiplex Polymerase Chain Reaction (PCR) protocols . For A. The amplicon sizes of each mono- and multiplex PCR reaction were confirmed by 2.5% agarose gel electrophoresis (Fisher Scientific) using a 100 bp DNA size marker . The agarose gels were stained in ethidium bromide (0.5 μg/mL), and Alpha Imager (Fisher Scientific) was used for scanning and documentation.A. faecis AF1078T (= LMG 28519T) reference strain contained 2,327,155 bp in one scaffold, and the genome of A. lanthieri AF1440T (= LMG 28516T) reference strain contained 2,234,737 bp in one scaffold. The overall GC contents of the two genomes were 27.0 and 26.4%, respectively, which were consistent with other Arcobactersensulato species (Table 1). The numbers of protein-coding genes predicted in A. faecis and A. lanthieri genomes were 2319 and 2230, respectively (Table 1). A. lanthieri and A. faecis had a similar percentage (73%) of functionally annotated protein-coding genes with Clusters of Orthologous Groups (COGs)  in the complete reference genomes of Aliarcobacter species. To avoid errors in gene copy number estimation, draft genomes of A. cibarius and A. thereius were not included. Overall, the genes were assigned to 23 out of 26 COG categories in the genomes of all Aliarcobacter species, as shown in Table pulE, pulF) and III  secretory pathways were identified from genomes of all strains (Table SvirB4), VI  and VII (hcp) protein secretion systems were identified in the reference strains of A. faecis but not in those of A. lanthieri or A. butzleri included in this study  involved in the Twin-arginine translocation (Tat) secretion pathway were found in A. faecis, A. lanthieri and A. butzleri , deletion of which resulted in significantly attenuated virulence in C. jejuni , and three cytolethal distending toxin  [A. faecis and A. lanthieri using species-specific PCR-based assays [A. lanthieri tested positive for all 11 VAT genes. By contrast, A. faecis showed positive for ten genes except for cdtB because no PCR assay for this gene was available for this species [cdt  genes in the reference genomes of A. faecis and A. lanthieri strains. To validate our detection of the cdtB in A. faecis AF1078T genome, we aligned the cdtB gene of A. lanthieri (UnitProt ID: A0A2K9Y5C5) against the protein sequences of A. faecis strain AF1078T using BLASTp and identified gene 2,690,353,140 as the cdtB gene of A. faecis    genes, id assays . A. lant species . Howevercdt operon [cdtB is the active subunit, while cdtA and cdtC work as two regulatory subunits that bind to cdtB [cdt operon may indicate that the A. faecis strain AF1078T and A. lanthieri strain AF1440T could potentially be pathogenic; therefore, further in vitro research is warranted to investigate risk assessment analysis associated with human and animal health. In contrary to these results, studies have shown the absence of the cdt genes in A. butzleri [Of the Cytolethal Distending Toxin encoded by the t operon , cdtB is to cdtB . The prebutzleri , 79.cadF, ciaB, mviN, pldA, and tlyA virulence genes was reported in A. butzleri and A. skirrowii strains [tet(O) and tet(W) antibiotic resistance genes were also detected in both species, which has also been reported in A. cryaerophilus [Aliarcobacter.In summary, the results of our PCR assays are in congruence with previous studies where a high frequency of  strains , 81. Simrophilus . Our finAliarcobacter species, A. faecis and A. lanthieri, using whole genome sequencing, comparative genomics analysis, and qPCR validation. Our results generally showed genes encoding motility and export apparatus, secretory pathways, abiotic stress resistance, and antimicrobial resistance were found in both A. faecis and A. lanthieri. However, unique genes were also identified for individual species. We acknowledge that further in vitro and in vivo assays are required to evaluate the roles of virulence-related factors in the pathogenicity of A. faecis and A. lanthieri in human and animal infections.This study provided insights into the virulence-related factors identified in the reference genomes of two new Additional file 1: Table S1. COG gene occurrence in Aliarcobacter spp.Additional file 2: Figure S1. The amino acid alignment of the cdtB gene of A. faecis AF1078T (top) and A. lanthieri AF1440T (bottom).


Solanum lycopersicum) and cucumber (Cucumis sativus)], and discuss the research trends and application perspectives of the sterile trait in vegetable breeding and hybrid production, in order to provide a reference for fertility-related germplasm innovation.Vegetable crops are greatly appreciated for their beneficial nutritional and health components. Hybrid seeds are widely used in vegetable crops for advantages such as high yield and improved resistance, which require the participation of male (stamen) and female (pistil) reproductive organs. Male- or female-sterile plants are commonly used for production of hybrid seeds or seedless fruits in vegetables. In this review we will focus on the types of genic male sterility and factors affecting female fertility, summarize typical gene function and research progress related to reproductive organ identity and sporophyte and gametophyte development in vegetable crops [mainly tomato ( Published by Oxford University Press on behalf of Nanjing Agricultural University. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: Day Month 2022; Revised: Day Month 2022; Accepted: Day Month 2022
 Vegetable crops are of essential importance to the human diet, not only because of their enrichment in nutritional substances such as vitamins, polysaccharides, and minerals, but also due to their high content of beneficial health components, including fiber and bioactive compounds . With thArabidopsis, with an inferior superior ovary surrounded by six stamens   and C-class [AG (AGAMOUS)] genes [SEP (SEPALLATA) genes act as co-factors with B- and C- homeotic genes in specifying stamen primordia [Structural male sterility is caused by defects in stamen morphology. Mutants of this type display deformed stamens with rare pollen production . Genes i)] genes , 18. E-crimordia . TherefoTAP3 and TM6 are the homologs of the Arabidopsis B-class AP3 gene. The expression pattern of TAP3, TM6, and other identity genes is indicated in TAP3/STAMENLESS led to defective stamens with no pollen . In. Insexuaelopment . The splher wall , 44. Cucelopment . In toma tapetum  46]. MS. MSsexuaertility . Both to defects , 49. Thebidopsis –50. DYT1bidopsis . In ams  tetrads , 53. Anobidopsis , 55. BrT1 mutant . In toman tomato  46, 48]sexual stn pepper  and AMS in melon  and CaAMn pepper  have beespff  showed shrunken anther locules with very few inviable pollen grains , while rice Osfigl1 mutants displayed male sterility, with abnormal chromosome behavior and pollen abortion in the anther . To. To60]. n grains . Some gee anther . Tomato seedless . Arabidogression . Cucumbeterility .SlMAPK20 or SlMAPK4 resulted in abnormally degraded cytoplasm at the binucleate stage of pollen development . I. ICsPID itiation . Cucumbemulation . CsWOX1 mulation . In sevetegument . Auxin w mutants , 60, 105ogenesis  45]. Cs. CsCsPIDogenesis  [60]. Ho mutants . Besides mutants , 108. GA mutants , 108. Topression . IMA-RNAs formed . Loss ofn tomato . AGL11, bidopsis . Its hom numbers . Suppreshenotype .jasmonate-insensitive1-1  in tomato , tolerance of extreme environments , and adaptability to different cultivation modes (e.g. dense planting and soilless culture) will attract more attention during vegetable breeding in the future.We thank Dr Luo Chen for the pictures of lettuce flowers in C.Z. and S.W. wrote the original draft and prepared the figures; Z.X. supervised the work and revised the manuscript. All authors have read and agreed to the published version of the manuscript.The authors declared no conflict of interest.


Pseudomonas, Xanthomonas as well as by symbiotic rhizobium.Soybean is a pivotal staple crop worldwide, supplying the main food and feed plant proteins in some countries. In addition to interacting with mutualistic microbes, soybean also needs to protect itself against pathogens. However, to grow inside plant tissues, plant defense mechanisms ranging from passive barriers to induced defense reactions have to be overcome. Pathogenic but also symbiotic micro-organisms effectors can be delivered into the host cell by secretion systems and can interfere with the immunity system and disrupt cellular processes. This review summarizes the latest advances in our understanding of the interaction between secreted effectors and soybean feedback mechanism and uncovers the conserved and special signaling pathway induced by pathogenic soybean cyst nematode,  Soybean is one of the world’s four main grain crops, along with wheat, rice, and maize and is the only legume in that set . In addiPattern Recognition Receptors (PRRs). For effector-triggered immunity (ETI), the host recognizes the microorganism effectors generally by NLR receptors and the recognition response is associated with the long-standing gene-for-gene hypothesis [Molecular-pattern-triggered immunity (PTI) and pathogenic-effector-triggered immunity (ETI) are two interconnected defense strategies of plant responses to microorganisms . Patternpothesis . Facing pothesis ,21. For pothesis . Pseudomonas, Xanthomonas), and soybean cyst nematode (Heterodera glycines Ichinohe) that are necessary for infection. The effector response genes of soybean will also be reviewed. In this review, we will focus on the general function of effectors derived from symbiotic bacteria (rhizobium), pathogenic bacteria (Heterodera glycines Ichinohe) disease is one type of globally classified and devastating Glycine max disease [Soybean cyst nematode   can interact with the CSN5 Subunit of the COP9 Signalosome of soybean [Heterodera glycines can interact with Rhg1 α-SNAP physically, possibly functioning as an avirulence protein. When absent, it helps SCN to evade host defenses [To invade the host without triggering defense reactions, SCN secretes a diverse set of proteins called effectors, interacting with the plant immunity signaling ,34,35. I pallida  and tomachiensis . Cell-wachiensis . Meloido soybean . HgSLP-1defenses . Rhg1 locus, which is a QTL (Quantitative Trait Locus) mapping to linkage group G (Chromosome 18) [Glyma.18g022200 (Glyma.18g02580), Glyma.18g022500 (Glyma.18g02590), and Glyma.18g022700 (Glyma.18g02610) that show higher expression in root from SCN-resistant compared to SCN-susceptible varieties [Glyma.18g022500 codes an α-soluble N-ethylmaleimide-sensitive factor attachment protein, named α-SNAP18. Copy number variation in these germplasms can underly the resistance to SCN directly. For example, at least two copies are required to make the germplasm resistant to SCN [Rhg1 resistance type, α-SNAP depletes the abundance of SNARE-recycling 20S complexes, disrupts vesicle trafficking, induces an elevated abundance of NSF , and causes cytotoxicity [GmSNAP18 could be used to identify the SCN-resistant and SCN-susceptible germplasms. Rhg4 is also a locus underlying SCN resistance [Glyma.08g108900 codes a serine hydroxymethyl transferase (SHMT08) [Rhg4 locus. SHMT plays a role in one-carbon metabolism, methionine synthesis, and the maintenance of redox homeostasis during photorespiration [Resistant resources, such as Peking, PI88788, Fayette, and PI437654, were identified by screening for resistant germplasms. These germplasms all have the some 18) ,42,43. Tarieties . Glyma.1t to SCN ,46. In ptoxicity . The difsistance . Glyma.0(SHMT08) ,48 and wpiration ,50,51. CRhg4 GmSHMT08 haplotype [GmSNAP18 copies dropped below 5.6, a ‘Peking’-type GmSHMT08 haplotype (rhg4 locus) was required to ensure the SCN resistance [Rhg1 and Rhg4, other genes underlying soybean resistance to SCN were found on the different chromosomes [In general, genes conferring resistance against pathogens regulate plant defenses. Signaling and transduction networks were also shown to play pivotal roles in plant resistance against nematodes . Howeveraplotype ,54. Oncesistance ,54. Thisomosomes , all chromosomes . Some geomosomes ,57. Thisomosomes . In the omosomes . Syn12 and Syn16 belong to the syntaxins of the t-SNARE family and can interact with Rhg1 α-SNAP [Rhg1 WI12 (Glyma.18G02270) can interact with DELLA11 (Glyma.11G216500) directly. The expression of WI12 was induced by JA (jasmonic Acid), SA , and GA (gibberellic acid) [SLY1 complex. Once recruited to SCFSLY1, DELLA is polyubiquitylated and then subsequently degraded [DELLA11 results in decreased levels of JA and SA [GmSHMT can interact with GmPR08-Bet VI, the interaction was enhanced when GmSNAP18 was also present [Rhg1 and Rhg4 might be in a complex composed of GmSHMT08/GmSNAP18/GmPR08-Bet VI [To further elucidate the molecular mechanism of soybean resistance to SCN, the interaction network of α-SNAP was identified. Genes 1 α-SNAP . Rhg1 WIic acid) . Interesic acid) . JA and ic acid) . Reciproic acid) . JA and degraded . WI12 caA and SA . While G present . This su8-Bet VI ,59.Pseudomonas syringae is a plant pathogen that can colonize the intercellular spaces of leaves and other aerial organs. P. syringae strains are classified into about 50 pathogenic bacteria, mainly according to the origin of the host [Pseudomonas syringae pv. tabaci and P. syringae pv. glycinea are identical, but the ability of these two strains to induce a hypersensitive response in tobacco and soybean is different [P. syringae effectors has gone through several phases. First, a small number of effector proteins was identified as “Avr” (Avirulence) proteins in test plants with matching R genes [Pseudomonas syringae effector AvrPto binds receptor kinases PRR (pattern-recognition receptor), including Arabidopsis thaliana FLS2 (Flagellin sensitive2) and EFR (EF-TU receptor) and tomato LeFLS2 to block immune responses in plant cells [P. syringae effector protein AvrB, which is delivered into the plant cell by the bacterial T3SS, interacts with MPK4 (mitogen-activated protein kinases 4) and HSP90 (heat shock protein 90) partners, inducing MPK4 activation in an HSP90-dependent manner, interfering with hormone signaling and enhancing plant susceptibility [P. syringae effector HopAI1 activates the nucleotide-binding leucine-rich repeat (NB-LRR) protein SUMM2-mediated defense responses [P. syringae pv. tomato AvrPtoB effector has a carboxy-terminal domain that is an E3 ubiquitin ligase [Arabidopsis SnRK2.8 is required for bacterial virulence [the host . The amiifferent . The stu R genes . Second, R genes . Third,  R genes . Fourth, R genes ,70 has bnt cells  -interacting protein 4) gene homolog and blocks the recognition of AvrB by soybean [GmRIN4 at T198 [P. syringae host and GmHID1 (2-hydroxyisoflavanone dehydratase from G. max) is a virulence target of P. syringae essential bacterial virulence protein HopZ1, promoting P. syringae infection of soybean [G. max alkaline isoform of the PR-5 protein), purified from soybean hull can inhibit the growth of P. syringae pv. Glycinea [AvrB can also suppress flg22-induced callose deposition and basal defense responses ,79 and isp297Ala . P. syri soybean . T3SS-se at T198 . Soybean soybean . The PR5Glycinea . P. syringae pv. glycinea, but also attenuates the activation of GmMPK3/6 in response to P. syringae pv. glycinea infection [Similarly to previous studies, silencing GmFLS2 not only compromises the resistance of soybean plants to nfection . NopT ofnfection .GmRPG1 (Resistance to P. syringae pv glycinea) are resistant to P. syringae strains expressing the avirulence gene avrB [Rpg4 may partly explain the resistance of soybean to P. syringae pv tomato and other avrD-carrying pathogens [RPS2 (Resistance to P. syringae) gene encoding a CNL (coiled-coil NBS-LRR) domain protein from wild soybean confer resistance to P. syringae [Plant-resistance (R) proteins sense specific pathogen effectors to activate plant defenses and limit pathogen invasion. Soybean cultivars expressing the disease resistance gene ene avrB . In addiathogens . Two ortsyringae ,89. Xanthomonas is a Gram-negative, aerobic, chemo-organotrophic phytopathogen [Xanthomonas is a combination of the Greek yellow ‘Xanthus’ and the unit ‘monas’, which translates as ‘yellow monad’. The Xanthomonas name was originally proposed by Burkholder in 1930 and created by Dowson in 1939. Pathogens in this genus are often associated with plant diseases [Xanthomonas infects plants, the plant PAMP (pathogen-associated molecular pattern)-triggered immunity (PTI) and effector-triggered immunity (ETI) are triggered to prevent initial pathogen invasion [pathogen . The celpathogen . The wordiseases . Common diseases . When Xainvasion ,96,97. Minvasion ,85. Amoninvasion ,84  [Xanthomonas and the pathogenicity against tomato. XopD binds DNA in the plant nucleus to inhibit the transcription of senescence and defense genes and results in the attenuation of SA-dependent senescence in tomato [Xanthomonas helps with understanding the molecular mechanism of plant resistance against Xanthomonas. Compared with the pathogenicity of XopD mutant, the pathogenicity of XopN-deficient strains is greatly reduced [Xanthomonas infected tomato, but also significantly reduced the virulence when the XopN homolog mutant infected radish [Xanthomonas effectors are widely distributed and have certain pathogenic abilities in different species. In rice, the Xanthomonas effectors XopN, XopQ, XopX, and XopZ can inhibit the immune response induced by cell-wall-degrading enzyme treatment. XopQ and XopX interact with each other and can also induce the rice immune response [Xanthomonas in rice [Xanthomonas have transcription activator-like (TAL) activity. Among non-TAL effectors, XopAF and AvrBs2 are the most representative ones, with AvrBs2 being the first reported non-TAL effector [Xanthomonas oryzae PV. Oryzae, Xoo) strongly promote bacterial growth and the formation of necrotic spots in rice [There are 53 known effector families in s (Xops) ,103,104.s (Xops) . Previoun tomato . Furthern tomato . The dis reduced . This sid radish . Xanthomresponse . XopP ta in rice . With fueffector , essentieffector ,114. As effector . AvrXa7, in rice ,117. Ano in rice .Xanthomonas effectors are well described in rice and tomato, there is little information on the effectors that play a major role in the pathogenic properties of soybean X. axonopodis pv. glycines. So far, 169 strains of X. axonopodis pv. glycines have been identified and divided into three races, each of which carries five to six TAL effectors. In soybean, GmLOB1 confers resistance to Race 2, which is the most pathogenic one, but its connection with TAL-type effectors needs further analysis [Xanthomonas was caused by avrXg1 [Xanthomonas virulence and provides new ideas for seeking practical methods to control soybean bacterial pustules in agricultural production.Although analysis . In addiy avrXg1 . This fiX. campestris pv. glycines (Xcg), which were renamed X. axonopodis pv. glycines (Xag) in 1985 [Xag, including extracellular cellulase, protease, endo-β-1, 4-mannanase, and pectin acid ligase. They can stimulate the degradation of cellulose and hemicellulose in host plants and have varying degrees of impact on soybean production [Xag invasion, soybean produces isoflavones, such as daidzein, genistein, and glycitein [Xag by inhibiting the tyrosinase pathway. Exogenous application of genistein decreases the expression of the virulence factor yapH and promotes the up-regulation of several soybean defense genes [Xag. When OmpA is mutated, the contents of cellulase and pectin acid ligase of Xag are significantly reduced and the pathogenicity decreases [Xag virulence genes have also been identified [Xag, determines its pathogenic cycle, and allows for studying the mechanism of its pathogenic interaction with plants.The main epidemic disease on the commercial crop soybean is soybean bacterial pustules caused by  in 1985 . The sym in 1985 ,123. Due in 1985 . Severaloduction ,126,127.lycitein . Recent se genes . The outecreases . In addientified ,135,136.Pseudomonas and Xanthomonas contain six protein secretion systems of type I, II, III, IV, V, and VI, among which the type III secretion system plays a very important role in their pathogenicity [Pseudomonas and Xanthomonas can secrete more than 50 effectors with virulence functions into plant cells through the type III secretion system. The study on Pseudomonas effectors found that there was functional redundancy between effectors [Xanthomonas effectors described earlier. The first REG consists of AvrPto and AvrPtoB, which act early in Pseudomonas infection. AvrPto and AvrPtoB block the function of the PRR complex through inhibition or degradation and then block the expression of downstream components, such as BIK1 to inhibit PAMP-triggered immune (PTI) signaling [Xoo in Xanthomonas pre-infection pathway. The second REG contains HopM1, AvrE, and HopR1, which interfere with the downstream defense pathway. HopM1 targets vesicle transport by destroying the stability of MIN7, thereby affecting the production of antibacterial compounds [Xanthomonas effector XopBXe which blocks glucose-mediated defense signals by interfering with vesicle trafficking to affect cell-wall-bound convertases [Pseudomonas HopN1 affects ROS production by degrading PsbQ, while Xanthomonas XopDxcc interferes with signaling pathways involved in plant defense by preventing ROS production [Pseudomonas HopAI1 targets MPK4 to interfere with MAPK signal transmission and prevent the activation of effector-triggered immunity (ETI). Xanthomonas AvrBsT acts as an ETI inhibitor to prevent the ETI reaction mediated by AvrBs1 and XopQXe [Pseudomonas and Xanthomonas both need type III effectors to exert virulence and most effectors can play the same or similar role to activate or block plant defense signals. Both genicity . Pseudomffectors ,137, whiignaling ,139. Thiompounds . This isvertases . In addioduction ,143. Psed XopQXe ,145. ThuSoil is a complex system containing a large number of pathogenic and symbiotic bacteria that can infect legumes. In particular, rhizobia can form nodules by infecting legumes roots and form a symbiotic organ in which the rhizobia fix nitrogen that can be absorbed by legumes for their growth and development . Due to Nod genes but also the TtsI expression. TtsI acts as a transcriptional activator, binds to the tts box sequence at the promoter of T3SS-related genes, and activates their transcription , is induced by genistein, and is regulated by TtsI [Lotus japonicus, the NopC mutant, HH103ΩNopC, can establish a symbiotic relationship with Lotus japonicus Gifu and form normal nodules [NopC promotes an increased nodule number and weight in soybean roots [GmCRP to promote nodulation. NopC-GmCRP can interfere with soybean immunity by affecting the expression of GmPR1 and PR2 [The secreted effector NopC was first identified in  by TtsI . NopC is by TtsI . NopC pl nodules . In soyban roots . During  and PR2 . These fS. fredii strain HH103. It was induced in the presence of genistein [Xanthomonas, the C-terminal region of NopD contains a domain with homology to the ubiquitin-like protease Ulp1 and can process small ubiquitin-related modifier (SUMO) proteins and cleave SUMO-conjugated proteins [Arabidopsis to promote infection of Xanthomonas [Xanthomonas immunity [FBD/LRR and PP2C genes were identified by QTL mapping using wild-type and NopD mutants, showing that this effector can suppress their expression during HH103 infection [NopD was first detected in culture supernatants of enistein  through enistein . Similarproteins . XopD cathomonas . XopD coimmunity . In rhizimmunity . In addiimmunity . In soybnfection . FurtherRhizobium sp. strain NGR234 [Flemingia congesta and Tephrosia vogelii [S. fredii HH103 can modify GmPR1 expression during the HH103 infection of soybean. Earlier studies showed that GmPR1 is a member of a protein family that includes enzymes  that can directly attack pathogen structures, thereby acting as an antimicrobial determinant [GmMAPK3 and TLP gene expression, to promote nodulation in soybean Charleston [Rj2 can restrict the nodulation involving specific rhizobial strains, such as Bradyrhizobium diazoefficiens USDA122 [GmNNL1 was shown to be involved in symbiosis. By interacting with NopP from USDA110, GmNNL1 could trigger immunity and suppress rhizobia infection [NopP is a specific rhizobial effector, was first identified in n NGR234 , and is  vogelii . NopP inerminant ,168. Dur USDA122 , suggestnfection .Rhizobium sp. strain NGR234. It is a rhizobia-specific effector protein with multiple phosphorylation sites. In addition to the N-terminal secretory signal sequence, NopL consists of two large repeats and a C-terminal domain [Phaseolus japonicum and accelerate the senescence of Phaseolus japonicum nodules [PP2C (protein phosphatase 2C family)-related gene and RPK are induced in soybean, but their functions have not been further studied [The type III effector NopL was first identified in l domain . Its mut nodules . In addi nodules . In soyb studied .S. fredii strain HH103 [Shigella flexneri, Salmonella enterica, and Ralstonia solanacearum [R. solanacearum, significantly suppress pattern-triggered immunity (PTI) responses, such as the production of reactive oxygen species and the expression of defense-related genes, when expressed in leaves of Nicotiana benthamiana [N. benthamiana, NopM of strain NGR234 represses the production of reactive oxygen species induced by flagellin [Lablab purpureus [Lablab purpureus and has a phenotype similar to the NGR234 mutant [Similar to NopD, NopM was first detected in culture supernatants of in HH103 . It is anacearum ,176. Ripthamiana . RipAW athamiana . NopM, slagellin . Studieslagellin ,176. Analagellin ,176. Explagellin ,176. Muturpureus . Nodulat4 mutant . AlthougP. syringae, AvrPphB mutation promotes the growth of P. syringae in host leaves [P. syringae infecting A. thaliana [Mesorhizobium amphore restores nodulation of the legume tree black locust. Compared with the wild strain, this NopT mutant induces black locust roots to generate more jasmonic acid, salicylic acid, and hydrogen peroxide [P. syringae infection and symbiosis, respectively, suggests that legumes have evolved immune responses that are somewhat similar with pathogens and rhizobia. It also shows an evolutionary contradiction or balance between the need to resist pathogen infections, on the one hand, and the need to promote the establishment of symbiosis on the other.NopT is an effector protease belonging to the AvrPphB effector family. The protease activity of this family is dependent on a catalytic triad of amino acids that is present in NopT . In P. st leaves ,180. Avrthaliana ,179,180.thaliana . Mutatioperoxide . Similarperoxide . Similarperoxide . The comPhytophthora sojae, one glycoside hydrolase, PsXEG1, was identified as a glycoside hydrolase 12 family member and can hydrolase the same substrates as NopAA [P. sojae, the growth of P. sojae could be promoted using a PsXLP1 decoy that was similar to PsXEG1 but without its enzymatic activity. Additionally, PsXLP1 (PsXEG1-like protein) can protect PsXEG1 from GmGIP1 (PsXEG1 interacting protein) binding in vitro and in plants [GmARP (NopAA-related protein) was shown to positively regulate the establishment of symbiosis after interaction with NopAA. Similarly, GmARP overexpression promotes nodule formation after inoculation with either the wild strain or the NopAA mutant. In contrast, in GmARP-silenced plants, no differences in nodule number or dry weight were observed between plants inoculated with HH103 or the corresponding NopAA mutant [GmARP is a positive regulator of nodule formation and that it mediates NopAA signaling in plants. Thus, in addition to the hydrolase activity of NopAA, NopAA may act as a signaling molecule with GmARP to regulate symbiotic nodulation. NopAA is an effector belonging to the Glycoside hydrolase 12 (GH12) family. It can be secreted into the extracellular environment and its expression is promoted by genistein . The enzas NopAA . Becausen plants ,185. Mutn plants . Using gA mutant . These rIn future studies, more and more type III effectors will be identified and studied in the frame of symbiosis. Additional type III effectors might be identified and might participate in nodulation using different mechanisms and might unravel other connections with the immune signaling pathway of host cells. Recent studies have shown that the type III secretion system and the type III effectors of rhizobia and pathogens are conserved, indicating a probable common origin. This conservation is also an important tool to decipher their action during symbiosis. The identification and functional analysis of interacting proteins of these type III effectors in the legume host are very important for understanding their mode of action in relation to immunity. The findings summarized in this review point to an increasing interest in the identification and determination of the functions of bacterial and nematode secreted effectors. Dozens of different soybean germplasms, including cultivars, landrace, and wild soybean, have been tested to determine the symbiotic and pathogenic responses and identify these secreted effectors. More and more scientists are now paying attention on the functional analysis of numerous secreted effectors and the signaling they trigger. Once the detailed function of different secreted effectors is clear, breeders could utilize these results to assist cultivar breeding. Fine regulation of the nodule number and nitrogen fixation efficiency are desired targets for symbiosis application in the field. In addition, pathogen and symbiotic effector targets participate in common signaling pathways. Thus, one may use gene-modification strategies to regulate the soybean responses to both rhizobium and pathogens, including leaf pathogens, if signaling includes the shoot and the root. Therefore, more efforts should be made to increase our knowledge about soybean responses to beneficial and pathogenic microbes and cluster these genes on new cultivar breeding. Doing this, we could reduce the use of nitrogen fertilizers and chemical pesticides.


Ziziphus jujuba cv. Bokjo chloroplast genome by de novo assembly using next-generation sequencing. The complete circular chloroplast genome consisted of 161,714 bp and contained four parts: a large single-copy (LSC) region of 89,323 bp, a small single-copy (SSC) region of 19,361 bp, and two inverted repeat regions (IRa and IRb) of 26,515 bp each. The genome annotation predicted a total of 110 genes, including 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis demonstrated the close taxonomic relationship between Z. jujuba cv. Bokjo and two other members of the Ziziphus genus, Z. spina-christi and Z. mauritiana. We found 135 polymorphic loci, 63 single nucleotide polymorphism (SNP) and 72 insertion–deletion (InDel), from the comparison of Z. jujuba cultivar Bokjo and Z. jujuba reference (NC_030299). The polymorphic loci could be used for the differentiation of Z. jujuba genetic resources and for breeding in the future.We have sequenced the  Ziziphus jujuba Mill. 1768) is a deciduous tree belonging to the genus Ziziphus of the Rhamnaceae family. Z. jujuba inhabits subtropical and tropical arid regions, but some species occur in temperate and arid regions with continental climates  . A dried plant specimen was deposited in the Herbarium of the National Institute of Horticulture and Herbal Science, Eumsung, Republic of Korea  under the voucher number MPS006272. Total genomic DNA was extracted using the DNeasy Plant Mini Kit . The isolated genomic DNA was used to construct a paired-end (PE) library with a mean insert size of 700 bp, using the Illumina HiSeq platform. Contigs were assembled with a total of 11.96 Gbp PE reads collected from Illumina Hiseq next-generation sequencing using the CLC Genomics Workbench . The assembled structure and the genes of the complete chloroplast genome were annotated using the DOGMA program (http://dogma.ccbb.utexas.edu/)  each of 26,515 bp. We annotated 110 genes within the Z. jujuba cv. Bokjo chloroplast genome, which included 76 protein-coding genes, 30 tRNA genes, and four rRNA genes.We have completed the chloroplast genome of Z. jujuba cv. Bokjo and of 11 other species, including five ingroup species of the Rhamnaceae to which Ziziphus belongs, and six outgroup species of the Rosales. To generate the phylogenetic tree, we used the time-reversal model of the maximum-likelihood algorithm with 1000 bootstrap replications in the CLC Genomics Workbench . Six taxa of Rhamnaceae formed a monophyletic group that was distinct from six other species of the Rosales (Z. jujuba cv. Bokjo together with Z. jujuba (NC_030299) and close to Z. spina-christi and Z. mauritiana.We performed a phylogenetic analysis based on the complete chloroplast genome sequence of  Rosales . The phyZ. jujuba cultivar Bokjo to a Z. jujuba reference (NC_030299) and we found 135 polymorphic loci, 63 single nucleotide polymorphisms (SNPs) and 72 InDels. The polymorphic loci could be used for the differentiation of Z. jujuba genetic resources and for breeding in the future.We compared the chloroplast genome of