Subtypes of adult mammalian stem cells can be maintained in this poised, quiescent state, and subsequently reactivated upon tissue injury to restore homeostasis. However, quiescence can become deregulated in pathological settings. In this review, we discuss the recent advances uncovering intracellular signaling pathways, transcriptional changes, and extracellular cues within the stem cell niche that control induction and exit from quiescence in tissue stem cells. We discuss the implications of quiescence as well as the pharmacological and genetic approaches that are being explored to either induce or prevent quiescence as a therapeutic strategy.Cellular quiescence is a dormant but reversible cellular state in which cell-cycle entry and proliferation are prevented. Recent studies both  Stem cell quiescence is a dormant but reversible cellular state in which cell-cycle entry and proliferation are prevented. Intrinsic regulators include the cell-cycle machinery, autophagy, chromatin modifiers, and microRNAs. Extrinsic regulators include cell-adhesion molecules and secreted factors. Therapeutic modulation of stem cell quiescence could restore tissue homeostasis. Entry into quiescence tends to be associated with an alteration in metabolic activity regulated by mitochondrial biogenesis genes and macroautophagy.1/S transition (Drosophila testis knockdown of RBF (pRB homolog) results in active proliferation of quiescent hub cells, the signaling center for germline stem cell recruitment. On double knockdown of RBF and dE2F1 there is no active hub cell proliferation, and normal population size is restored  is one of the main suppressors of E2F transcription factor activity, making it a central player in mediating Gansition . RB-E2F restored . RB-E2F restored . Despiterestored . Ablatiocapacity . In contcapacity  and hippcapacity , withoutCdk2, Cdk4, or Cdk6 each affect tissue-specific proliferation in mice (reviewed in Cdk6 underlies heterogeneity in the quiescence of human HSCs and modulates the frequency of HSC division (CCNC (Human Cyclin C gene) in HSCs increases the quiescent SC pool , which regulate the switch between proliferation and quiescence . Single knockouts of division . Knockdo SC pool . The inviescence . Knockouof HFSCs  and HSCsof HFSCs . Likewisll cycle . Conditilated RB , subsequhaustion . Togethehaustion .Figure 1−/− mice have a higher proliferation rate than those in control mice  production. To achieve this, the environmental sensing target of rapamycin pathway becomes inactive, leading to increased macroautophagy and a decrease in mitochondria .Macroautophagy is a process of intracellular degradation characterized by the formation and elongation of a phagophore that engulfs cytoplasmic components to form an autophagosome. Fusion of the autophagosome with a lysosome allows for the recycling of cargo to sustain cell survival A. An incDirect suppression of metabolism is achieved through removal of mitochondria by repression of mitochondrial biogenesis/function genes  via macrThere is strong evidence for differences in the epigenetic landscape of quiescent and active SCs. One such epigenetic mark is chromatin methylation, which is coordinated by repressive Polycomb group (PcG) and activating mixed-lineage leukemia (MLL) proteins. PcG proteins recruit PcG-repressive complexes (PRC1/2), triggering H3 lysine 27 trimethylation (H3K27me3) to suppress gene expression, whereas MLL proteins mediate H3K4me3 to antagonize gene repression . BesidesMyoD, leading to exit from quiescence and expansion of activated MuSCs  signaling pathway or H4K20 dimethyltransferase Suv4-20h1, increase expression of MuSC differentiation regulators, such as PAX7 and ed MuSCs . Similared MuSCs . These omiRNAs also possess the ability to modulate gene expression, and several quiescent SC populations  have a common miRNA profile, suggesting a role for miRNA regulation in quiescence . Canonicin vivo are likely to be more complex and dependent on the specialized microenvironment, described as the niche, in which SCs reside  of the brain, quiescence is induced by specialized protrusions in physical contact with endothelial cells of the perivascular niche. The endothelial and membrane-bound ligands Jagged1 (JAG1) and EphrinB2 activate Notch and Eph signaling, respectively, and act as negative regulators downstream of the MAPK pathway to attenuate proliferation signals from soluble growth factors . ExternaIn contrast to its quiescence-promoting function in NSCs and MuSCs, the interaction of the HFSC Notch receptor with tissue resident regulatory T cells induces proliferation of HFSC and regeneration of hair growth . This il2+ pathway  and Secreted frizzled-related protein 1 (SFRP1) to promote differentiation of cells in the inner hair follicle bulge, which results in a compartmentalization of the hair bulge layers  regulate the maintenance of SCs and can trigger quiescence exit to promote proliferation and differentiation. Fibroblast growth factors (FGFs) are known activators of MuSCs, and increased FGF signaling causes loss of quiescence and SC depletion . Releasell cycle . Conversll cycle .0 cells to re-enter the cell cycle, thereby prematurely depleting the NSC pool (The transforming growth factor β (TGF-β) superfamily of growth factors, including bone morphogenetic proteins (BMPs), regulate key events in development and adult SC function . BMPs arNSC pool . TGF-β1 NSC pool . Thus, mMost cells in the body are in contact with extracellular matrix (ECM) proteins, which can be organized in a variety of ways, from basement membranes to collagenous fibers. The ECM provides attachment sites for residing SCs via specific receptors and ensures tissue integrity and cell survival . BesidesDisruption of tissue integrity through injury results in activation and release of stored growth factors  capable Integrins are central mediators of ECM signals to SCs and their regulation can impinge on additional pathways, creating complex regulatory networks and regulating the cell cycle . β1-InteIn several tissues, including the small intestine and the hair follicle , quiesceUncovering the mechanisms underlying SC quiescence provides opportunities for innovative therapeutic strategies. Such interventions fall into two main categories: “lock-out” strategies, which consist of pushing the cells out of the quiescent state to induce proliferation and differentiation; and “lock-in” strategies, which consist of re-establishing the quiescent state to prevent premature senescence or aberrant proliferation and differentiation . It has Several attempts have been made to genetically and pharmacologically induce activation of quiescent NSCs for tissue repair using a “lock-out” approach. For instance, depletion of neuroblasts and TAPs with the chemotherapeutic drug cytarabine stimulates rapid regeneration of the SVZ network , thoughtQuiescence “lock-out” strategies have been employed in other tissues such as the skeletal muscle, where regenerative potential depends on MuSCs . p38 MAPFBXW7, a protein that promotes the degradation of c-Myc and Notch  . MuSC quof MuSCs . Maintenof MuSCs . In coopof MuSCs .in vitro without a loss in potency. The potency of MuSCs correlates with their ability to remain quiescent, which is rapidly lost after isolation (An improved understanding of stem cell quiescence not only provides novel potential therapeutic interventions but could also improve previously established approaches. For instance, a key hurdle in autologous SC transplantation is the ability to manipulate the cells solation . While ssolation .0 that is actively maintained by various signaling inputs. Targeting quiescent stem cell populations is an attractive therapeutic strategy within the fields of oncology and regenerative medicine.Quiescence is a state of reversible arrest in GI.J.C., P.P.L., J.O., F.R., W.S., T.L.W., F.S., and F.M.W. conceived the manuscript. I.J.C., P.P.L., J.O., F.R., W.S., and T.L.W. wrote the manuscript. P.P.L., T.L.W., W.S., and F.R. designed the figures. J.O., T.L.W., and F.M.W. edited the manuscript.


Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes.Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis.Here, we initially characterized 2,483,032 SSRs (repeat units of 1–10 bp) from seven genomic sequences of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms.The present work constitutes the first deep characterization of SSRs in seven genomes of http://biodb.sdau.edu.cn/tmpd/index.htmlThe Tobacco Markers & Primers Database (TMPD) is available at The online version of this article (10.1186/s12864-018-4878-4) contains supplementary material, which is available to authorized users. Brachypodium [Brassica [Simple sequence repeats (SSRs), otherwise known as short tandem repeats (STRs) or microsatellites, are abundant and broadly distributed in eukaryotic and prokaryotic genomes. The length of an SSR shows extensive intra- and interspecific variation, primarily because of high rates of DNA replication error within SSRs –3. Hencehypodium , maize [hypodium , foxtailhypodium , BrassicBrassica  and cottBrassica .Nicotiana, a member of the Solanaceae family, is one of the most important research model plants and is of high agricultural value worldwide [Nicotiana have large genome sizes, averaging ~ 2.5 Gb for diploids and ~ 4.5 Gb for tetraploids, which made it challenging to sequence whole genomes [Nicotiana species or varieties and made available to the public [N. otophora (N. oto), N. sylvestris (N. syl) and N. tomentosiformis (N. tom) and from four allotetraploids, namely N. benthamiana (N. ben) and three major commercial varieties of N. tabacum (N. tab): TN90, K326, and BX [N. syl and N. tom lineages diverged about 15 million years ago [N. syl and N. tom are the ancestors of N. tab. An interspecific hybridization between N. syl and N. tom formed N. Tab. 0.2 million ago [N. tab varieties are nearly identical [N. ben is a tetraploid (38 chromosomes) that formed ~ 10 million years ago so it is far distinct from tetraploid N. Tab (48 chromosomes) [orldwide , 16. Spe genomes . With ree public . These s, and BX –21. The ears ago . As confears ago , N. syl lion ago . The thrdentical . N. ben mosomes) –21. AlthNicotiana currently are SSR markers. Two sets of SSR markers, 5119 named PT markers and 4886 named TM or TME markers, were designed from N. tab partial genomic DNA or EST sequences by Bindler and colleagues, and by Tong and coworkers, respectively [N. tab [N. tab genetic map [N. tom map, involving 489 SSRs and conserved ortholog set II (COS II) markers. The COS II markers are gene sequences of a small number of orthologous loci across the investigated species [N. acuminata contains a mixture of 308 SSRs and COS II markers [Genetic markers have been used in many types of biological research, including the construction of genetic maps, population genotyping, phylogenetics, genome comparisons, gene mapping, quantitative trait loci analysis and marker-assisted breeding , 24, 25.ectively , 27. Of etic map . In addi species . Similar markers . Some ofNicotiana, all with large genomes, the currently available markers represent only a small part of all possible SSR loci, and these may not be sufficient for some marker-based applications. In addition, most reported SSR markers were developed for one or two particular species or varieties only. Hence, the development of a whole-genome set of SSR markers across multiple species of Nicotiana genus is warranted. One complicating issue is that many Nicotiana species are polyploid, which can make it difficult to associate any given set of allelic polymorphisms with a particular homoeologous genome. Therefore, the study of markers in multiple genomes of Nicotiana will be most helpful if it provides exact allele information. Cross-species marker transferability has also proven to be an important issue during marker development in multiple plant lineages [Nicotiana species, analysis of both the homoeology and transferability of SSRs markers among species is more feasible, as previously shown [For the species of lineages . With thly shown .Nicotiana species. Our study discovered and characterized a comprehensive set of SSRs in silico in seven sequenced Nicotiana genomes mentioned above. We used our novel software package called GMATA® [Nicotiana genomes, and also developed an efficient protocol for SSR marker development that can be employed across any genome. The discovered Nicotiana SSRs and developed SSR markers were used to investigate marker polymorphism in these seven species. We also developed an online database called the Tobacco Markers & Primers Database (TMPD) to facilitate the use of the SSR information and markers.So far, genome-wide SSR distribution has not been well investigated across d GMATA®  to facilNicotiana genome sequences, including three diploids and four tetraploids species. The sequences used in this study total ~ 20 Gb, and are from N. ben, N. syl, N. tom, and N. oto, and from N. tab cultivars TN90, K326, and BX. These sequences represent a respective ~ 74%, ~ 80%, ~ 78%, ~ 81%, ~ 84%, and ~ 73% of each of the genomes, and are primarily deficient in the highly repetitive regions such as nested transposon blocks that tend to be poor (< 1%) in SSRs [Nicotiana genomes using the software GMATA [Nicotiana genomes were compared in Additional file We analyzed perfect repeated SSRs with repeat unit length between 1 and 10 bp across seven publicly available  in SSRs , 30, 31.Nicotiana, with a frequency of 61–65% . SSR length was classified into two categories in accordance with previous designations [Nicotiana. Class II type SSRs account for approximately 70, 68 and 72% of all SSRs in N. ben, N. tom, N. oto, respectively, while there is a higher but very similar percent of ~ 75% in N. syl and the three N. tab varieties TN90, K326, BX. The similarity of SSR length in the three N. tab varieties is consistent with the overall similarity of these genomes [Nicotiana genomes ranges from 23 to 32%. N. tom has a higher percentage (~ 32%) of class I SSRs than does N. syl and N. tab. There is a similar frequency (~ 25%) of class I SSRs in N. syl and N. tab. The overall trend of SSR length distribution is that the frequency of occurrence decreases as the SSR length increases  from seven genomic assemblies and compared the location of SSRs in these scaffolds. The results showed that the location of SSRs did not follow any obvious pattern in linear genomic sequences Fig. . We furtNicotiana SSRs was carried out using the GMATA software [N. ben, N. syl, N. tom, N. oto, and N. tab TN90, K326, BX, respectively. Generally, the abundance of grouped motif pairs in Nicotiana increased with the size of the genome sequence. N. tab has the highest number of grouped motif pairs, but this number differs somewhat between N. tab varieties. The motif pairs ranking at the 20 highest frequencies in each of the seven Nicotiana genomes are shown in Additional file Nicotiana genomes. Grouped motif pairs GC/GC and CG/CG are the rarest di-nucleotide motifs, at frequencies of ~ 0.1–0.17%, ranking after twenty tri-nucleotide motif pairs. The distribution of tri-nucleotide motif pairs displayed major genetic variation among these Nicotiana genomes. Motif pairs CAA/TTG and GTT/AAC are the most abundant tri-nucleotides, with a total frequency of ~ 5% in six of the genomes, but N. tom has more motif pair ATT/AAT than motif pair CAA/TTG and GTT/AAC. AAAT/ATTT is the most abundant tetra-nucleotide motif pair in six of the genomes, but is the second most abundant in N. ben, after the ATAC/GTAT motif pair. The remaining motif pairs with repeat lengths > 4 bp are the rarest motifs  genome) markers. The information on all designed NIX markers is provided in “sts” format, according to the NCBI’s rule for marker information, and is freely available to the public in our online database TMPD as described later.To develop a comprehensive set of SSR markers at a genomic sequence scale in multiple software . In tota similar , 20; theNicotiana. After removing redundancy of published markers based on primer sequence similarity, 5397 unique SSR markers from Bindler et al. [To investigate the novelty of the NIX markers, a comparison was conducted between NIX markers and previously published markers in r et al. , 33 and r et al. , 34 werer et al. , 33, 34.Nicotiana genomic sequences. Two copies of genes in tetraploid Nicotiana will produce two alleles of PCR product if repeat numbers are different. We found that all the designed NIX markers would produce at least one amplicon in at least one investigated genome. In the diploids, ~ 30% of designed NIX markers would amplify DNA in N. syl while a lower percentage (~ 25%) would provide an amplification product in both N. tom and N. oto. For tetraploids, ~ 53% of NIX markers are amplifiable in each of the three N. tab varieties, while only ~ 23% would amplify an SSR product in N. ben. Because the information regarding common and species-specific NIX markers will be extremely useful for marker selection during application, we checked this for all NIX markers. A total of 9948 NIX markers (~ 0.8%) will be amplifiable in all seven investigated Nicotiana species or varieties, so we infer these markers are very likely to be amplifiable in any other Nicotiana species. There are also many species-specific NIX markers . N. ben has more species-specific NIX markers than any other, which may be explained by the fact that N. ben is the most distantly related of the Nicotiana species analyzed [N. syl  are in common, while only a few markers (2.3–3.5%) are variety-specific  of the NIX markers were shared with both progenitors N. syl and N. tom. Besides the common NIX markers, N. tab appears to have inherited a different number of NIX markers from its two putative progenitors, 34.8% from N. syl and 25.6% from N. tom . Thus, an in silico simulated PCR was carried out to investigate polymorphism across the seven analyzed . The fewsyl Fig. . Of the fic Fig. . Despitetom Fig. .Fig. 3VeNicotiana genomes. Of the amplifiable NIX markers in a given genome, on average, ~ 81% of the NIX markers are predicted to produce one fragment while ~ 8% will produce two fragments. Species N. ben has the lowest percent (~ 6%) of NIX markers producing two fragments while N. oto has the highest percent (~ 11%). In the seven Nicotiana genomes combined, ~ 3.8% of NIX markers yield many predicted fragments (> = 11), suggesting that they may be amplified from repeated DNA sequences.A total of 744,993 (61%), 211,845 (17%) and 106,472 (8.7%) of the designed NIX markers are predicted to produce a respective one, two or three PCR fragments from the combined sequences of these seven genomes. Some NIX markers will amplify only from one or a few Nicotiana genomes. The polymorphism information is available in the TMPD database.For all 1,224,048 NIX markers, the predicted amplicons were scored for predicted length polymorphisms across the seven genomic sequences Table . A totalNicotiana accessions, including four Nicotiana species of N. syl, N. tom. N. Tab K326 and N. ben with known genomic sequence and additional species N. glutinosa or accession N. Tab HD with unknown genomic sequence   of the SSRs are short (< 20 bp), which is routinely correlated with a relatively low level of polymorphism for these markers. Our comparison of distribution revealed that SSRs in Nicotiana are mainly located in the regions between genes. This observation may partly explain the low rate (~ 4%) of polymorphism identified during Nicotiana SSR marker screening in an earlier study [SSRs have been comprehensively characterized for some plant species after their genome sequences were published, including in hypodium , foxtailhypodium , 35, 36,Brassica , and casBrassica . CurrentBrassica . Howeverpossible . The gene GMATA®  was useder study  that useNicotiana SSRs were focused on a specific genome or variety. In this study, we compared SSRs between tetraploid N. tab and its ancestral diploids, between varieties of tetraploid N. tab, and between different tetraploid species. Comprehensive comparison revealed genome-specific SSRs in each of the seven Nicotiana genomes. Some of the absences of SSRs in certain accessions may result from incompleteness in the genome sequences. However, most genomic sequences that are missing in these seven assemblies are repetitive sequences that are generally deficient in SSRs [N. Tab BX and N. ben, for instance, have incomplete genome sequences, believed to represent 74 and 73% of full genome sequence, respectively [N. Tab BX did not show a biased distribution of amplicons by in silico analysis compared with the other genomes. N. ben has the fewest NIX markers that are predicted in silico to produce two fragments, which may be caused by both the less complete sequences and perhaps by the fewer chromosomes (38) in this species, compared to the 48 chromosomes in other tetraploids. Perhaps the chromosome number reduction was associated with some DNA loss during tetraploid evolution.Previously, studies on  in SSRs . Therefoectively , 20. HowN. oto has more grouped motifs than diploid N. syl, which indicates that the two genomes became very different after their lineages diverged from the same ancestor. This conclusion is also supported by genome sequence comparison of these two species [N. tab have very similar numbers of grouped motifs, indicating their limited degree of divergence. This high homology, also seen in earlier studies [Nicotiana genomes have similar di-nucleotide type abundances. However, mono-nucleotide, tri-nucleotide and other higher-order repeats were found to vary a great deal among Nicotiana genomes. These long SSRs are the major differences in SSRs between these Nicotiana genomes. In bacteria, previous studies have shown that many SSRs in intergenic or upstream regions can have regulating functions [N. ben and N. tom shared a very similar abundance order. The similar distribution of short SSR repeats in N. syl and N. tab may be partially explained by the fact that N. tab has retained more genomic sequence from N. syl than from N. tom [Nicotiana. In conclusion, all genomes shared most of their SSR motifs while each genome has its own specific motifs, especially for larger repeat lengths and distribution frequencies.Diploid  species . In tetr studies , is likeunctions , and thim N. tom , 22, 23.Nicotiana genomes will provide insights into SSR evolution. SSRs in allopolyploids of N. tab showed considerable departure from the predicted additivity of their ancestral progenitors, N. syl and N. tom, which was demonstrated by the distribution of shared and specific NIX markers  and N. tom-specific NIX markers . This difference may partially be caused by both the incomplete genome sequences and real biological differences. An increase in amplifiable NIX markers (net increase of 2429 or 1.7%) means increased SSRs in polyploids relative to their diploid progenitors. In contrast, SSR frequencies in Brassica species were observed to decrease after polyploidization [N. tab is less than the sum of their ancestral progenitors, N. syl and N. tom . It has been previously noted that the genome reduction from the N. tom ancestor was greater than that from the maternal N. syl genome in natural N. tab [N. tab may be from the amplification of DNA from the N. syl-like ancestor and loss of DNA from N. tom ancestor, which is also supported by the genomic sequence comparison between species [SSR evolution can be revealed by comparison of the SSR and its flanking sequence. The NIX markers were designed from the sequences flanking SSRs, so the amplicons’ lengths in different ers Fig. . There idization . The genl N. tab , 23. ThiNicotiana species. For tetraploid N. tab, the genetic map contains around 2000 SSR markers [N. acuminata and N. tom genetic maps, a mixture of 489 and 308 SSR plus COSII markers were also reported, respectively [Nicotiana. Thus, the NIX markers reported here have increased, about 240-fold, the SSR marker resource for the Nicotiana community. We identified 9948 SSR markers that were informative on all seven Nicotiana investigated. These transferable SSRs will facilitate future characterization of genomic diversity, relatedness and evolution across the entire Nicotiana genus.SSR markers have been used in several genetic maps of  markers , 33. In ectively . The totNicotiana.The great value of SSR markers is their co-dominance and allelic multiplicity. The information for predicted allele number and size were determined and provided for each NIX marker in each of the seven genomes, so this will be an immediately useful resource for marker-assisted selection and genetic studies. This is the first report of comparative marker amplification information across multiple genomes of the same genus, and our TMPD database makes it easy to search for and compare the information for each marker, which will facilitate the efficiency of NIX markers use to follow linked agronomic or other genetic traits in future studies. In total, ~ 94% of NIX markers amplify 1–2 alleles per genome. The remaining NIX markers may be less useful for application due to multiple copies in a single genome, which is a possible outcome of their presence in repeated sequences such as transposable elements. In the past decade, molecular breeding using DNA markers has become the norm with many crop species –42. The A highly efficient experimental protocol for the use of SSR markers was developed here, as well. Because all NIX markers were designed for uniform PCR conditions, the PCR reaction can be conducted at the single annealing temperature of 60 °C. For the standard PCR setting, the user will just add DNA, primers, and water to our standard master mix. This will facilitate rapid PCR application. Our PCR-based experimental validation of 120 NIX markers across five species or varieties demonstrated that the method worked in 100% of the cases investigated. Thus, the PCR product scoring method for NIX is of high efficiency, high resolution and high throughput with little background noise. Unlike the broad/fuzzy peaks seen with much PCR/SSR analysis, the sharp peaks in our method may result from the fully functional Taq polymerase employed, which retains the 3′-5′ exonuclease activity. In addition, our PCR settings for NIX marker have a high stringency that leads to the exclusive production of specific PCR fragments.Nicotiana genus, developed NIX markers for these genomes, and constructed an online database for using the information. The NIX markers greatly expand Nicotiana marker resources, thus providing an immediately useful tool for research and breeding. We demonstrated a novel protocol for SSR marker development and SSR utilization at the whole genome scale that can be applied to any lineage of organisms. We also developed the TMPD database to facilitate NIX marker utility.We characterized SSR in seven genomes of Nicotiana used here are from publicly available databases. The draft assembly (version 0.44) of the genome sequence for N. ben was retrieved from the web site of Solgenomics. The genome sequences of N. syl , N. tom , N. oto (Accession No. AWOL000000000.1), N. tab TN90 (Accession No. AYMY00000000.1), N. Tab K326 (Accession No. AWOJ00000000.1) and N. tab Basma Xanthi (Accession No. AWOK00000000.1) were retrieved from Genbank at NCBI using the web links as described previously [The genomic sequences of seven eviously .Nicotiana species by using our published software package, GMATA [http://sourceforge.net/projects/gmata/). The parameters of SSR unit length were set to at least 12 bp for mono-nucleotide repeats, and at least five tandem copies for 2 bp to 10 bp nucleotide motifs. The five tandem copies criterion was used from our previous experiments [Perfect SSRs, consisting of perfect repetitions of the same kind of nucleotide unit, were mined from whole genomic sequences of e, GMATA  . DNA was diluted to 30–50 ng/μl in water before use. 120 markers were randomly chosen from the predicted commonly amplifiable makers across seven Nicotiana genomes for validation by using PCR amplification Additional file 2:Figure S1 SSR length distribution. (PDF 364 kb)Additional file 3:Table S2 Duplication between NIX and reported markers. (XLS 41 kb)Additional file 4:Table S3 Information for experimentally validated markers. (XLS 51 kb)


Helicobacter pylori activity, with emphasis on involved mechanisms of action. Lastly, the issue of safety profile of these plant products has also been addressed.In this narrative review, we have comprehensively reviewed the plant sources used as antiulcer agents. From traditional uses as herbal remedies, we have moved on to preclinical evidence, critically discussing the in vitro and in vivo studies focusing on plant extracts and even isolated phytochemicals with antiulcerogenic potential. A particular emphasis was also paid to  Peptic ulcers (PU) are sores or lesions in the gastrointestinal mucosa extending throughout the muscularis mucosae, typically characterized by different stages of necrosis, neutrophil infiltration, blood flow reduction, increased oxidative stress and inflammation . PU maniHelicobacter pylori infection, where the chronic use of non-steroidal anti-inflammatory drugs (NSAIDs) and acetylsalicylic acid (ASA) are some of the disease-causing factors.The disease is mostly categorized based on its anatomical origins, such as gastric  and duodenal  ulcers . StudiesH. pylori infection, pharmacological agents used in an effective management and also pointing out the latest challenges and opportunities of using plant phytochemicals as upcoming antiulcerogenic agents. Lastly, a special emphasis was given on plant products safety and security, in order to trigger the interest in deepening skills on this matter and to ensure an effective managing competence for health-related systems. Thus, based on the latest advances on this field and stress the fact that PUD is an important cause of morbidity and health care costs, the present report aims to provide a general overview on peptic ulcers, namely considering their epidemiology, main symptoms and clinical features, pathogenesis, where a particular emphasis will be given to H. pylori infection prevalence, increasing with NSAIDs and ASA use, as also with ageing population. PUD had a tremendous effect on morbidity and mortality until the last decades of 20th century, when a significant decline in its incidence was observed [H. pylori spread [H. pylori infection treatment and prevention. However, by the turn of the century, the increased use of NSAIDs has resulted in a decline in duodenal ulcers (H. pylori-associated infection) and increase in gastric ulcers (NSAIDs-caused ulcers) [H pylori infection is highly prevalent [H. pylori before the age of 10 and the prevalence peaks at more than 80% before the age of 50 in the developing countries [H. pylori infection is uncommon before age 10 in developed countries, such as US but increases to 10% between 18 and 30 years and to 50% in ages above 60 years [H. pylori infection will lead to an ulcer, while a larger proportion of people will get non-specific discomfort, abdominal pain or gastritis.Epidemiological studies have established that the prevalence of PU is a reflection of observed . This dri spread . Also, t ulcers) . Neverthrevalent . Studiesountries . However60 years . Indeed,Most patients with PU present abdominal discomfort, pain or nausea, with epigastric pain being the most common PU symptom . This is characterized by a gnawing or burning sensation occurring after meals. Usually, duodenal ulcer pains can be relieved with food or antacids , while gH. pylori infection has been known to play central role in the development of chronic gastritis, gastric ulcers, duodenal ulcers and gastric cancer [H. pylori triggers chronic gastritis by gastric epithelium infiltration and underlying lamina propria by immune cells, such as neutrophils, macrophages, lymphocytes and mast cells. Also, H. pylori produces some toxic biomolecules to the epithelial cells, such as ammonia produced to regulate stomach pH, proteases and vacuolating cytotoxin A, which damages epithelial cells and could cause apoptosis and certain phospholipases [H. pylori-derived biomolecules, such as lipopolysaccharide (LPS) and cysteine-rich proteins (Hcp), particularly HcpA (hp0211), have been shown to trigger immune response and contribute to inflammation [The pathogenesis of PU has been found to be complex and multifactorial. However, one common feature in its pathogenesis is the imbalance between aggressive luminal factors (gastric acid and pepsin) and defensive mucosal barrier function . Criticac cancer . H. pyloolipases . Else, Hammation ,18. TherH. pylori infection. In fact, it has been reported that chronic NSAIDs use could damage gastric and duodenal mucosa via several mechanisms, such as drugs-induced topical irritation of the epithelium, impairment of the barrier properties of mucosal membrane, suppression of prostaglandins synthesis in the gastric area, reduction of blood flow to the gastric mucosal and interference with superficial injury repair [Studies have established an association between chronic NSAIDs use and incidence of PU in the developed world. This was consequent upon the discovery and treatment of y repair . Anyway,y repair .Pharmacological management of PU continues to evolve despite the availability of diverse types of new therapeutic agents, with the aim of centering treatment on pain relieving, ulcer healing and in ulcer recurrence delay. However, many of the pharmacological agents available for treating PU are targeted at either counteracting the aggressive factors or stimulating the mucosal defense. Such drugs , targeteSince ancient times, plants and plant derived-products have been used in folklores around the world for the treatment of several ailments and diseases. Nowadays, herbal medicine is becoming a viable alternative treatment over the commercially available synthetic drugs on PU management/treatment. This is premised on its lower cost, perceived effectiveness, availability as well as little or no adverse effects. A number of these herbal remedies have demonstrated gastroprotective properties ,27,28,29Helicobacter pylori,” “infection”, “peptic ulcer”, “bioactive molecules”, “phytochemicals”, “plant species”, “antiulcerogenic”, “gastroprotective”. In addition, the biography of all selected articles was accurately handled in seeking for additional relevant articles.An extensive search of existing literature was performed and carefully collected from all scientific journals , books and reports from worldwide accepted databases . The following keywords were searched, “This section reports the plant extracts with antiulcerogenic activity that are also briefly summarized in H. pylori effects. Below, are briefly described all the studied plant extracts with antiulcerogenic activity, its corresponding modes of action and studied models.Among the studied plant extracts, those belonging to the Asteraceae, followed by the Combretaceae and Fabaceae families, were the most frequently studied and were reported to have promising wound healing, antioxidant, anti-inflammatory, cytoprotective, gastric secretion inhibition, mucus production improvement, HSP70 up-regulation, Bax protein down-regulation, anti-secretory and anti-Centella asiatica (L.) Urban is a very important medicinal herb used in the Orient. In China, it is called gotu kola and is one of the reported “miracle elixirs of life,” known of over two thousand years ago. C. asiatica leaf extract (50 or 250 mg/kg) evidenced a pronounced gastroprotective activity against indomethacin-induced ulcer in rats [ in rats , that co in rats . Several in rats .Baccharis dracunculifolia DC is a native plant species from Brazil and represents the main source of southeastern Brazilian propolis, commonly known as green propolis. The essential oil from its leaves, rich in non-oxygenated and oxygenated terpenes, showed antiulcer activity in rats , lowering the lesion index, total lesion area and the percentage of lesion, with a consequent reduction of gastric juice volume and total acidity [B. dracunculifolia leaves, in terms of phenolic compounds, was accessed and investigated its bioactive potential in rats with trinitrobenzenosulfonic acid (TNBS)-induced ulcerative colitis [ acidity . In anot colitis . The ora colitis .Baccharis trimera (Less.) DC, popularly known as “carqueja” in Brazil, is widely recognized as a treatment for gastrointestinal, hepatic and kidney disorders and diabetes. The anti-secretory and antiulcer activity of B. trimera aqueous extract (1000–2000 mg/kg) was already reported in stress-induced ulcer model and pylorus ligature model [B. trimera extract (90%), it was shown that the oral administration of 30 mg/kg significantly reduced the lesion area and the macroscopic appearance of acute and chronic ulcer models [B. trimera inhibits gastric acid secretion by acting on the cholinergic regulatory pathway. However, Lívero et al. [B. trimera extract in preventing or reversing ethanol- and acetic acid-induced ulcers may be attributable to the inhibition of free radical generation and subsequent prevention of lipid peroxidation and that flavonoids and caffeoylquinic acids detected in the studied extract play an important and contributive role on these effects.re model  and evenre model . In a mor models . Also, io et al.  proposedHieracium L. genus (Compositae) are used as anti-inflammatories and diuretics in traditional European Medicine. A study performed with a chloroform extract of H. gymnocephalum blooms at 25, 50, 100 and 200 mg/kg, in Wistar rats with indomethacin-induced acute ulceration, suggested that the extract has anti-inflammatory and gastroprotective effects, though poor antioxidant activity [H. gymnocephalum chloroform extract were the main contributors to observed anti-inflammatory and gastroprotective effects.Some species from activity . Based oTanacetum larvatum (Griseb. ex Pant.) Kanitz is an endemic perennial herb distributed on rocky places in Serbia, Montenegro and Albania. The chloroform extract from the aerial blooming parts of T. larvatum showed a dose-dependent anti-inflammatory activity, with significantly less gastric lesions at 200 mg/kg dose in Wistar rats ulcered with indomethacin [methacin . The autmethacin  and to emethacin .Vernonia condensata Baker are traditionally used in folk medicine, being this plant widely known in Brazil. The gastroprotective and gastric healing properties of a crude ethanolic extract from leaves of this plant  were evaluated in Wistar rats and mice ulcered using ethanol and indomethacin [V. condensata (200 mg/kg) in the same model [V. condensata extract presents an antiulcer effect, mediated through inhibition of gastric secretion via cholinergic and gastrinergic pathways and produces a cytoprotective effect by increasing antioxidant activity and mucin content and also inhibits neutrophil migration [The leaves from methacin . The resmethacin , similarme model . Therefoigration . Solidago chilensis Meyen—popularly known as “vara dorada”—is a native plant from South America, widely used in folk medicine as an anti-inflammatory, diuretic and for gastrointestinal disorders. The gastroprotective effect of S. chilensis methanol leaf extract (100 and 300 mg/kg) was evaluated in gastric ulcer models of Swiss mice and in L929 cells [S. chilensis inflorescences  in albino mice subjected to ethanol-induced gastric ulcer model, a significant antiulcer activity was also demonstrated [29 cells . The res29 cells . In anotnstrated .Cordia dichotoma G. Forst, commonly known as “Bhokar” in Marathi, are attributed many medicinal properties in Ayurveda Medicine. The methanol fraction of the crude methanol extract of C. dichotoma bark (500 mg/kg) showed a protective role against acid acetic-induced ulcerative colitis in Swiss mice trough anti-inflammatory and antioxidant mechanisms [To chanisms .Moringa oleifera L.—also known as horseradish tree and rumstick tree—is a perennial plant indigenous to Northwest India, Pakistan, Bangladesh and Afghanistan and commonly used for medicinal and nutritional purposes. The ethanolic root-bark extracts of M. oleifera  were tested as antiulcer agent in albino Wistar rats with ethanol-induced and pylorus ligation-induced gastric ulceration models, being stated prominent antiulcer, anti-secretory and cytoprotective abilities [M. oleifera seeds showed therapeutic effects in Wistar rats with acetic acid-induced colitis, even causing a significant reduction of ulcer severity, area and index as well as on mucosal inflammation severity and extent, crypt damage, invasion involvement, total colitis index and myeloperoxidase activity [bilities . Moreoveactivity . On the activity .Capparis zeylanica L. is widely recognized in traditional Ayurvedic Medicine. The methanolic extract from its leaves (200 mg/kg) exhibited a stomach-protective effect against ethanol necrotic damage in a study performed using three different models  of induced ulcers in albino rats [C. zeylanica leaves, among them flavonoids, tannins and saponins.ino rats . The autSalvadora indica Royle—commonly known as “jhak” in Hindi—is traditionally used as an important key ingredient in tooth care products by Arabian people. A study performed with the ethanolic extract of S. indica leaves , using pylorus ligation, ethanol and cysteamine induced ulcer models in albino rats, showed a dose-dependent cytoprotective effect against ethanol-induced cellular damage in gastric mucosa [c mucosa . FlavonoMaytenus robusta Reissek is used in Brazilian folk medicine to treat gastric ulcers and its gastroprotective properties have been demonstrated in acute gastric ulcer models [M. robusta in chronic gastric ulcer has been attributed to its ability to empowering protective factors of the gastric mucosa, such as mucosa layer regeneration, antioxidant defenses and cell proliferation [M. robusta hydroalcoholic extract were demonstrated in acute gastric ulcer models, where particularly leaves  [M. robusta aerial parts was evaluated in Wistar rats with acetic acid-induced chronic ulcer model and in L929 cells, to determine its effect on cell proliferation, free radicals scavenging and inflammatory and oxidative damages [2O2 and free radical scavenging [n-hexane and dichloromethane fraction of M. robusta root barks, respectively; their gastroprotective activity was evaluated in mice with ethanol and NSAIDs-induced ulcer models [M. robusta is rich in pentacyclic triterpenes [M. robusta have been ascribed to the ability of pentacyclic triterpenes to stimulate mucus synthesis and prostaglandin secretion, thus strengthening gastric mucosa defense factors [r models ,28. The feration . In fact0 mg/kg)  and 15-d damages . The resavenging . In anotterpenes ,117 and, factors . However factors .Mukia maderaspatana (L.) M. Roem leaves are commonly used in Siddha and Ayurvedic Medicine. The ethanolic extract from M. maderaspatana was able to reduce gastric mucosal lesions, malondialdehyde (MDA) and TNF-α levels, while increased gastric juice mucin content and gastric mucosal catalase (CAT), nitric oxide and PGE2 levels in rats with indomethacin-induced gastric ulcer [ic ulcer . These bMomordica cymbalaria Hook f. is well-known as “Athalakkai” in Tamil and it is available in various parts of India, where M. cymbalaria fruits decoction are used in traditional medicine as a treatment for gastric ulcers. Wistar rats with ethanol-induced ulcer were treated with 500 mg/kg of the aqueous extract from M. cymbalaria fruits and showed a decrease in total acidity, ulcer index and gastric lesions, while histopathological parameters improved [improved . Furtherimproved  and otheimproved ,121.Cibotium barometz (L.) J. Smith is a tropical and sub-tropical plant, also known as “golden hair dog fern,” used as medicinal plant in Malaysian Peninsula and parts of China. The gastroprotective effect of the ethanolic extract from its leaves [C. barometz leaves presented a dose-dependent antiulcer effect, increased antioxidant enzymes activity, such as superoxide dismutase (SOD), CAT and glutathione peroxidase (GPx) and decreased lipid peroxidation [C. barometz hairs presented a dose-dependent antiulcer effect too, free radical scavenging activities, increased pH, gastric mucus glycoprotein and antioxidant enzymes activity  and reduced MDA levels [C. barometz leaves and hairs were proposed as being related to HSP70 up-regulation and Bax protein down-regulation [s leaves  and hairs leaves  was evalxidation . On the A levels . Moreovegulation ,54. Cyperus rotundus L. a widely used plant against gastric ailments in traditional Indian Medicine, especially in Ayurveda. The oral administration of methanolic extract from C. rotundus rhizomes (250 and 500 mg/kg) inhibited aspirin-induced ulceration in Wistar rats in a dose-dependent manner, being even comparable with standard drug ranitidine (50 mg/kg) [0 mg/kg) . Moreove0 mg/kg) . Also, i0 mg/kg) .Caesalpinia sappan L.—widely known as pattanga—has been used in the Ayurveda system of medicine for a long time. The hydroalcoholic extract from C. sappan heartwood is rich in polyphenols, including flavonoids such as brazilin, brazilein, hydroxybrazilin and peonidin-3-galactoside which display an interesting antioxidant activity [+/K+-ATPase (proton pump) inhibitory assay at 500 µg/mL. Indeed, the authors proposed that the gastroprotective activity of C. sappan heartwood is possibly mediated by cytoprotective and antioxidant mechanisms involving an increase in PGE2 synthesis and a decrease in myeloperoxidase (MPO) levels, conferred by antioxidant phytoconstituents present in the plant [activity . The effhe plant .Archidendron jiringa (Jack) I.C. Nielsen is native from Southeast Asia and belongs to the Fabaceae family. A. jiringa ethanol extract (250 and 500 mg/kg) was protective against ethanol-induced gastric mucosal ulcers in Sprague Dawley rats, increasing adherent mucus and inhibiting oxygen-derived free radicals generation (through increasing SOD activity and decreasing MDA levels) [ levels) .Alhagi maurorum Medik, namely its aerial parts, have been traditionally used and studied for multiple purposes. Shaker et al. [r et al.  investigr et al. .Cassia sieberiana DC. is a savannah tree whose roots have been traditionally used in the management of various stomach disorders, including gastric ulcer, stomach pains and indigestion [igestion . In factigestion . Tamarindus indica L. is a plant tree indigenous from the tropical Africa and America but also cultivated in several regions, such as China, India, Philippines and Spain. The methanolic extract of the seed coat of this plant (100 mg/kg and 200 mg/kg) has been evaluated for determining their antiulcer potential on ibuprofen, alcohol and pyloric ligation-induced gastric lesions using albino Wistar rats [tar rats . The restar rats .Parkia speciosa Hassk—also known as stink bean—is popular in Southeastern Asia, besides having medicinal properties. A study performed to establish the antioxidant and antiulcer activity of P. speciosa ethanol leaf extract  against ethanol-induced gastric ulcers in rats concluded that the extract is effective [ffective . The resffective .Morinda citrifolia L.—also known as ′noni′—is a plant native from Southeast Asia and is commonly used in popular medicine in Brazil. The health benefits of fruit aqueous extract (0.63 to 2.50 g/kg) and its isolated compound, scopoletin, were evaluated in models of gastro-esophageal inflammation in rats  [ic acid) . The stuic acid) . Kigelia africana (Lam.) Benth is a native plant from the South-western part of Nigeria, where hot-infusion preparations of its leaves are popularly used to treat stomach ulcers. Ethanolic leaf extract from this plant presented antiulcerogenic potential against aspirin-induced ulcer, while aqueous leaf extract against ethanol-induced ulcer in Wistar albino rats [K. africana can be attributed to the presence of antioxidant flavonoids . ino rats . The antCordia verbenacea DC is a shrub medicinal plant popularly used in Brazil, where leaf infusion or decoction are widely used for anti-inflammatory, analgesic, antiulcer and anti-rheumatic purposes. The antiulcer activity of C. verbenacea ethanol leaf extract  was evaluated using ethanol/HCl, ethanol and piroxicam-induced gastric lesion models, pylorus-ligated assay [ed assay . In thised assay . Moreoveed assay . Barleria lupulina Lindl is a plant widely distributed in Indian mountains and is used in the folk culture of India, Thailand and Pakistan. The gastroprotective effect of the methanol extract from B. lupulina aerial parts was tested in Wistar rats using various models of ulcers, such as drug induced ulcers, restraint ulcers, duodenal ulcers and pylorus ligated ulcers [B. lupulina aerial parts (300 mg/kg) exhibited anti-inflammatory activity without displaying ulcerogenic activity in rats [d ulcers . This std ulcers . Moreove in rats .Eremomastax speciosa (Hochst.) Cufod. is a widely distributed plant in tropical Africa and used in Cameroonian ethnomedicine, where it is commonly referred to as “blood plant” due to its reputed use in the treatment of anemia. In 1996, it was reported that the water extract from E. speciosa leaves (190 mg/kg) inhibited the formation of HCl/ethanol-inflicted and pylorus ligation gastric lesions in rats [E. speciosa aerial parts (200–400 mg/kg) against carbachol- and histamine-induced hypersecretion, associated with the pylorus ligation technique, in Wistar rats [2Cl2 extracts and even CH2Cl2 fraction of E. speciosa protected the gastric mucosa and inhibited gastric acid secretion [ in rats . In 2013 in rats . The auttar rats . As the ecretion . Interesecretion .Hyptis suaveolens (L.) Poit. is originally a native plant from tropical America but now considered a worldwide weed and used in folk medicine in several parts of the world. The ethanolic extract and hexane fraction from the aerial parts of this plant  were evaluated in models of acute gastric ulcer  and mucosal lesions, using Rattus novergicus rats, Wistar strain and Mus musculus [H. suaveolens, where its mode of action involves nitric oxide, prostaglandins and sulfhydryl groups [musculus . The resmusculus . Suaveoll groups .Tectona grandis L. evidenced a prominent ability to mediate gastric protection in experimental animals via inhibiting proton pump (H+/K+-ATPase) activity with a corresponding decrease in plasma gastrin level [Solanum nigrum L. fruit extract [Verbascoside, a phenolic glycoside isolated from in level , similar extract . Calamintha officinalis Moench, widely known as “Mentuccia” in central Italy, is an aromatic plant used for preservative and medicinal purposes since ancient times. The methanol extract obtained from its leaves (12.9% w/w) displayed an important antiulcerogenic activity in rats ulcered with ethanol, being the observed effect similar to sucralfate, a drug that has a protective action on gastric lesion induced by ethanol [C. officinalis extract, namely polyphenols, catechin, tannins and terpenes, even being able to remove damaging agents from the gastric mucosa conferred by its prominent antioxidant activity [ ethanol . The autactivity .Myristica malabarica Lam., mainly its fruit rind, is used as an exotic spice in Indian cuisine. Malabaricones B and C are active constituents present in methanol extract [M. malabarica extract involves vascular endothelial growth factor (VEGF) enhancing and endostatin levels reduction, relevant mechanisms in angiogenesis and prostaglandin synthesis [ extract , which a extract . The ext extract . The gasynthesis . Moreoveynthesis .Talinum portulacifolium (Forssk.) Asch. ex Schweinf, namely its leaves, have been used for a long time by Indian people against diabetes, fevers and ulcer. Whole plant ethanolic extract (800 mg/kg) showed antiulcer activity on albino rats in three models of induced gastric ulcers: ethanol, pylorus ligated aspirin and histamine [istamine . This exCratoxylum arborescens (Vahl) Blume is widely distributed in Sabah and Sarawak  and its bark, roots and leaves are used in traditional medicine. Different xanthones, α-mangostin and β-mangostin have been isolated and identified from C. arborescens and have been studied as antiulcer protectors [H. pylori agents [H. pylori activity [H. pylori activity [otectors  and antii agents ,84. A stactivity .Mammea americana L.—commonly known as mammee—is an evergreen tree of the Calophyllaceae family, the fruit of which is edible. In folk medicine, this plant is used against stomachache. Three different bark/latex extracts from this plant  has been evaluated, in Swiss mice, for their ability to confer gastric mucosa protection against necrotizing agents, hypothermic restrain stress, NSAIDs and pylorus ligation [M. americana bark/latex extracts retain antiulcerogenic compounds [ligation . In all ompounds .Terminalia catappa L. is a plant widely distributed in tropical and subtropical regions and listed in Caribbean pharmacopeia as a medicinal plant to treat gastritis. The aqueous extract from leaves (25 mg/kg) showed preventive and curative effects on acute and chronic induced gastric ulcers on rats (absolute ethanol and ischemia-reperfusion injury) and an important inhibitory profile against H. pylori [T. catappa gastroprotective effects are related to nitric oxide pathway, increasing endogenous prostaglandins levels and mucus production and inhibiting MMP-9 and MMP-2 activities [. pylori . The auttivities .Terminalia coriacea (Roxb.) Wight & Arn. is a plant found in India, usually used as cattle feed and in Ayurveda and Siddha traditional medicine to heal ulcers. A leaf methanol extract  from this plant was tested in a study using Wistar rats as model of pyloric ligation and ethanol induced gastric ulcers [c ulcers . The extc ulcers .Terminalia arjuna (Roxb.) Wight & Arn. bark contains antioxidant polyphenolics and flavonoids and has been reported to have antibacterial activity [H. pylori lipopolysaccharide-induced gastric ulcer in rats [T. arjuna extract reflects its ability against gastric mucosa damage and its mucosal protective factors [activity . The baractivity . Moreove in rats . The aut factors ,86.Terminalia belerica Roxb., introduced in Europe and India by Arabs, is a plant used in traditional Ayurvedic medicine, its fruits being one of the three constituents of the important Indian Ayurvedic preparation “Triphala.” The antiulcer activity of 70% methanol extract from T. belerica fruits  was evaluated on Wistar rats by employing ethanol, aspirin, cold restraint stress and pylorus ligation ulcer models [T. belerica methanol extract may be due to reinforcement of the mucosal barrier resistance through protective coating [r models . This ex coating .Terminalia fagifolia Mart. is a medicinal plant used in folk medicine due to its effectiveness in the treatment of gastrointestinal disturbances. Pharmacological activity, including antioxidant effects on gastrointestinal tract of Wistar rats, using the ethanol extract from T. fagifolia bark and its aqueous, hydroalcoholic and hexane partition fractions have been evaluated [valuated . Paradoxvaluated . Terminalia chebula Retz. is native to southern Asia, from India and Nepal, east to south-western China and south to Sri Lanka, Malaysia and Vietnam. The fruit of this plant is one of the three constituents of the important Indian Ayurvedic preparation “Triphala.” Aspirin, ethanol and cold restraint stress-induced ulcer methods were used in Sprague Dawley rats to assess the antiulcer effects of the hydroalcoholic (70%) extract from T. chebula fruits (200 and 500 mg/kg) [T. chebula fruits and showed anti-secretory and cytoprotective effects on gastric ulcers through the inhibition of H+/K+-ATPase activity and antioxidant mechanisms [0 mg/kg) . The res0 mg/kg) . Chebulichanisms .Argemone mexicana L. is a plant that contains numerous alkaloids and is widely used in traditional medicine. A study carried out to assess the effects of methanol and aqueous extracts from this plant (500–3000 mg/kg), in Wistar rats with duodenal ulceration, concluded that both extracts produced significant activity in cysteamine-induced duodenal ulceration [ceration .Piper betle L. is a plant growing in the tropical humid climate of South East Asia and its leaves are widely consumed as a mouth freshener. The ethanol extract from leaves (200 mg/kg) exhibited protective effects against indomethacin-induced gastric lesions through increasing the antioxidant machinery (SOD and CAT) [P. betle, allylpyrocatechol, as a gastroprotective agent [and CAT) . Similarand CAT) . Furtherve agent ,97,98. Tve agent . MoreoveFicus religiosa L. is a plant species belonging to the Moraceae family that has been recently studied, namely its phytochemicals, as a potential H2 receptor antagonist using molecular docking approach and lanosterol and α-amyrin acetate were found to have higher stability during simulation studies. Hence, these compounds may be suitable therapeutic agents on PU treatment, acting as H2 receptor antagonist [tagonist . Scutia buxifolia Reissek exhibited antiulcerogenic and protective effects on gastric mucosa against ethanol-induced oxidative injury in experimental model of gastric ulcer, this protection being attributed to the antioxidant properties of the constituent phenolic compounds of the plant.Boligon et al.  reportedZiziphus jujuba Miller is a plant species belonging to Rhamnaceae family, commonly used in Persian folk medicine for the treatment of gastrointestinal diseases, such as ulcers [Z. jujuba stem bark  against acidified ethanol-induced gastric ulcers in albino Wistar rats, as well as its anti-H. pylori activity was tested by disc diffusion assay [H. pylori activity. Moreover, the authors proposed that the flavonoids present in the stem bark extract may be responsible from the observed effects due to increased gastric wall mucus; in turn, the mechanism of gastric mucosal protection may be due to the enforcement of mucosal barrier through a protective coating, in addition to the antioxidant activity [s ulcers , and botCecropia glaziovii Snethl. is a fast-growing and short-lived tree native to tropical Central and South America regions, which is used in folk medicine. A study reported the antiulcer and anti-secretory activities of the aqueous extract from this plant  on gastric acid secretion of pylorus-ligated Swiss albino mice [+/K+-ATPase activity in vitro, proportionately to the concentration used (IC50 = 58.8 µg/mL). With these findings, the authors concluded that C. glaziovii extract constituents inhibited the gastric proton pump provoking the anti-secretory and antiulcer activities [ino mice . Furthertivities .Osyris quadripartita Salzm. ex Decne is a plant native of Africa, southwestern Europe and Asia, commonly known as wild tea and widely used in Ethiopian folk medicine. A study evaluated the antiulcer activity of 80% methanol leaf extract from O. quadripartita in Wistar albino rats, using pylorus ligation-induced and ethanol-induced models, both applying a single  and repeated dosing (200 mg/kg for 10 and 20 days) approaches [50) was estimated to be higher than 2000 mg/kg and where secondary metabolites, including flavonoids, tannins and saponins were detected in the extract [proaches . The ext extract .Anacardium occidentale L.—commonly known as cashew tree—is native to Brazil but presently cultivated in many regions of the world. It is used by folk medicine in South America, namely its leaves, in the form of tea. The hydroethanolic extract from A. occidentale leaves inhibited gastric lesions induced by HCl/ethanol in Wistar rats [50 was 150 mg/kg. The chemical analysis of the extract detected, respectively, 35.5% and 2.6% of total phenolics and flavonoids. The use of aqueous leaf extract seemed not to involve the lowering of acid secretions [A. occidentale at 200 mg/kg did not provoke any ulcerogenic consequence in rat's stomach and at doses of 300, 400 and 800 mg/kg presented less gastric ulcerogenity than similar doses of indomethacin [tar rats . Furthercretions . Also, tmethacin . + ATP channels [In a study designed to investigate the effect of anacardic acids in gastroprotection against ethanol-induced gastric damage , the autchannels .Anacardium humile St. Hill, namely its leaves and bark infusions, are used in folk medicine. The crude methanol extract obtained from A. humile leaves  has shown to possess antiulcerogenic activity against ethanol and piroxicam-induced gastric lesions in Wistar rats and Swiss albino mice, respectively [A. humile leaves  was also evaluated in another study using ethanol-induced acute gastric mucosal injury as a model, in Wistar rats [ectively . The gastar rats . The restar rats .Spondias mombin L. is a fructiferous tree found in the rain forest and coastal areas of Nigeria, where it has found usage in folk medicine for the treatment of many diseases due to its bioactive substances including tannins, saponins, flavonoids, phenolics and anthraquinone glycosides [S. mombin leaf extracts was capable of ameliorating indomethacin-induced gastric ulceration via antioxidant and proton pump inhibition mechanisms [ycosides . In factchanisms .Toona ciliata M. Roem is a tall tree with colored wood, widely distributed in the Himalayan region. Ethanol heart wood extract of T. ciliata (300 mg/kg) was evaluated for its antiulcer activity against aspirin plus pylorus ligation induced gastric ulcer, HCl-ethanol induced ulcer and water immersion stress induced ulcer in Wistar albino rats [T. ciliata heartwood extract exerted antiulcerogenic effects through anti-secretory, cytoprotective and proton pump inhibitory mechanisms [ino rats . The autchanisms .Bryophyllum pinnatum (Lam.) Oken is a medicinal plant used in India, Africa, China and tropical America that contains different groups of phytoconstituents, among them flavonoids, phenolic acids, alkaloids and terpenoids. In Wistar rats, the isolated mucilage (500 mg/kg) and the aqueous extract (500 and 750 mg/kg) from whole plant exerted both potent gastroprotective effects against ethanol-induced ulcer model [B. pinnatum, a pronounced gastroprotection was observed on aspirin-induced ulcer in pylorus-ligated rats and histamine-induced duodenal lesions in guinea pigs [er model . The reser model . In anotnea pigs . Aframomum pruinosum Gagnep. and even other species from the Aframomun genus, are traditionally used in Cameroon to cure gastritis. A methanolic extract from A. pruinosum seeds  was evaluated as antiulcerogenic agent using two different models, NSAID- and H. pylori-induced gastric lesion in rats [Helicobacter and antiulcer activities, with a cytoprotective action due to the increase in mucus production stimulated by the endogenous prostaglandins and nitric oxide generation mechanisms [ in rats . This stchanisms .Medicinal plants are safe, cheap, effective and available source of biologically active molecules ,132,133.H. pylori and so on. Indeed, PSM exert antiulcer activity through multiple mechanisms; predominantly via antioxidant, anti-inflammatory, antimicrobial, anti-secretory, anticholinergic and cytoprotective effects [There are four main classes of drugs used in antiulcer therapy: antacids; H2 receptor antagonists; proton pump inhibitors; and potassium-competitive acid blockers . Numerou effects . The phyAlkaloids represent a group of natural products that are nitrogen containing PSM, which display a considerable antiulcer activity. Falcao and et al.  reviewedPilocarpus microphyllus leaves, protects against naproxen-induced gastrointestinal damage in rats by reducing pro-inflammatory cytokines and oxidative stress and increasing gastric mucosal blood flow. Pretreatment with epiisopiloturine prevented naproxen-induced macro and microscopic gastric damages with maximal effects at 10 mg/kg [rydalis impatiens reduced gastric injuries in mice with ethanol-induced acute gastric ulcer at 10 mg/kg. Also, cavidine treatment resulted in increased mucosa GSH, SOD and PGE2 levels, while decreased IL-6 and TNF-α levels [Himatanthus lancifolius resulted in increasing GSH levels and an antioxidant response and a decrease in H+/K+-ATPase activity at the pylorus ligature-induced ulcer in rats at 30–82 mg/kg. Alkaloids from Mahonia bealei possess anti-H+/K+-ATPase effects on pyloric ligation-induced gastric ulcer in rats at 18.6 mg/kg/day. Besides, 2-phenylquinoline effects were attributed to SOD and glutathione-S-transferase (GST) normalization activity and reduction in lipid peroxide (LPO) and TNF-α levels in the gastric mucosa from rats with gastric ulcer induced by 60% ethanol/0.03 M hydrochloric acid (HCl) and indomethacin [Evodia rutaecarpa have shown highly selective antibacterial activity against H. pylori, the minimum inhibitory concentration (MIC) found being 0.05 µg/mL [Tylophora conpicua was able to decrease histamine insulted gastric acid secretion in rats [Epiisopiloturine hydrochloride, an imidazole alkaloid isolated from 10 mg/kg . Cavidinα levels . Uleine methacin . Chelerymethacin . Also, q05 µg/mL . Still,  in rats .Citrus aurantium decreased gastric and duodenal lesions, increased gastric mucus production and mucosal MDA levels, GPx and GR levels and decreased SOD activity in experimental ulcers models induced by ethanol, NSAIDs, stress, H. pyroli, ischemia reperfusion injury and cysteamine at 7.5 mg/kg [H. pylori at ethanol-induced gastric ulcer, with an EC50 value of 12.32 mg/kg [Cedrus deodara significantly reduced ulcers at a dose of 100 mg/kg, which justifies the traditional usage of this herb to treat peptic ulcers. Ulcer inhibition of 100 mg/kg Cedrus deodara and 20 mg/kg of rabeprazole was, respectively, 41.5% and 67.7% [Gallesia integrifolia evidenced potent gastroprotective and curative effects in vivo and in vitro experimental models, which is probably due to its antioxidant, nitrergic, mucogenic, anti-secretory and anti-inflammatory effects [Croton rhamnifolioides with major components spathulenol (22.5%) and 1,8-cineole (18.3%) exhibited antiulcer activity by modulation of opioid receptors and nitric oxide [o-glucoside isolated from Rubus coreanus increased SOD and GPx activities in rats with ulcer induced by combination of ethanol and sodium salicylate [Monoterpene β-myrcene isolated from .5 mg/kg . α-Pinen32 mg/kg . α-Pinen32 mg/kg . The volnd 67.7% . α-Santa effects . On the ic oxide . Triterplicylate .Piper umbellatum L. showed antiulcer effect by exerting antioxidant, anti-secretory, anti-inflammatory and mucosa regenerative activities [Caryocar coriaceum extract, with gallic acid, chlorogenic acid, caffeic acid, rutin and quercetin as major constituents, exhibited antiulcer activity through opioid and α2-adrenergic receptors and primary afferent neurons sensitive to capsaicin in gastric ulcers induced by ethanol, acidified ethanol, acetic acid or indomethacin [Rubus coreanus have shown antiulcer effect in association with the regulation of the matrix metalloproteinase-2 activity, preventing lipid peroxidation and even increasing CAT, SOD and GPx activities [Flavonoids are natural antioxidants present in different kinds of fruits and vegetables, possessing a characteristic C6-C3-C6 carbon skeleton structure. Recent studies indicated that flavonoid shows a wide range of pharmacological activities, including as antiallergic, anti-inflammatory, antimicrobial, anti-cancer, antidiarrheal and antiulcer. Due to the presence of a hydroxyl group(s) in their aromatic ring(s), they possess antioxidant activity. Quercetin, rutin and kaempferol are widespread in the plant kingdom. They inhibited the mucosal content of platelet-activating factor in rats with gastric damage produced by acidified ethanol . Rutin ativities . Hesperitivities . Caryocamethacin . Anthocytivities . Garcinotivities .Bauhinia purpurea leaf exhibited in vivo antiulcer activity, which confirm the traditional uses of B. purpurea in the treatment of ulcers [Probably due to the presence of antioxidant saponins, the aqueous extract from f ulcers .p-Coumaric acid elicited antioxidant activity by attenuating ulcers due to elevated MDA levels, reduced GSH levels and decreased SOD, CAT, GPx and GR activities [H. pylori strains [tivities . Gallic  strains . Ellagic strains . A syner strains .Mouriri pusa augmented cell proliferation, anti-inflammatory activity by reducing COX-2 levels, enhanced angiogenesis and increased mucus secretion [Persea major bark exerted antiulcer effects in rodents through empowering gastric protective factors. The main compounds found in the hydroalcoholic extract of P. major (HEPM) were polyphenols, such as condensed tannins, flavonoids heterosides derivatives from quercetin and kaempferol. HEPM (300 mg/kg) prevented gastric lesions induced by ethanol or indomethacin in rats by 58.98% and 97.48%, respectively, compared to the vehicle group  [Tannins fraction of ecretion . Ellagitecretion . Hydroalctively) .Oleic acid accelerated ROS and nitric oxide (NO) synthesis and reduced oxidative damage; it also reduced inflammatory cells infiltration and TNF-α expression in mice using ischemia-reperfusion-induced skin injury model .In an attempt to find an effective treatment for various diseases, the modern medicine turns to traditional medicine. There are decades of using specific plants or certain plants parts in the treatment of several health conditions throughout the world. Many side effects because of using conventional antiulcer drugs has shifted the search for new drugs to folk and traditional medicines. Indeed, there is an effort in pharmacology to confirm the real benefits of traditionally used plants in antiulcer therapy and to identify active compound(s) responsible for their positive effects. The new modern approach with improved technology is unthinkable without the use of laboratory animals. Nonetheless, there are few animal models developed in ulcers research, usually including rats. All ethical principles for using of animals in experiments should be followed and protocols approved by the Institutional Ethics Committee.The assessment of the acute gastroprotective activity of plant extracts is generally performed using two different animal models of gastric ulcer: ethanol-induced and indomethacin -induced gastric ulcer. On the other hand, the evaluation of the chronic gastroprotective activity is usually performed on animals with gastric ulcer induced by acetic acid.Serjania marginata Casar. (fam. Sapindaceae) [Crassocephalum vitellinum (fam. Asteraceae) [50) [The growing interest in herbal medicines is partly derived from the results of many animal studies, indicating that plant extracts have lower toxicity than synthetic drugs . Howeverndaceae)  or with eraceae) , both plae) [50) . NotwithVernonia condensata (Asteraceae) [Maytenus robusta (Celasteraceae) over 7 days twice a day at dose of 10 mg/kg, in rats, did not produce any sign of toxicity [Bauhinia purpurea (Fabaceae) [Parkia speciosa (Fabaceae) [Clausena excavata (Rutaceae) methanol extract, in rats, using a single dose ; the oral LD50 higher than 5 g/kg body weight indicated that it is relatively safe and, therefore, considered to be non-toxic [The experiments performed in animal models of gastric ulcer confirm the gastroprotective and healing properties of many herbs traditionally used in folk medicine. One of them is the ethanol extract from eraceae) , where ttoxicity . Howevertoxicity . Aqueousabaceae) ,189 and abaceae)  at the son-toxic . HoweverAnnona muricata (Annonaceae) leaves showed the safety of this plant and that the oral LD50 is higher than 2 g/kg, which correlated with the previous results obtained in mice (where LD50 was 1.67 g/kg) [Brassica oleracea (Brassicaceae) [Caesalpinia sappan  [Piper tuberculatum (Piperaceae) fruit [50 were 1.62 g/kg p.o. and 0.26 g/kg i.p.The acute toxicity test carried out in rats at two doses (1000 mg/kg or 2000 mg/kg) of ethyl acetate extract from 67 g/kg) . No signicaceae)  and Caesniaceae) , confirme) fruit , followiAchillea millefolium (Asteraceae), popularly known as yarrow. It has been shown that the aqueous extract of yarrow has protective effects in ethanol and indomethacin induced gastric lesions and healing properties in acetic acid-induced chronic gastric lesions. In the study of chronic toxicity, tests were performed in both genders of Wistar rats for 28 and 90 consecutive days [While there is a certain number of data that involves acute toxicity studies of plant products used as antiulcer agents, the information on chronic or sub-acute toxicity studies are missing or sparsely performed. One of the exceptions in this field are data obtained from aqueous extract of ive days . BesidesSedum dendroideum (Crassulaceae), which showed gastroprotective effects [Subacute toxicity evaluation was carried out using the hydroethanolic extract of  effects . Wistar  effects .Bambusa arundinacea (Gramineae) exhibited antiulcer activity and toxicity studies carried out in Swiss Albino mice of both genders showed that there is no significant change in autonomic responses, though these animals were less active compared to the control group [50 was 2.55 g/kg (p.o.) and 1.81 g/kg (i.p.). Otherwise, curiously, the combination of B. arundinacea methanol extract and phenylbutazone (a NSAID) produced a more powerful anti-inflammatory agent, with fewer toxic effects and without ulcer formation.One of the possible approaches in gastric ulcer treatment is the combination of synthetic drugs with plant products, which alleviates the side effects of conventional drugs for long-term treatment. The methanol extract of ol group . CalculaEuphorbia umbellata (Euphorbiaceae) bark, it was concluded that the observed antiulcerogenic properties depended on polyphenols, primarily ellagic and gallic acids derivatives and flavonols, though there are no toxicity studies [Based on this data, the examination of the main constituents of plant extracts could also provide an approach in investigating possible antiulcerogenic effects of plant products and performing toxicity studies with specific substances. Interestingly, in a study performed using the methanol fraction of  studies . Also, o studies .The overall findings shared in this report clearly stress that plant products represent a rich source of bioactive molecules with antiulcer potential. Moving from traditional uses to preclinical studies, the efficacy of certain herbal remedies has been substantially investigated by in vitro and even in vivo studies, and, in some cases, their activity has been ascribed to specific classes of phytochemicals, such as alkaloids, tannins, simple phenols and polyphenols (particularly flavonoids).Analysis of literature data indicated that phytochemicals are natural, safe and effective resources that can be used in the prevention and even treatment of ulcers. However, the paucity of human studies, at the top of the evidence-based medicine pyramid, slows down these promising findings, thus requiring, in the near future, more clinical trials to support and even to validate the myriad of preclinical data.


Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank.The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications.The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for “planetary-scale” projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project. With the advent of next-generation sequencing technologies, enormous efforts have been made to sequence the whole genomes of plant species, thereby providing new insights into plant evolution  and new As a key part of the Earth BioGenome project , a globade novo genome assembly.DNA barcoding has emerged as an important molecular tool for ecological studies, particularly for the rapid identification of standard specimens . AlthougHere, we sequenced the genomes of 761 samples, representing 689 vascular plant species, at high depth . By making these data freely accessible and linking them to voucher details stored in the China National GeneBank (CNGB) herbarium and Ruili Botanical Garden, we provide a valuable genomic resource for evolution and diversity research and applications that may reveal new insights into the evolution of vascular plants.We sampled almost all of the species growing at the Ruili Botanical Garden, Yunnan, China  were generated for each of these samples  using specimen morphology, and the remaining 504 samples were identified to the family level using specimen and chloroplast sequences. Thus, we identified 738 samples from 761 sequenced, which belonged to 137 families and 49 orders. Among these families, most species belonged to Fabaceae (71 taxa), Poaceae (45 taxa), and Asteraceae (37 taxa), respectively.de novo assembler. We used the complete coding sequence of the rbcL gene of Arabidopsis thaliana (downloaded from the NCBI accession number: U91966) [We assembled the chloroplast genomes of each species from clean read data using NOVOPlasty , a seed  U91966)  as the s U91966) . Complet U91966) . Assembl U91966)  and Gene U91966) . Seventy U91966) .ndh and rps genes (Assembled chloroplast genomes were then compared and a phylogenetic tree constructed using RAxML  and IQ_Tps genes . 456) selected for parsimony inferences, and 26 fern samples to root the tree. ML analyses were also performed with IQ-TREE using the substitution model GTR+F+R10, which was determined according to the Akaike information criterion and the Bayesian information criterion by IQ-TREE. With the increase in the amount of phylogenetic data, it has become increasingly important to choose different substitution models for variation in rates and patterns of substitution among sites. We partitioned 59,695 nucleotide positions to 78 groups of sites based on gene content, then applied the edge-linked–equal partition model. However, between partitions, a separate model was used with the parameter: -m “GTR+I+G” by IQ-TREE (named IQ-TREE partitions).Each gene was aligned using MAFFT , and eacBoth RAxML and IQ_TREE provided consistent phylogenetic reconstructions Fig. . All nodIn this study, the ML tree provided support for the notion that the Gentianales are a sister group to the Lamiales (BS = 83%), which in turn is a sister group to the Solanales and Boraginales (BS = 100%). Fifty-four species of Poales were also analyzed, revealing a close relationship of this group with the Arecales, rather than the Pandanales and Dioscoreales.k-mer analysis in this study and found good agreement between them (R2 = 0.63) (Cunninghamia lanceolata (Lamb.) Hook. var. lanceolata to 19.26 Gb in Juniperus pingii var. wilsonii (Rehder) Silba. On average, repeat content also varied from 10% to 88% between the species sampled, with several exceptions . Myrtaceae  had the most repetitive genomes (∼88% repetitive content), while Celastraceae  had the least repetitive genomes (∼10% repetitive content). There was relatively high heterozygosity in these species, ranging from 0.15% to 36.6% per individual, which probably reflects their nature as wild species.To ensure the quality and accuracy of the dataset Table , we cond = 0.63) . OverallAlternanthera sessilis (L.) R.Br. ex DC was assembled to contig N50 of 15.2 kb and scaffold N50 of 95.5 kb, and Senna alata (L.) Roxb. was assembled to a contig N50 of 14 kb and scaffold N50 of 101.1 kb  for genome assembly. We used SOAPdenovo2  , a datapository ), and a pository . With alpository , any futThe high-depth whole-genome sequencing data, together with images and voucher specimens, can be reused in different ways and will be valuable for future applications. First, future evolutionary analysis may be used to study the evolution of specific genes after assembling them from raw reads, as well as investigating particular features of plant genome evolution, including the evolution of repeats, polyploidization, whole genome duplication, and similar features. Second, the data may be used to improve future genome assemblies of these plant species. For example, the information on repeat content, heterozygosity, and genome sizes provided here may help to tailor new sequencing and genome assembly strategies for these plant genomes. Sequencing data may also be integrated into other genome assemblies. Using the sequencing data obtained from this study would make it easier and more efficient to assemble the remaining sequenced plant genomes. The ∼60 Gb data can be used for genome assembly, in combination with either contig reconstruction of second-generation-based sequence reads or for error correction of third-generation long sequence reads. Finally, this dataset may also be used to develop new methods of species identification based either on sequencing data or plant images and to resolve phylogenetic relationships based on whole-genome sequencing data. At present, we have insufficient information to identify all species, so we are building a living plant database that records the position of species grown in the Ruili Botanical Garden and monitors the status of each species .In combination with information accumulated in the future, deep learning may be applied to this dataset as a training tool to develop plant identification. Indeed, we used data from 175 of the known Ruili species for deep learning, with each sample contributing 1 million reads to build the model. At the first trial stage, 181 species have been successfully identified to the species level using our models. By providing this comprehensive easily and publicly accessible dataset, we believe it would be reused in many ways beyond what has been mentioned here.Current understanding of the evolution of plants and their diversity in a phylogenomic context is limited because of the lack of genome-scale information across phylogenetically diverse species. In this study, we provide a high-depth whole-genome sequencing dataset comprising 689 vascular plant species with voucher specimens, covering 137 families and 49 orders. These samples were obtained from Ruili Botanical Garden in the Yunnan Province of China, near the border between China and Myanmar, reflecting the rich plant diversity in that region. The data generated here were used to estimate genomic features including genome size, repeat content, and heterozygosity, which will be helpful for future studies aiming to establish reference genomes for these species. The dataset may also be used to assemble chloroplast genomes, as well as some conserved nuclear genes, thus providing useful information for evolution and gene function studies.In this study, we scaled up a whole-genome sequencing effort to sequence hundreds of plant species. We only constructed a single short insert library (200 bp) for each species and generated ∼70 Gb of whole-genome sequencing data. Although it would be insufficient to assemble high-quality genomes for most species based solely on single library data, the current data have potential uses in analyses such as such as gene finder, plastid, and mitochondrial assembly. We are now using these data, in combination with 10X Genomics, to obtain high-quality genome data for follow-on work including looking at wood development.This study tested, for the first time, the feasibility of large-scale whole-genome sequencing, which is already underway for the Earth BioGenome Project  and the GigaScience GigaDB repository and will be continuously updated and linked to the GigaDB entries as new assemblies are completed [The specimens, leaf samples, and DNA solutions of all collections are stored at the CNGB herbarium. The raw sequencing data described in this article are available in the NCBI SRA repository, under project number PRJNA438407. The data reported in this study are also available in the CNGB Nucleotide Sequence Archive under accession number CNPhis0000538. DNA extraction  and BGISAdditional file 1: Supplementary Table S1. List of samples included in this study, with voucher information, current kmer-based estimation of genome sizes, repeat content and heterozygosity. Identified collections were listed with species names, while unidentified collections with only family and order information. Samples with assembled chloroplast genomes (738) are marked with *; 17 samples with assembled unclear genomes are marked with §.Supplementary Table S2. The chloroplast genome list used as references for further assembly by MITObim.Supplementary Table S3. Gene content information for all assembled chloroplast genomes.Supplementary Table S4. Genome information previously measured and publicly available in Plant DNA C-values Database.Supplementary Table S5. Summary of preliminary genome assemblies of 17 species of vascular plant.Supplementary Table S6. Summary of BUSCO analysis for 17 species of vascular plant.Additional file 2: Supplementary Fig. S1. Phylogeny of vascular plants from the Ruili Botanical Garden. Species tree based on the maximum likelihood analysis of 78 chloroplast genes generated by RAxML. Colors of the inner circle and outer circle represent different families and orders. Clade color represents bootstrap values from red to gray (bootstrap range 50–100).Supplementary Fig. S2. A comparison of genome sizes measured by experimental approaches to the k-mer estimated genome sizes in this study.10KP: 10,000 Plant Genome Project; BS: bootstrap support; BUSCO: Benchmarking Universal Single-Copy Orthologs; CNGB: China National GeneBank; ML: maximum likelihood; NCBI: National Center for Biotechnology Information; SRA: Sequence Read Archive.The authors declare that they have no competing interests.2015DA008, P.R. China).This work was supported by grants from the Basic Research Program, Shenzhen Municipal Government, China (grants JCYJ20150529150505656 and JCYJ20150831201643396), as well as funding from the Guangdong Provincial Key Laboratory of Genome Read and Write (grant 2017B030301011) and the Construction of China National GeneBank (Yunnan province, X.L. conceived this study. X.L. and H.L. drafted the manuscript. H.L. managed the project. J.P.W., X.B.W., L.C., X.F.H., H.C.C., J.L.Y., Y.W., R.C.M., J.L., and J.M.Z. collected the samples. T.Y. led the identification of voucher specimens. T.Y., W.X.M., B.S., Y.F., Y.C., and H.Y.C. analyzed the data. T.Y., X.L.C., M.W., and Z.H.H. constructed the phylogenetic tree. G.H.H., W.S.L., H.C.Z., H.C.C., and Y.L. extracted DNA and performed genome sequencing. S.K.S. and X.X. revised and edited the manuscript. All the authors read and approved the final manuscript.GIGA-D-18-00121_Original_Submission.pdfClick here for additional data file.GIGA-D-18-00121_Revision_1.pdfClick here for additional data file.GIGA-D-18-00121_Revision_2.pdfClick here for additional data file.GIGA-D-18-00121_Revision_3.pdfClick here for additional data file.Response_to_Reviewer_Comments_Original_Submission.pdfClick here for additional data file.Response_to_Reviewer_Comments_Revision_1.pdfClick here for additional data file.Response_to_Reviewer_Comments_Revision_2.pdfClick here for additional data file.Reviewer_1_Report_Original_Submission -- Michael Pirie9/27/2018 ReviewedClick here for additional data file.Reviewer_1_Report_Revision_1 -- Michael Pirie11/26/2018 ReviewedClick here for additional data file.Reviewer_2_Report_Original_Submission -- Alex Twyford10/2/2018 ReviewedClick here for additional data file.Reviewer_2_Report_Revision_1 -- Alex Twyford12/4/2018 ReviewedClick here for additional data file.Reviewer_3_Report_Original_Submission -- Monica Carlsen10/15/2018 ReviewedClick here for additional data file.Supplemental FilesClick here for additional data file.


Mycobacterium tuberculosis is a rare but severe condition. It is difficult to distinguish between M. tuberculosis-associated and bacterial necrotizing pneumonia. The optimal treatment for this condition is controversial. Here, we report a case of M. tuberculosis-associated necrotizing pneumonia treated with the adjunctive corticosteroid and the antituberculosis drugs.Necrotizing pneumonia induced by  M. tuberculosis was reported in children recently [M. tuberculosis pulmonary gangrene had been reported in adults before [M. tuberculosis-associated necrotizing pneumonia treated successfully with initiation of corticosteroid followed by antituberculosis drugs.Necrotizing pneumonia is a rare but severe condition of lung parenchymal destruction commonly caused by bacterial pathogens. Necrotizing pneumonia induced by recently , and sevs before . Howevers before . Here, wM. tuberculosis polymerase chain reaction (PCR). He had been diagnosed with community-acquired pneumonia but not improvement after a 10-day course of antibiotic therapy and was transferred to our tertiary hospital.A 44-year-old male patient was hospitalized because of progressive dyspnea, cough, and fever during one month. His past medical history was unremarkable. He appeared initially with mild fever, dry cough, and night sweating but untreated. After two weeks, he felt shortness of breath and coughed up yellow sputum. He had been admitted in the general hospital where he had undertaken the first bronchoscopy which revealed the negative results of bronchoalveolar lavage (BAL) for both acid-fast bacillus (AFB) smear and 2 70 mmHg, PaCO2 32.7 mmHg, and HCO3− 19.4 mmol/L. Physical examination revealed dullness on percussion, fine crackles, and decreasing breath sound at the right lower lung field. Cell blood count with white blood cells 8.84 G/L (77.5% neutrophil and 13.3% lymphocyte) and hematocrit 38.2%, C-reactive protein level 78.4 mg/L, and mildly elevated liver transaminase level were recorded. The rapid testing for human immunodeficiency virus was negative. Chest X-ray showed consolidation in the right lower hemithorax, and the first contrast-enhanced chest computed tomography (CT) revealed small necrotizing cavities in this consolidation area  and the positive BAL result for M. tuberculosis. The destruction of pulmonary parenchyma induced by M. tuberculosis usually develops from months to years in most cases. Nonetheless, there are a few cases (necrotizing pneumonia and pulmonary gangrene) in which this destruction may progress rapidly causing severe respiratory failure. The pathogenic mechanism can be explained by the intensive tuberculous inflammation causing the widespread vascular thrombosis and arteritis [M. tuberculosis-associated and bacterial necrotizing pneumonia [M. tuberculosis-associated necrotizing pneumonia in adults.In our case, diagnosis of necrotizing pneumonia associated with rteritis . With thneumonia . AccordiM. tuberculosis-associated necrotizing pneumonia. Although the corticosteroid was initiated without antituberculosis drugs, the clinical and radiological tests showed significant improvement in our case. This can be through the beneficial effects of corticosteroid in reducing the intensive tuberculous inflammation. Moreover, the adjunctive therapy with corticosteroid should be considered in managing bacterial necrotizing pneumonia. However, using corticosteroids in these cases should be researched more before arriving at a definite conclusion.The adjunctive therapy of corticosteroid showed significantly improving outcomes of patients with not only severe community-acquired pneumonia  but also


Borrelia miyamotoi disease is a hard tick–borne relapsing fever illness that occurs across the temperate climate zone. Human B. miyamotoi disease in immunocompetent patients has been described in Russia, North America, and Japan. We describe a case of B. miyamotoi disease in an immunocompetent patient in western Europe. Three weeks earlier she had noticed a tick bite after gardening. Several days later, an erythematous lesion appeared, increasing to palm size within 1.5 weeks and dissolving in a similar period. Full medical history was not suggestive of other causes of fever. Her previous medical history included cervical carcinoma and breast cancer, curatively treated.A 72-year-old woman in the Netherlands sought treatment in her third day of fever (9 cells/L), elevated monocytes (11%), and thrombocytopenia (144 × 109 platelets/L)  in convalescent-phase serum samples that was positive but could not be confirmed by either IgM or IgG immunoblot   on the thigh, and mild generalized lymphadenopathy. Initial laboratory tests revealed increased C-reactive protein (22.7 mg/L), leukopenia (2.1 × 10Germany)  Table 2.Ixodes ricinus tick, the most prevalent tick species in western Europe , a tickborne febrile disease  and Izh-16  compared with reactivity to the B. afzelii strain PKo  and B. hermsii HS-1  control lysates (In this patient, results of pan–relapsing fever ific PCR . We had ific PCR . Finally lysates  Figure.B. miyamotoi in I. ricinus ticks throughout Europe, clinical presentation, and laboratory findings, strongly suggest that B. miyamotoi was the causative agent of the patient’s symptoms. That the patient recovered even without antimicrobial treatment is consistent with a recent BMD case described in the United States (B. burgdorferi s.l. co-infection; however, prior evaluation by an independent dermatologist, a negative B. burgdorferi s.l. immunoblot despite high C6 reactivity, and a negative PCR on DNA obtained from the skin biopsy argue against co-infection. Regardless, the clinical picture of fever and mild leukopenia and thrombocytopenia is compatible with BMD and not with Lyme borreliosis. Of interest, C6 reactivity in combination with a negative B. burgdorferi s.l. immunoblot has been described in BMD patients in the United States (These findings, combined with the established presence of B. miyamotoi as an emerging tickborne pathogen in western Europe. Because of the widespread presence of multiple other tickborne pathogens across Europe, more attention and awareness for other tickborne diseases is warranted.This case identifies Borrelia miyamotoi disease.Additional information on diagnostic tests for 72-year-old woman in the Netherlands who showed evidence of