Aim: There is growing evidence that physical activity modulates gut microbiota composition through complex interactions between diet and microbial species. On the other hand, next-generation sequencing techniques include shotgun metagenomics and 16S amplicon sequencing. These methodologies allow a comprehensive characterisation of microbial communities of athletes from different disciplines as well as non-professional players and sedentary adults exposed to training. This systematic review summarises recent applications of next-generation sequencing to characterise the athletic gut microbiome.Methods: A systematic review of microbiome research was performed to determine the association of microbiota composition profiles with sports performance.Results: Bibliographic analysis revealed the importance of a novel research trend aiming at deciphering the associations between individual microbial species and sports performance. In addition, literature review highlighted the role of butyrate-producing bacteria such as Anaerostipes hadrus, Clostridium bolteae, Faecalibacterium prausnitzii, Roseburia hominis and unidentified species belonging to Clostridiales, Lachnospiraceae and Subdoligranulum species in gut health and sports performance across several disciplines. Interestingly, metabolic activities of Prevotella copri and Veillonella atypica involved in branched amino acid and lactate metabolism may contribute to reducing muscular fatigue. Other microbial metabolic pathways of interest involved in carbohydrate metabolism showed increased proportions in athletes´ metagenomes.Conclusion: Future research will aim at developing personalised nutrition interventions to modulate key species associated with certain components of exercise. In this sense, human microbiome is sensitive to the physiological changes associated with training, including increased intestinal permeability and altered profiles of inflammatory markers. It has been described that gut microbiota regulates the energetic balance and the inflammatory, redox, and hydration status. Specifically, physical activity may lead to an increase in microbiota diversity. These increased microbial diversity estimators include α-diversity, indicating the number of clades in one sample within an individual. Previous studies suggest that athlete microbiota shows higher proportions of certain members of the Firmicutes phylum and the genus Akkermansia,4. The interactions between diet, exercise, and gut microbiota in athletes have been reported. Common dietary strategies and recommendations for elite athletes are primarily based on high protein and simple carbohydrate intake and low consumption of plant polysaccharides. However, other factors that should be considered in these recommendations include the sports discipline , sex, nutrient sources with different amino acid contents, and sports periodization (involving pre- and post-training and pre- and post-competition phases). Some of these dietary recommendations may result in reduced microbiota diversity and functionality,6. It has been reported that elite athletes suffer from psychological and gastrointestinal conditions associated with gut microbiome. Administration of specific probiotic strains, prebiotics and synbiotic combinations could promote a healthy microbiota, which may exert a direct influence on the hypothalamus-pituitary-adrenal axis in athletes,5,6.There is growing evidence that physical activity modulates gut microbiota composition. These pattern-recognition algorithms might be especially useful to distinguish between responders and non-responders to specific nutrients or supplements in order to develop personalised nutrition strategies aiming at improving sports performance. Similarly, machine learning could be of great interest to rationally design prebiotic interventions targeting species and strains associated with health benefits, and perform systematic literature reviews dealing with microbial carbohydrate metabolism. Systematic reviews in the field of gut-microbiota-brain axis study revealed the associations between physical and emotional stress during exercise in animal models. This fact may induce changes in gut microbiome including microbial clades involved in the degradation of intestinal mucus and immune response. Other systematic reviews suggested that probiotic administration may improve athletes’ general health and performance while controlling inflammation and redox levels. To our knowledge, no systematic review has addressed the association of gut microbes with sports performance with an emphasis on metagenomics. In this regard, shotgun sequencing shows several advantages compared to amplicon sequencing and culture depending techniques, including the taxonomic identification of non-culturable microbes at species and strain level, the recovery of microbial metagenome-assembled genomes and the study of microbial metabolic pathways . These culture-independent techniques allow for characterising gut microbes without the need to culture them. In this regard, shotgun metagenomics offers some advantages compared to 16S sequencing, including a higher strain-level resolution, and the possibility of studying microbial genes and metabolic pathways. Selected articles were published between 2017 and 2022, highlighting the current relevance of this topic. To further investigate this emerging research trend, advanced mathematical models for text analysis were computed.A total of 16 original articles reported the applications of shotgun metagenomics or 16S amplicon sequencing for the analysis of fecal samples of athletes and individuals practicing sports [,5. Moreover, a high degree of compliance with dietary recommendations for athletes greatly affects gut microbiota functionality and sports performance,6. Interestingly, this mathematical model suggests the association of specific taxonomic clades with sports performance indicators such as endurance in professional athletes. It has been reported that athletes show increased microbiome diversity estimators like α-diversity as well as microbial pathways and fecal metabolite production compared to controls,3,14.Network modelling highlighted the co-occurrence of several terms in these scientific publications: dietary intake, physical activity, and taxonomic and functional profiles of the microbiota. In this regard, previous authors suggested that training modulates microbial diversity and microbial metabolismThe importance of each term represented in the co-occurrence network was calculated considering the number of other terms with which it appears. Some relevant terms highlight the role of physical activity on the health status, taxonomic and functional profiles of the gut microbiota. It should be noted that the number of microbiome studies dealing with sports performance of elite athletes based on parameters like endurance has incremented in the last five years. In contrast, studies published before tend to focus on the relationship between gut microbes and general dietary and lifestyle factors in professional athletes.. Then, terms showing correlation coefficients greater than 0.6 were determined. These terms were “intestinal microbiota”, “metabolic” and “specific”. It should be noted that these co-variables do not have a great impact on keyword relationships established by the co-occurrence network. On the other hand, synonyms and terms describing very similar concepts were excluded from the network to avoid bias.To assess the potential impact of co-variables in the network analysis, Spearman correlation coefficients between terms were calculated using caret package, marathon runners ,18,22, endurance athletes,28, competitive cyclists, rowers,17,25, skiers, football and cricket players,29, and other athletes across 16 different sports. In addition, some studies characterised the microbiota of physically active senior orienteers, as well as healthy but sedentary adults exposed to endurance and strength training, and short-term exercise regime. It should be noted that most of these studies compared microbiota profiles of athletes and physically-active participants to sedentary controls [Among the original articles included in this systematic review, nine and five microbiome studies involved shotgun metagenomics and amplicon 16S sequencing, respectively. Moreover, two studies involved both metagenomics and 16S sequencing. These next-generation sequencing experiments involve microbiota analysis of fecal samples of professional athletes and physically active individuals . Specificontrols . Most stcontrols . It shouRuminococcaceae or Faecalibacterium was increased in endurance athletes compared to physically inactive individuals,24. Moreover, Firmicutes/Bacteroidetes ratio is correlated with obesity as well as controlling fungal occupancy in athletes,31. In this regard, bacteria from the phyla Firmicutes and Bacteroidetes represent 90% of the gut microbiota and Firmicutes/Bacteroidetes ratio has been associated with maintaining normal intestinal homeostasis. Increased or decreased Firmicutes/Bacteroidetes ratio may lead to various pathologies. Gut microbiota unbalance usually observed with obesity, including increases in the abundance of specific Firmicutes or Bacteroidetes species. On the other hand, high Akkermansia abundances were found in the microbiota of professional rugby players and competitive cyclists. Low-abundance Akkermansia species such as A. muciniphila comprise mucin-degrading microorganisms that are negatively correlated with obesity and metabolic syndrome. In contrast, Veillonella genus and Veillonella atypica might be slightly increased in marathon runners and rowers, although these increments are not statistically significant,18. It has been suggested that lactate is the primary source of energy for V. atypica. Blood lactate resulting from muscle activity is associated with fatigue, and its concentration and accumulation depend on various factors, including exercise intensity, load and density. Scheiman et al. demonstrated in a murine model that plasma lactate may reach the intestinal lumen, where it may also be metabolized by V. atypica. The relationship between physical activity levels and the prevalence of Veillonella involved in metabolic, protective, structural, and histological functions was also reported by Dorelli et al., and Manor et al.,32. The proposed mechanism of action has been proposed: Veillonella species metabolize lactate into acetate and propionate via the methylmalonyl-CoA pathway. Unlike V. atypica, many other microbes are capable of utilizing lactate through lactate dehydrogenase, but do not possess the full pathway to convert lactate into propionate. In this sense, systemic lactate resulting from muscle activity during exercise may enter the gastrointestinal lumen and is metabolized by Veillonella into propionate in the colon. Gut colonization of Veillonella promotes the Cori cycle by providing an alternative lactate-processing mechanism whereby systemic lactate is converted into SCFAs that re-enter the circulation. SCFAs are absorbed in the sigmoid and rectal region of the colon and enter circulation via the pelvic plexus, bypassing the liver and draining via the vena cava to reach the systemic circulation directly. As a consequence, microbial SCFAs derived from lactate improve athletic performance.A total of 12 articles described the association of specific microbial clades with sports and exercise performance . Figure Prevotella copri was increased in rowers who completed an east–west transatlantic rowing race, and sedentary adults with a short-term exercise regime involving combined aerobic and resistance training. It has been reported that gene expression of metabolic pathways of P. copri involved in L-lysine is increased after ultra-endurance exercise. This essential amino acid plays a critical role in reducing muscular fatigue and contributes to muscular integrity. Furthermore, microbial derived lysine contributes to the human body protein pool.Similarly, Erysipelotrichaceae in rugby players [. However, different rugby player positions require different physiological and physical demands. High abundances of several bacterial genera  were also found in competitive cyclists compared to sedentary adults [. Similarly, several clades like Dorea longicatena, Faecalibacterium prausnitzii, Roseburia hominis and unclassified species belonging to Subdoligranulum were increased in rowers throughout a race as well as physically active senior orienteers compared to the general older adult population,21. F. prausnitzii, R. hominis and Subdoligranulum are butyrate producers that contribute to reducing gut inflammation and oxidative stress. It should be noted that butyrate is the main nutrient for colonocytes that exert an anti-inflammatory activity. With regard to Dorea longicatena, this taxon is associated with insulin sensitivity,33. In addition, high abundances of Lachnospiraceae were determined in marathon runners and skiers, while Coprococcus, Parasutterella genera and Ruminococcaceae family were increased in physically active individuals.Other microbial clades that may be characteristic of the microbiota of athletes include unidentified taxa belonging to  players . These uy adults . These get al. determined the prevalence of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria in the fecal microbiota of rowing athletes. However, unidentified species belonging to Clostridiales and Lachnospiraceae, as well as Faecalibacterium genus, showed higher abundances in metagenomes from elite adult participants than young elite athletes [. It should be noted that Lachnospiraceae increments are strongly associated with fiber consumptions, although general dietary recommendations for athletes are characterised by low intake of non-amylaceous polysaccharides,6. In contrast, Bacteroides was enriched in the microbiota of young elite athletes [.Some studies reported characteristic differences in the microbiota profiles of young and adult elite athletes in order to monitor the potential of elite athletic candidates . In thisathletes . These tathletes . High abStreptococcus suis, Clostridium bolteae, Lactobacillus phage LfeInf and Anaerostipes hadrus were associated with moderate dynamic components of exercise. It should be noted that dynamic components of exercise involve aerobic exercise, while static components of exercise are performed by increasing tension in a muscle while keeping its length constant. Therefore, sports disciplines can be classified into nine different categories according to the contributions  of both components.Efforts to establish associations between individual microbial species and different types of physical activities have also been made . In thisS. suis showed high proportions of metabolic pathways involved in the fermentation of sugar alcohols, while C. bolteae and A. hadrus may produce butyrate to promote gut homeostasis and anti-inflammatory effects. Other clades, including Bifidobacterium animalis, Lactobacillus acidophilus, Prevotella intermedia and butyrate-producing species such as Faecalibacterium prausnitzii, were associated with high dynamic and low static components of exercise. On the contrary, Bacteroides caccae was enriched in athletes from disciplines involving high dynamic and static components of exercise [It has been reported that exercise .. It has been described that fecal microbiota samples of professional rugby players and sedentary controls show even greater separation at the functional metagenomic and metabolomic than at compositional levels. Similarly, microbial diversity, including butyrate-producing species, increased throughout the ultra-endurance events such as transoceanic rowing races. The functional potential of bacterial species involved in specific amino and fatty acid biosynthesis also increased. Additional studies dealing with rowing athletes report that ATP metabolism, multiple sugar transport systems and carbohydrate metabolism are enriched in the microbial community of these athletes. Differences in functional bile acid and histidine metabolism also differentiate power athletes from sedentary controls, while galactose metabolism markers differentiate endurance athletes from controls. Moreover, D-alanine and primary bile acid biosynthesis differentiate power and endurance athletes from controls. Scheiman et al. and Kostic reported that every gene in a major pathway metabolizing lactate to propionate is at higher relative abundance postexercise in marathon runners,16. On the other hand, an increment in the abundance of Prevotella was correlated with a number of amino acid and carbohydrate metabolism pathways in cyclists, including branched-chain amino acid metabolism. In contrast, some studies report characteristic microbiota patterns mainly at taxonomic level, including increased abundances of Faecalibacterium prausnitzii in physically active senior orienteers.Most articles selected in this systematic review do not involve intervention studies. In this regard, characteristic patterns in the fecal microbiota of athletes were elucidated at taxonomic and functional levels . In addi. In addition, microbial-derived SCFAs are enhanced within rugby players and their gut microbiota was predominantly correlated with creatine kinase (CK), total bilirubin and total energy intake.Some studies report characteristic microbial-derived metabolic profiles of athletes from different disciplines. In this regard, cis-aconitate, succinic acid and lactate in urine samples and creatinine in faeces were found to be significantly different between groups of sports. These differences were evident despite the absence of significant differences in diet,18. Other studies report the assessment of macronutrient intake per day to enhance inter-individual comparison as well as quantitative diet evaluation. It has been reported that the versatility of the microbial community of athletes, which might affect their performance, is associated with dietary factors. However, other studies report the lack of in-depth dietary analysis and a matching non-athlete cohort .Dietary factors that may confound the association between exercise and the abundance of microbial taxa of interest were considered in several of these studieset al. demonstrated modest changes in gut microbial composition and function in healthy but sedentary adults exposed to short-term exercise regime, with and without concurrent daily whey protein consumption. An association between whey protein intake and the β-diversity of the adult gut virome was found, while no major changes in the functional activity of the gut microbiota were determined, with the exception of urinary levels of trimethylamine N-oxide (TMAO) and phenylacetylglycine (PAG) excretion. Similarly, Moitinho-Silva et al. elucidated taxonomic differences, a significant increase in lymphocytes and a decrease in mean corpuscular haemoglobin concentration in healthy sedentary adults exposed to strength training. No change in dietary patterns towards the end of the intervention period and after it was observed. Finally, Fukuchi et al. investigated the effects of both official competition and a multi-strain lactic acid bacteria-fermented soymilk extract in taxonomy and urine metabolites in endurance athletes. Changes in urinary metabolites included a significant reduction in yeast and fungal markers, neurotransmitters, and mitochondrial metabolites including the tricarboxylic acid (TCA) cycle. Tricarballylic acid was positively correlated with the ratio of Firmicutes, while Parabacteroides distasonis was negatively correlated with several urinary metabolites, including 3-metylglutaconic, vanillylmandelic, quinolinic and kynurenic acids and thymine.On the contrary, three of the selected articles comprised intervention studies. In this regard, Cronin Applications of next-generating sequencing technologies to assess the relationships between gut microbiota composition and sports performance have been summarised. Computational methods for text processing and bibliographic analysis revealed recent research trends focusing on the impact of microbial diversity and metabolic pathways on different components of physical activity. These studies highlight the role of butyrate-producing bacteria in promoting gut health and contributing to an optimal composition of the athletic microbiota.Mathematical modelling for text processing opens new possibilities for evidence synthesis in microbiome research. This could be of special interest to monitor research trends in emerging fields like metagenomics applied to sports science. However, this novel approach has several limitations. In this sense, the authors from selected articles may use general and unprecise terms to describe their findings, making keyword co-occurrence analysis difficult. In addition, unprecise terminology in the field of sports science, including “performance”, “exercise”, “athlete”, “elite”, is used in several articles. In this regard, authors should provide detailed participant metadata for accurate interpretation of results. Moreover, specific indicators of physical activity performance, such as endurance, should be properly described in the study design. Other limitations of current research summarised in this review include different dietary patterns among participants from different studies that show an association with gut microbiota regardless of physical activity. Similarly, different geographical origins of individuals and control groups such as non-elite athletes or sedentary adults are potential confounding variables that may be considered to assess bias in these studies.Bacteroides, while simple carbohydrates are associated with Prevotella enrichment. It is difficult to establish standard diet regimes due to the considerable complexity of stress responses in elite athletes. It has been proposed that gut microbiota acts like an endocrine organ by secreting serotonin, dopamine or other neurotransmitters and may control the hypothalamus-pituitary-adrenal axis in athletes resulting in the release of stress and catabolic hormones, inflammatory cytokines and microbial molecules. Therefore, dietary interventions may contribute to an improvement in sports performance,36. However, some dietary recommendations for elite athletes are primarily based on low consumption of plant polysaccharides, which is commonly associated with reduced microbiota diversity and SCFA and neurotransmitter synthesis. In this regard, dietary recommendations for athletes should consider fiber intake to promote microbial species reduced in athlete’s gut,35. Some studies reported a reduced diversity of the athlete’s gut microbiota that could be attributed to their higher protein intake, although there is a need for longer-term studies on athletes from different disciplines to assess the impact of diet on the athletic gut microbiota. It has been reported that protein intake was negatively correlated with diversity in marathon runners and fat intake was negatively correlated with Bifidobacteria in bodybuilders,37. As explained, high-protein diets may decrease microbial diversity in endurance athletes who consume lower amounts of carbohydrates. Similarly, a decrease in SCFA-producing species has been observed in resistance athletes that follow a high-protein, low-carbohydrate, and high-fat diet. However, some dietary recommendations for endurance athletes resulting in the consumption of high amounts of both simple and complex carbohydrates in combination with training may lead to an increased abundance of Prevotella. This genus is associated with fiber-rich diets and participates in several amino acid and carbohydrate metabolism pathways, including branched-chain amino acid metabolism. Interestingly, five bacterial families  were associated with physical activity in studies that controlled diet as a possible confounding factor.Diet modulates the composition of the athletic gut microbiota. Long-term diets modulate gut microbiota composition. For example, protein and animal fat lead to an increase in Future research trends may focus on the interactions of diet and gut microbial composition in the context of athletic performance as well as potential applications of pro- pre- and symbiotic supplements specifically developed for athletes. For this purpose, more studies dealing with metabolic activities and other mechanisms of action of specific clades associated with several indicators of sports performance are needed. In this regard, metagenomic sequencing enables the identification of microbial metabolic pathways showing higher abundances in the gut microbiota of athletes from several disciplines than in sedentary controls. This fact may contribute to a better understanding of the role of gut commensals in athlete physiology. In addition, further studies including a multi-omics approach  are needed to better elucidate the associations between physical activity, dietary patterns and gut microbiota. It should be noted that most articles published up to date comprise observational studies and the mechanisms of action of specific microbial clades contributing to sports performance remain unknown. In this regard, genomic sequences recovered from athlete metagenomes could be of great benefit to perform metabolic modelling in order to characterize those activities that may have a physiological impact. The integration of these techniques may lead to personalized nutrition interventions including specific nutrient recommendations aimed at improving performance by promoting certain taxa and enhancing certain metabolites of interest during exercise. Finally, more randomized controlled studies analyzing wider cohorts and controlling for potential confounding factors are needed to identify microbial species that could be used as biomarkers of sports performance.A. hadrus, C. bolteae, F. prausnitzii, R. hominis and unidentified species belonging to Clostridiales, Lachnospiraceae and Subdoligranulum may contribute to maintaining gut homeostasis in athletes. On the other hand, species involved in branched amino acid and lactate metabolism, such as P. copri and V. atypica, may reduce muscular fatigue. In addition, athletic gut microbiota shows an increase in microbial metabolic pathways involved in carbohydrate metabolism. Future research will aim at developing personalised nutrition strategies and recommendations to optimise microbiota composition profiles associated with different components of exercise . Future research trends may focus on the interactions of diet and gut microbial composition in the context of athletic performance. For this purpose, multi-omic studies dealing with metabolic activities and other mechanisms of action of specific clades associated with several indicators of sports performance are needed. As a consequence, these microorganisms could be used as biomarkers of sports performance to assess the potential of athletic candidates.This systematic review gives a general overview of the applications of next-generation sequencing, including shotgun metagenomics and 16S amplicon sequencing, to study the athletic gut microbiota. Bibliographic analysis using computational models revealed the growing research interest in elucidating the associations between specific microbial clades and sports performance. In this sense, butyrate producers such as


Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes  that aim to sequence most of the extant families in a clade. Squamates (Order Squamata) are a near-globally distributed clade of reptiles including ~11,000 extant species of lizards, snakes, and amphisbaenians ,3, untilSquamates and humans share a common history with birds, mammals, and other reptiles, which together form a unique lineage on the Tree of Life called amniotes. Amniotes (Amniota) first appeared during the Carboniferous Period ~318 million years ago (MYA) . The watLiving sauropsids include all reptiles and birds and are classified into two main lineages . The firSphenodon punctatus, as the single living species) and Squamata. Squamates include all extant lizards, snakes, and amphisbaenians , with a fossil record extending to the Early Triassic ~240 MYA [The sister taxon to the archelosaurs are the lepidosaurs, which share several synapomorphies including overlapping scales . Within Lepidosauria there are two extant taxonomic orders: the once-diverse Rhynchocephalia  [Vertebrate comparative genomics started with a purposeful orientation toward humans and other mammals. While complete genome sequences were already available for model eukaryotes with smaller genomes  ,22,23,24sophila) ,26 set osophila) , which wMus musculus) and rat (Rattus norvegicus) genomes were made available in 2002 and 2004, respectively [Pan troglodytes) genome in 2005 and rhesus macaque (Macaca mulatta) genome in 2007 filled some of the gaps in mammalian and primate evolution [www.vertebrategenomesproject.org) have released their own mammalian genome assemblies  was released in 2004 to fill the evolutionary gap between mammals and other model organisms [Taeniopygia guttata) in 2010 [A few years, after the publication of the human genome, draft genomes for birds started to appear on GenBank . The drarganisms . The nex in 2010 . The Avi in 2010 .Anolis carolinensis), published in 2011 [Python bivattatus) and king cobra (Ophiophagus hannah) in 2013 [The first available reptile genome sequence was that of a squamate, the green anole lizard , amphisbaenians, and most acrodont iguanian groups. Lack of sampling from these lineages introduces many phylogenetic gaps that encompass important and ancient events in squamate evolution, such as at the root of the squamate phylogeny ≤ 240 MYA  and key The green anole genome put forth by the Broad Institute was one of the last of the “old generation” 7X Sanger-sequenced projects . Next-geLong-read sequencing platforms (or third generation) from Pacific Biosciences  and Oxford Nanopore Technologies  have significantly decreased in cost . With reAll sequenced genomes must be assembled to align and merge reads into a full genome representation. Usually, short or long reads are assembled into stretches of contiguous sequence called contigs, which are then properly ordered and oriented during a process called scaffolding. Building genome scaffolds starts by sequencing read pairs which span longer insert sizes than the typical NGS library. Scaffolding libraries can include Illumina mate-pair libraries that span a few thousand base pairs , while other methods like Hi-C often result in insert sizes of hundreds of thousands of base pairs . Hi-C liTo ensure high assembly quality, important decisions must be made early on in the project, in particular what coverage or “depth” of sequencing will be obtained. Coverage is an estimate of the number of times each site in the genome is represented by a sequenced read. Higher coverage improves the chances that sequencing errors will be corrected. Postassembly, genomes are evaluated mainly using three metrics: contiguity, completeness, and correctness. Contiguity is quantified using the N50 statistic, which is similar to a weighted median length. Starting with the largest contig (or scaffold), the contig lengths are added together until the cumulative sum is half of the total assembly length, and the N50 is the length of shortest contig in that list. Long read assemblies result in much higher contig N50s, making them useful for capturing structural variation and longer genic regions, which are typically fragmented in Illumina-based assemblies.Completeness can be assessed with BUSCO , a tool that measures the amount of clade-specific conserved orthologs in an assembly compared to the expected amount for the taxon of interest . If a hiAt the beginning of 2023 there were 83 squamate species with available genomes on NCBI, representing ~0.75% of living species , and by p = 1.8× 10−11; R2 = 0.4). N50 was also predictive of interspersed repeat content . In the meantime, predicted gene content predicted interspersed repeat content but without a large effect . We also found that while assembly size did not have a strong effect on predicted gene content , assembly size did predict interspersed repeat content , highlighting the fact that repetitive DNA, and not the number of protein-coding genes, plays an important role in determining genome size [2 = 0.24). Our analysis suggests that N50, particularly for contigs, should be a prioritized metric in order to maximize detection of both coding and noncoding regions of the squamate genome.We analyzed the relationships between assembly metrics of 91 publicly available squamate genomes in terms of their assembly size in bp, scaffold N50, and the proportion of single-copy BUSCOs found in the genome  has been improved to the chromosome level [When planning a squamate genome project and depending on its goals, it may be best to initially focus on quality contig assembly from long reads for initial analysis to maximize genic coverage followed by the possibility of acquiring scaffolding libraries  that increase contiguity as the model system develops and new questions arise. For instance, the genome of the brown anole lizard , and sex determination research.Phylogenies can be used to visualize evolutionary relationships, understand trait evolution, and form the foundation of many predictive models in biomedical research for drug development, forensics, and gene function ,71. PhylGenome-wide studies of squamate relationships have the potential to resolve longstanding debates about squamate diversity. The earliest cladistic analyses of squamates used morphological, fossil, ecological, and behavioral data, supporting two main squamate lineages : IguaniaA strong argument for the molecular hypothesis of squamate evolution was the discovery of Toxicofera, or the “venom clade” . SeveralGenome-scale datasets that have been used to reconstruct the squamate tree of life include anchored hybrid enrichment loci , proteinPhylogenomic discordance can be driven by biological factors, such as incomplete lineage sorting and introgression , and also artifactual factors such as model violations and issues with data quality. Multilocus phylogenetic methods such as “supergene” concatenation most often assume that all sampled loci can be explained by the same underlying tree , and so Interestingly, squamates may present a “perfect storm” of problems commonly found to drive discordance in molecular phylogenetic datasets. For instance, the phylogenetic signal for older divergences (such as the Triassic or Jurassic-aged divergences of most squamate suborders) may be reduced by genetic saturation, where multiple substitutions at the same site accumulate over time, which most substitution models for phylogenetic analysis are not equipped to handle ,89. AlsoDespite a large number of markers, phylogenomic methods used for squamates still have largely relied on reduced representations of the genome, and are less likely to incorporate differential evolutionary patterns and rates such as across coding and noncoding regions. The future of squamate phylogenomics, therefore, lies in the ability to sample the entire genome, encompassing the widest possible range of coalescent histories and substitution rates, and the ability to parse the signal from the noise in phylogenomic reconstruction. These methods have already been applied to other amniote groups. For instance, an analysis of millions of orthologous parsimony-informative sites across annotated features of the mammalian genome showed that coding regions were predominant drivers of discordance while noncoding regions contained far more data that agreed with the species tree . A recenTo demonstrate the utility of complete genome assemblies in reconstructing the squamate tree of life, we downloaded 91 squamate genome assemblies—plus human, chicken, alligator, and the tuatara as outgroups. We then assessed each genome for the presence of 7453 single-copy orthologous protein sequences from the sauropsid orthoDB database with BUSCO v5 and computed multiple sequence alignments for each ortholog with MAFFT . We reliWe obtained complete local posterior support for all splits in the squamate species tree , except Our analysis of a large number of protein sequences reveals that there is much disagreement among gene genealogies for squamates. By employing these genome-wide approaches, squamate comparative genomics may yield resolutions to these longstanding conflicts, as well as causal explanations for the underlying disagreements about the topology of the squamate tree of life. For instance, machine learning techniques can help decipher between biological and artefactual discordance , and forWhat applies to squamate species and phenotypic diversity equally applies to their genomic diversity . Across TEs are divided into two main classes based on their mechanism of transposition. Class I elements are the retrotransposons, which use a copy-and-paste method via an RNA intermediate that is reverse transcribed into a new DNA locus. Retrotransposons are further classified into those containing “long terminal repeats” (LTRs) and those lacking repetitive flanks (non-LTRs), and are the dominant elements across most eukaryotic genomes . Within Class II elements are the DNA transposons. The “cut-and-paste” transposons include a transposase that removes the transposon and inserts its sequence at a different genomic location. DNA transposons are particularly abundant in nonavian reptilian genomes , with 23Drosophila, human, chicken, and house mouse, leading to ascertainment biases that underestimate species-specific or clade-specific TEs in nonmodel organisms [Determining the diversity and abundance of TEs in the genomes of squamates and other vertebrates requires bioinformatics tools capable of detecting and analyzing TEs in sequence data. RepeatMasker is a popular software that can use TE consensus sequences as queries in BLAST searches against the genome, outputting annotated lists of repetitive DNA . TE consrganisms .One approach to repeat findings in nonmodel organisms is to model repeat consensus sequences de novo with RepeatModeler , which uThe initial analysis of the green anole genome revealed a repeat-rich squamate genome with a high diversity of Class I and II TEs, many of which are recently active and producing copies ,104,105.The range in TE abundance across squamates is in stark contrast to relative uniformity in terms of repeat content within mammals and birds, respectively ,115. ForTo visualize the diversity in TE content across squamate genomes, we downloaded the assemblies from 91 squamate species representing 24 families  and modeWe found considerable variation in TE content across squamate genome assemblies, mirroring previous results based on short read datasets . For insThe long-term patterns of TE accumulation and loss in squamate genomes have been measured in numerous ways, including comparisons of TE abundance and diversity between genomes above the species level ,104,105,The differences in TE abundance and diversity between squamate genomes may be driven by stark lineage-specific differences in TE activity. To understand the differences in TE activity between major groups of squamates, we generated repeat landscapes for representatives of six major squamate clades  identified a lineage-specific autonomous DNA transposon from the  species . The HarLaticauda genomes. In this model, the mechanism of DNA loss of recently expanded TEs is explained by nonallelic homologous recombination events , where sequences with high similarity from different locations in the genome recombine [Laticauda kraits, evidence suggests that the L. laticaudata genome underwent a series of NAHR deletions following mass transposon expansion, allowing the species to retain a genome size similar to related terrestrial species [The abovementioned study also identified a key difference in TE dynamics at the species level, finding evidence for the accordion model between the two ecombine . NAHR is species .Large-scale differences in TE dynamics have been shown between major vertebrate clades as well; a positive correlation between DNA gain and DNA loss was found in birds, but not in mammals, suggesting that the avian genome structure is governed by deletions more so than mammals . RegardiGenome assembly quality can greatly affect the estimation of genomic repeats. As previously mentioned, short reads sequencing can make accurate characterization of TE content difficult due to the short read lengths and highly repetitive makeup of TEs, particularly when the focal element is longer than the read length . Long-read sequencing technology not only improves the quality of assemblies but also allows reads to span full repetitive regions and increase TE annotation accuracy. Even in gold standard reference assemblies of model organisms, long reads increased TE insert detection by 26–57% and identified hundreds of new TE variants associated with adaptive evolution . These mPogona vitticeps, Eublepharis macularius, Gekko gecko, Salvator merianae, Shinisaurus crocodilurus) [Linking genomic and phenotypic evolution has expanded from early efforts of simple genotype–phenotype mapping to the use of genome-wide loci and comparative genomics . Many trdilurus) . Howeverdilurus) ).Using whole genome assemblies, researchers can identify both the specific genes controlling traits of interest as well as their position, contextualizing the genomic architecture of trait evolution as was recently performed for pit viper chemoreception . OutsideAnolis sagrei) and gecko species (Paroedura picta) [The latest advances in genomics, such as CRISPR, have now developed genome-wide screening methods to target thousands of genes in a single injection . Phenotya picta) ,150, opeHeloderma  [Varanus   and Varated; see ,153), asted; see . Venom ited; see ,156. Vented; see ,158. Bected; see . The higeuticals , includium venom .Ophiophagus hannah) was the first venomous snake to have its genome sequenced, revealing and providing genome-wide support for the importance of gene duplication of housekeeping genes followed by recruitment into snake toxin-producing functions  [The king cobra (m genes) . Howeverm genes) ,162. In m genes) . IdentifNiveoscincus ocellatus), which transitions to a temperature-dependent system in certain climates [The developmental and evolutionary basis for various forms of sex determination across vertebrates is an active area of research, with direct implications to issues of climate change and conservation . Squamatclimates . Multiplclimates ; howeverSphaerodactylus townsendi (Puerto Rican Sandy Geckolet) genome enabled the identification of the candidate primary sex-determining gene that has independently evolved in two fish clades [Recently, a reannotation of the h clades . ReferenSquamates are an important taxon representing a large proportion of extant amniote diversity, and recent advances in DNA sequencing technologies have enabled access to complete genome information for the group that was not possible at the onset of the era of the human genome. We have found that despite a growing number of complete genomes for squamates in the public databases, there is not only considerable variety in genome assembly quality but also gaps in the taxonomic distribution of available genomes for squamates. We suggest that effort should be placed toward obtaining high-quality contigs for key lineages of squamates such as dibamids and amphisbaenians. The fact that an amphisbaenid genome became available at the time of this writing reflects a rapidly changing squamate genomics field which portends many promising future discoveries.Targeted genome projects for squamates will help establish ancestral states in genome evolution and allow greater accuracy in the reconstruction of squamate evolutionary history. In addition, we assert that squamates deserve a genome consortium on par with Zoonomia for mammals ,35 and t


Bioinspired self-assembly is a bottom-up strategy enabling biologically sophisticated nanostructured biogels that can mimic natural tissue. Self-assembling peptides (SAPs), carefully designed, form signal-rich supramolecular nanostructures that intertwine to form a hydrogel material that can be used for a range of cell and tissue engineering scaffolds. Using the tools of nature, they are a versatile framework for the supply and presentation of important biological factors. Recent developments have shown promise for many applications such as therapeutic gene, drug and cell delivery and yet are stable enough for large-scale tissue engineering. This is due to their excellent programmability—features can be incorporated for innate biocompatibility, biodegradability, synthetic feasibility, biological functionality and responsiveness to external stimuli. SAPs can be used independently or combined with other (macro)molecules to recapitulate surprisingly complex biological functions in a simple framework. It is easy to accomplish localized delivery, since they can be injected and can deliver targeted and sustained effects. In this review, we discuss the categories of SAPs, applications for gene and drug delivery, and their inherent design challenges. We highlight selected applications from the literature and make suggestions to advance the field with SAPs as a simple, yet smart delivery platform for emerging BioMedTech applications. Peptides, short amino acid sequences, are useful tools to create therapeutics and biomaterials . PeptideThese minimalist sequences are known as self-assembled (or assembling) peptides (SAPs). SAP materials are ideal candidates for BioMedTech applications, as they are inherently biodegradable with predictable degradation products from the activity of, for example, proteases . They arIn order to deliver drugs to specific tissues, several challenges must be overcome. These drugs must be presented at a specific concentration, time and place; typically determined by the biological needs of the therapeutic or regenerative process. This presentation must ensure that the therapeutic payload is both protected from the biological environment that may degrade it, administered in a dose-dependent, safe manner  to minimAn emerging category of hydrogelators are short peptides that assemble into nano-micro-macroscale hierarchical materials . There aStable, highly hydrated, interconnected hierarchy of structures, SAP delivery systems offer desirable characteristics for high drug loading, low drug leakage, sustained delivery, and high permeability to reach the target cells . Further6KNH2 and KA6-NH2, were also designed by Zhang’s group. These have a nonpolar tail composed of hydrophobic amino acids and a hydrophilic head consisting of charged amino acids and are capable of assembling in water to form nanostructures including tubes, vesicles and micelles [Amphiphilic peptides have both hydrophobic and hydrophilic faces. Significant success has been achieved with peptide amphiphiles (PAs). These are a peptide-alkyl chain with four basic structural factors: a hydrophobic portion, a short peptide sequence able to form intermolecular hydrogen bonds and promote β-sheet formation, a charged amino acid sequence to balance aqueous solubility and a domain for the inclusion of bioactive signals . Therefomicelles .Cyclic peptides are able to form rigid nanotubes via hydrogen bonding and allow the molecules to present a variety of orientations that are not available in linear peptides . They haThe N-terminal residue of the peptide chain can be modified with a capping group. This enables a hydrophobic or aromatic group to be introduced and allows shorter fragments to self-assemble. For example, Fluorenylmethoxycarbonyl (Fmoc) Fmoc-protected peptides are a class of minimalist peptides, with short amino acid sequences of 1–10 residues and can form hydrogels underpinned by nanofibers under physiological conditions ,39. For Triggering the assembly of SAPs in the presence of other functional molecules further expands the library of structural and functional diversity. Carefully selected, proteins and polymers can become part of the hydrogel, adding richness and complexity to target the requirements of a greater number of applications . SAPs haDue to their versatility, SAPs have been used as a platform technology to stabilize and control delivery of biological compounds that are expensive, complex or liable to degradation. Cancers are one of the most fatal diseases in the world; increasing numbers of new cases each year mean new, cheaper and safer therapies are urgently required . NanotecThe inherent ability of SAP to mimic the epitopes of ECM proteins has been utilized to bind to overexpressed proteins on vascular endothelial cells and tumor cells ,68. ThisHeart failure remains one of the leading causes of death worldwide, most commonly developing after myocardial infarction (MI) . Cells lSAPs have numerous inherent advantages for delivery to the heart; in particular, their general biocompatible properties and the ability to form stable and injectable nanofibrous hydrogels that support cell transplantation. SAP-based protein delivery has been used for the myocardium to enhance cell therapy, progenitor/stem cells delivery, endothelial cells delivery and myocytes delivery . Burgess4 gel, and found that varying peptide nanofiber density could be an efficient approach to control protein release [In order to achieve controlled delivery of proteins using SAPs, it is crucial that the scaffold components and pores match the particular size and composition of the protein molecules being delivered , requiri release . FurtherThe intrinsic ability of SAPs to promote endothelial progenitor cell recruitment within its microenvironment has inspired further work specifically targeting vasculogenesis, angiogenesis and arteriogenesis following MI. RADA 16-II nanofibers were employed to deliver vascular endothelial growth factor (VEGF), resulting in sustained presentation over >14 days in the myocardium and resulted in improved angiogenesis, arteriogenesis and cardiac function at 28 days post-MI in rats . InteresThe delivery of osteoinductive SAPs have gained attention and shown promise for accelerating bone repair . A void-220 is a thermal-responsive elastin-like polymer with the sequence VPAVG repeated 220 times. This resulted in self-assembled spherical nanoparticles that were capable of encapsulating and sustaining BMP-2 delivery [While these studies adopted relatively short peptide sequences , longer peptide chains can also be used for BMP delivery to enhance bone regeneration. For example, Poly(VPAVG)delivery . Bone remodeling has also been targeted by an SAP to deliver RANKL, a factor contributing to bone turnover. Kaipatur, et al. showed a (RADA)4 hydrogel with RANKL could induce osteoclastogenesis in vitro —with proDamage to the peripheral nervous system, most notably spinal cord injury (SCI) has thus far evaded satisfactory therapeutics in clinical trials . Whilst Taxol-loaded SAPs have been studied, an antitumor drug, which is also recognized for its ability to promote neurite regeneration via stabilization of microtubules. Taxol released from the SAP prolonged its activity to promote neurite extension, reduce glial scarring and consequently result in enhanced functional recovery after SCI in canines without notable cytotoxicity . In a coIn another study, Lindsey et al. examined the feasibility of using MAX8 as a delivery system for nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF); two key neurotrophic growth factors currently used in experimental treatments of spinal cord injuries. Importantly, the encapsulation of NGF and BDNF within MAX8 did not negatively impact gel formation, nor the shear thinning property of gels result in immediate growth factor release . MeanwhiIn SCI, the formation of the glial scar is considered one of the greatest barriers to regeneration. The scar is composed of proteoglycans that impede axonal growth. Chondroitinase ABC (ChABC) is a depolymerizing lyase enzyme that cleaves a broad range of galactosaminoglycan substrates, including chondroitin sulfate proteoglycans, to reduce the gliotic scar . HoweverThere are additional challenges to successfully deliver a cargo to the brain compared to other tissues. A carrier must not only navigate through the body while eliciting minimal immunogenic response and avoiding off-target delivery, but also needs to achieve transport across the BBB, perhaps the most tightly regulated biological barrier in the human body . Although still less exploited in the treatment of CNS disorders, a growing amount of work shows that SAPs have significant promise in delivery of compounds to the brain. Both polypeptide-bearing amphiphilic block-copolymers and PAs that self-assemble into peptide nanoparticles (NPs) , can be In addition to the non-invasive capacity for drug delivery into the brain and across the BBB, SAPs have been investigated for their potential to promote repair following intracerebral delivery. Most relevant in stroke where, much like spinal cord injury, there is a lesion side, tissue void and glial scarring, here SAPs can impact regeneration directly because of their customized peptide-based properties, but also in their capabilities to deliver compounds  in a targeted temporal and spatial manner to the infarct site. Most recently, Yaguchi et al. fabricated a cell-adhesive fiber forming peptide that mimics aspects of the ECM—forming micrometer-long supramolecular nanofibers that dispersed homogeneously in the hydrogel and could efficiently mediate the sustained release of vascular endothelial growth factor, to provide regeneration in a mouse stroke model. In a zebrafish brain injury model (severed optic tectum), a RADA16-SVVYGLR hydrogel promoted angiogenesis and invoked local neurogenesis resulting in functional recovery. Fmoc-protected SAPs matching the common brain ECM protein laminin have shown significant promise for the repair of stroke , cell deTopical delivery of ocular therapeutics is commonly impaired by rapid tear clearance, poor corneal absorption and low bioavailability (less than 5%) ,123. FurConsidering the negative charges of the ocular mucosa, the rational design of cationic peptide-based molecular hydrogels is promising to prolong the ocular residence time of drugs, which simultaneously provides a mucoadhesive property via the electrostatic interaction with negatively charged mucin on the ocular surface. Li et al. used a cationic peptide (Nap-FFKK) for treating ocular disorders, exhibiting minimal cytotoxicity against human cornea and displaying excellent biocompatibility properties . More reKaravasili et al. engineered two SAPs, (RADA)4 and (IEIK)3I, that both formed hydrogels at physiological conditions and were used as carriers for ocular delivery of timolol maleate (TM). They showed controlled release and transport of the drug through the cornea with (IEIK)3I showing a slower release than (RADA)4. Moreover, in vivo studies demonstrated that there was an extended reduction in intraocular pressure (up to 24 h) compared to the drug solution . RecentlTransplantation of the insulin-producing β-cell islets is a promising treatment for Type 1 Diabetes. However, several factors such as immune-mediated transplant rejection and immunosuppressive-related beta-cell toxicity severely limit the long-term success ,125. FurLiu et al. functionalized the cationic SAP, KLD12 (KLDLKLDLKLDLR) with collagen IV and fibronectin mimicking motifs abundant in the native islet ECM to encapsulate islets and deliver sustained release of hepatocyte growth factor (HGF). In vivo, this hydrogel showed slow release of HGF, which inhibited the expression of pro-inflammatory cytokine pathway activation and T-lymphocyte infiltration in grafts and thereby improved β-cell survival and insulin secretion . Khan etImmunogenic stimulation arising from the development of vaccines has become a milestone in disease prevention and human health. Currently, whole pathogen vaccines are most often used clinically . While tYang et al. designed a set of reduction-responsive SAP precursors, which can be reduced by glutathione (GSH), forming hydrogels with different surface properties . When co-assembled with vaccines  prepared by mixing different precursors with antigens before GSH reduction, K-vacc promoted antibody production and antitumor immune responses more effectively than the other two vaccines. Therefore, co-assembly of SAPs and antigens could act as efficient vaccine delivery systems for improving antibody production, and different immune effects can be obtained by changing the surface properties of the SAPs . An IKVARecently, SAPs themselves have been reported to exhibit immune-stimulating effects, therefore, they could also be designed as vaccines . PeptideIncreasingly, new therapies have focused on the delivery of genetic material that can elicit a response in the host cells . Gene deA variety of delivery vehicles for nucleic acids depend on electrostatic interactions between positively charged groups and negatively charged nucleotide back bones. This approach can be extended to SAPs, which have demonstrated the ability to adsorb nucleotides by interactions with charged arginine or lysine residues . The delSAPs have been used to deliver siRNAs for cancer treatment ,146. ForNot every application is best suited for the use of a virus as a transfer vector. Novel systems that provide equally as effective gene transfer and minimal cytotoxicity are the main goals of these synthetic gene transfection systems, yet they have delivery and stability challenges which can be synergistically overcome with SAPs . Liang eViral vector gene delivery is a promising technique for the therapeutic treatments of proteins to damaged tissues for the enhancement of regeneration outcomes in various disease circumstances, including brain and spinal cord injury, as well as autoimmune diseases. Viral vector gene delivery is different to nonviral-based formulas, due to its significant numbers of empty capsids and limited size of therapeutic gene delivered based on the viral capsid capacity. However, SAPs can be used for viral vector gene delivery as well. For clinical applications in gene therapy, transduction protocols include the polypeptide CH-296, a sequence of the human fibronectin protein that enhances transduction by promoting the co-localization of viruses and cells and making the target cell more available to the carrier. Identification of new additives that are easy to manipulate and able to improve the infectivity of a wide spectrum of lentiviral vector (LV) phenotypes is therefore required . RodriguSAP nanostructures have shown promising results in the delivery of therapeutics to a range of different tissues and cells. The predominant superiorities of SAPs are due to their simplicity and the relatively easy production and functionalization approaches . HoweverCharacterization of SAP hydrogels is quite limited. Commonly used techniques such as dynamic light scattering and transmission electron microscopy give only partial information. Newer methods such as nanoparticle tracking analysis and tunable resistive pulse sensing have potential; however, the ability to determine more than just the average surface functional group density is incomplete ,149.With regard to SAPs as gene-delivery vectors, the peptide engineering library and therapeutic DNA formulations provide a toolbox of options. However, peptide-based gene therapy has several challenges that still need to be overcome, including unacceptable aggregation, pH stability, size control, and chemical and enzymatic stability . New DNADespite the challenges listed above, regarding brain drug delivery, peptide nanocarriers are perfectly positioned to achieve the successful delivery of treatments to the brain. The toolbox of peptide building blocks affords opportunities of design and tuning the abundant supramolecular interactions. Improved peptide nanomaterial synthesis approaches will, in turn, afford researchers new probes for recognizing novel routes and concepts for the delivery of therapies to the brain. The diversity of both material properties and experimental approaches makes peptide nanomaterials an extremely promising platform for use as delivery vehicles . SAP-based nanomaterials are likely to play a valuable role in the delivery and targeting of future drug and vaccines. Further research is needed before this growing field can be translated to clinical application. However, future peptide delivery systems will likely transform into natural-synthetic hybrids that meet non-toxic functional demands and safety and efficacy purposes. For successful clinical application, peptide nanostructures must have improved stability within environments of varying pH, and the relationship between the morphology, physicochemical and biological activity must be exploited in more detail. Future work needs to focus on rational systematic design, which will help to understand peptide self-assembly thoroughly and allow specific and controlled development. In this way, SAPs could form the basis for a broad range of therapeutics and be a significant step forward in the treatment of numerous conditions.


It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives. Studies exploring genetic variation have built foundational knowledge in genetics, molecular biology, cell biology, breeding, and evolution in plants, animals, and microorganisms. The methods applied, and the ability to capture the true genetic variation present in species, has evolved as technology has advanced. The power to sequence whole genomes with increased efficiency and decreased cost has allowed researchers to begin to understand new levels of genomic variation. Recently, the ability to accurately sequence long regions of genomes and single molecules has illustrated the impact of larger variations across and within genomes, referred to as structural variants (SVs).Any deviation from the reference genome for a particular species can be described as ‘structural variation,’ but generally structural variants are defined as changes larger than a few bases, which can range from 30 base pairs to several megabases. Insertions, deletions, translocations, inversions, changes in copy numbers, tandem duplications, and presence/absence deviations are all examples of structural variation , which is comprised of > 80% repetitive sequence and is derived from three separate genomes to contain 3 copies of each chromosome. Plants also contain transposable elements which can play a large role in SVs, as is likely the case in maize. Although SVs can occur throughout the genome, studies suggest that their distribution is nonrandom, and there is a higher prevalence of SVs in centromeric and subtelomeric regions , cross-species chromosomal hybridizations , and ancient duplication events . Additionally, selective breeding and crop improvement have led to the development of polyploid genomes, such as hexaploid bread wheat  in the Andes. Cherry tomato moved across the region, and in Mesoamerica cherry tomato was improved and selected for larger fruit size and mass that led to the large-fruited tomato (Solanum lycopersium). Recent advances in sequencing capabilities have also made way for the development of a tomato pan-genome , and the number of species sequenced continues to grow exponentially , at the genome scale  . Array-CGH relies on comparative hybridization of the reference and test samples to hybridization targets. The signal ratio is then used as a proxy for estimating copy number variation. SNP arrays also utilize hybridization to detect genomic variation. However, SNP probes are designed to capture unique differences between samples. This increases the sensitivity for SNP arrays to detect copy number variations and unique alleles. However, SNP arrays do have increased background noise compared to array-CGH  now allow researchers to identify larger genomic variants up to several megabases in length. LRS amplifies a single DNA molecule, which avoids amplification bias of repetitive sequences and generates enough DNA overlaps to assemble whole chromosomes. Single-molecule real-time (SMRT) sequencing, such as Pacific Bioscience’s Sequel platform, and nanopore sequencing, such as Oxford Nanopore’s MinION platform, are available long-read sequencing methods. While SRS typically has lower error rates and therefore more accurately calls SNPs compared to LRS, LRS is essential for de novo genome assembly and chromosome-level sequencing.The plunging costs of sequencing have made identifying SVs less cost-prohibitive, and the development of ‘in-house’ long-read sequencers such as Oxford Nanopore’s MinION platform brings costs down significantly. The development of easy-to-use genomic DNA preparation, library, and barcoding kits have made sequencing broadly accessible to biologists.Published in 2009, maize became the first plant genotyped for SV analysis  Flagellin sensing 3 (Fls3), which detects the bacterial flagellin peptide flgII-28, can lead to dramatic changes in Fls3 function  production in transient assays expressing chimeric Fls2/Fls3 constructs in leaves  paralog, Fls2.2, which is located approximately 3.8 kb away from Fls2.1 and likely arose from a tandem gene duplication event . Additionally, the coiled-coil nucleotide-binding subclass of NLRs (CNLs) in tomato and five of its wild relatives were recently found to harbor structural variation in their N-termini in the form of extended CNLs (exCNL) that arose from tandem duplications of exon segments  . By definition, SVs are larger than other forms of genomic variation. This presents a problem when current CRISPR protocols for plants have been optimized for smaller regions of genetic material. Zhang et al. generated 245 T0 CRISPR/Cas9 events that induced mutations in 63 immunity-associated genes, and evaluated the efficiency of different CRISPR systems to induce mutations (Zhang et al., There is also the potential to use CRISPR/Cas Prime editing to genetically engineer changes in structural variations. Prime editing vectors for plants have been developed, but with overall low mutation efficiency with the highest being 53.2% for maize (Jiang et al., There is still much to learn about how structural variation affects plants, but the evidence thus far reveals a strong association with structural variation and disease responses. Recent innovations in genomic tools and the development of large collections of genomic resources has led to great insights into the discovery of structural variants in plants, molecular mechanisms of genetics, and the effects of genomic changes on disease resistance or development. Additionally, improvements in gene editing tools such as CRISPR pave the way for ‘designer genomes’ to improve agricultural germplasm in the future. Such improvements could allow scientists to better and more quickly adapt to the adverse impacts of climate change, including emerging pathogens and biotic stresses, abiotic stresses, increased need for biofuel production, and a significant need for carbon sequestration from the atmosphere.


Preclinical in vitro models play an important role in studying cancer cell biology and facilitating translational research, especially in the identification of drug targets and drug discovery studies. This is particularly relevant in breast cancer, where the global burden of disease is quite high based on prevalence and a relatively high rate of lethality. Predictive tools to select patients who will be responsive to invasive or morbid therapies  are relatively lacking. To be clinically relevant, a model must accurately replicate the biology and cellular heterogeneity of the primary tumor. Addressing these requirements and overcoming the limitations of most existing cancer cell lines, which are typically derived from a single clone, we have recently developed conditional reprogramming (CR) technology. The CR technology refers to a co-culture system of primary human normal or tumor cells with irradiated murine fibroblasts in the presence of a Rho-associated kinase inhibitor to allow the primary cells to acquire stem cell properties and the ability to proliferate indefinitely in vitro without any exogenous gene or viral transfection. This innovative approach fulfills many of these needs and offers an alternative that surpasses the deficiencies associated with traditional cancer cell lines. These CR cells (CRCs) can be reprogrammed to maintain a highly proliferative state and reproduce the genomic and histological characteristics of the parental tissue. Therefore, CR technology may be a clinically relevant model to test and predict drug sensitivity, conduct gene profile analysis and xenograft research, and undertake personalized medicine. This review discusses studies that have applied CR technology to conduct breast cancer research. Breast cancer is the second most common type of cancer among women in the world, with an estimated 2.3 million new cases accounting for 11.7% of all cancer cases and approximately 700,000 deaths worldwide ,5. The mA major obstacle hindering cancer research progress is the limited availability of cancer models . Cancer Recent progress in biotechnology has led to significant changes in the development of cancer models. Patient-derived models (PDMs) have emerged as a particularly promising approach, as they maintain consistent genetic characteristics with their parental tumors. Different types of PDMs such as organoids, induced pluripotent stem cells (iPSCs), patient-derived xenografts (PDXs), and conditionally reprogrammed cells (CRCs) have been widely used in cancer research due to their ability to better replicate the complexity of human tumors ,23,24,25Organoids are three-dimensional (3D) cell structures derived from primary tissues or stem cells that mimic the architecture and function of the original organ . The conDespite the organoid system’s promise, it has some drawbacks and technological challenges. It is significant to note that numerous phases of differential centrifugation and cell straining are used in many contemporary techniques to separate and purify mammary epithelial cells from surrounding stromal cells before growth in 3D culture. Breast organoids made from pure stromal and epithelial cells might not accurately replicate the in vivo tissue architecture and cell-cell/matrix interactions . AlthougPDX models are generated by transplanting fragments of human tumors into mice with immunocompromised immune systems ,52. OverWhile PDX tumor models have many advantages, they also have some drawbacks, such as the possibility for selection of minor clones as mentioned above. Moreover, creating PDX models may be an expensive and time-consuming process that takes anything from six months to two years. In addition, depending on the specific characteristics of the disease and the origins of the tumor, the success rate of developing PDX models might vary greatly, ranging from 10% to 90% ,59. The Identifying a single model system that is fast, easy to perform, and has a high success rate from a variety of clinical samples  remains a challenge. We have recently developed a new primary cell culture system called conditional reprogramming. To efficiently and rapidly produce infinite cells, we added irradiated Swiss-3T3-J2 mouse fibroblast cells and Y27632, a Rho-associated kinase (ROCK) inhibitor, to the cell culture plate using this method . The genThe ease of execution, genotype stability, exponential growth, and high success rate in a single model system are some of the reported advantages of CR. These properties qualified CR as an outstanding in vitro model compared to other models such as organoids and patient-derived xenografts . ClinicaThe conditional reprogramming system can be successfully applied to various epithelial tissues such as prostate, kidney, skin, lung, and several others ,80. MoreThe adult human mammary gland consists of a complex structure made up of tubuloalveolar units. These tubuloalveolar units are composed of polarized epithelial cells responsible for producing milk, which is surrounded by myoepithelial cells. The overall organization of the gland is characterized by a two-layered arrangement, with a basement membrane encompassing the entire structure . UnderstUsing primary epithelial cells directly derived from human mammary glands offers a tissue-specific model; however, it has certain limitations. One of the limitations is that these cells have a short lifespan when cultured under conventional tissue culture conditions . CR systJin and colleagues investigated the feasibility of the CR system for the characterization of primary human mammary epithelial cells (PHMEC) isolated and propagated by conditionally reprogrammed cell culture . They esThey showed that PHMEC initially isolated using CRC could be transferred and grown in a variety of different mammary cell specific media. Then, exploiting the ability of utilizing CRC-isolated cells for parallel studies of behavior and gene expression, showed that estrogen growth response was associated with tissue necrosis factor signaling and interferon alpha response gene enrichment while neoadjuvant chemotherapy exposure significantly altered transcriptomes, shifting them towards expression of genes linked to mammary stem cell formation. Finally, they showed gene expression patterns in mammary cells normally linked to pregnancy can be found as an abnormal finding in non-pregnant at-risk and breast cancer cells . Alamri In addition to applications on basic mammary epithelial biology, recent studies suggested CR technology also can be used for modeling human breast cancer , biologyEfficient and rapid establishment of CRCs has been achieved using various human normal and tumor specimens, including the breast, without the need for exogenous viruses or genetic manipulation. These CRCs can preserve the characteristics of their primary tissues. By removing these conditions, the cells’ differentiation ability can be restored. They also can be cultured in both 2D and 3D systems. Consequently, CR can serve as an ideal in vitro model for studying breast cancer. Mahajan et al. applied CR technology to conduct a comparative analysis between early-passage conditionally reprogrammed breast cancer cells and their corresponding primary tumors . They evDuctal carcinoma in situ (DCIS) is a non-invasive form of breast cancer, and currently, there are no reliable predictors to determine its progression into an invasive disease. Therefore, the majority of patients undergo radiation and/or hormone therapy following surgical removal, often resulting in overtreatment. Two commercially available cell lines for studying DCIS, namely SUM225CWN and MCF10DCIS.COM, are not ideal due to their origins that are not derived directly from primary DCIS tumors ,102,103.Brown et al. sought to develop new models of DCIS by culturing primary DCIS tissue from patients following lumpectomy or mastectomy . FollowiPrecision medicine is a recently developed strategy for characterizing malignancies biologically and is seen as a new frontier in the treatment and prevention of cancer. Precision medicine has a wide range of applications, including those for prevention, diagnosis, prognosis, monitoring treatment response, and early treatment resistance discovery. Precision medicine aims to do away with the “one size fits all” approach to managing cancer patients. Genetic analysis has recently revolutionized how different malignancies are classified and treated. Precision medicine is built on targeted therapy, a therapeutic approach that uses drugs to specifically target proteins and genes linked to the growth and survival of tumor cells . Due to To investigate heterogeneity and drug sensitivity, Mimoto and colleagues generated CRCs from patients with recurrent HR+/HER2-  breast cancer . In CR cThe findings of this study highlight the potential application of CR cells for drug sensitivity tests and determining appropriate treatments. Their research represents a key step in innovative clinical tools development to aid in decision-making for patients with metastatic HR+/HER2- breast cancer. Phyllodes tumors of the breast are uncommon tumors that involve both stromal and epithelial components. Surgical removal is the primary recommended treatment for Phyllodes tumors. However, despite complete resection, the malignant form of Phyllodes tumors still carries a high recurrence risk, reaching up to 40%. Furthermore, there is currently no consensus regarding the most effective drugs for treating Phyllodes tumors. Recently, Urbaniak et al. applied CR technology to evaluate the response of phyllodes tumor of the breast to seven drugs namely Salinomycin, Bcl-2/Bcl-xL inhibitor ABT-263, paclitaxel, DOX, colchicine, vincristine, and cisplatin. Of these, ABT-263, Salinomycin, and DOX were found to be highly selective toward phyllodes tumor cells . This stCustomizing assays for tumor molecular phenotyping is essential due to variations in the differentiation status of tumors and normal tissues in different patients. In response to this challenge, Anjanappa and colleagues  employedRecent progress in DNA sequencing technology have made it feasible to sequence a considerable number of tumor samples at a reasonable cost. Nonetheless, to enhance its clinical applicability, it is crucial to decrease sequencing errors and identify rare mutations that might exist within a small subset of tumor cells. Tumor complexity and intratumor heterogeneity contribute to the diversity of subclones. Despite advancements in next-generation sequencing, pinpointing low frequency mutations in primary tumors and metastases that contribute to subclonal diversity remains a challenge in precision genomics. To address this, Anjanappa and colleagues  employedEarly diagnosis is crucial for effective breast cancer treatment and plays an important role in reducing mortality rates . While mLiquid biopsies are non-invasive and safe methods for tumor detection. These minimally invasive sampling techniques utilize circulating biomarkers to analyze tumors and deliver reliable diagnostic information. Liquid biopsies encompass various components, such as exosomes , microRNIn 1869, Thomas R. Ashworth first identified CTCs in the blood of a cancer patient through a comparison of CTC morphology with different tumor cells . Despiten = 6) versus white (n = 15) were identified (padj<0.05). One hundred seventy-seven genes were significantly up-regulated and one hundred forty-four genes significantly down-regulated in non-cancer ipsilateral cells from women identifying as black as compared to white  or intertumor heterogeneity (different tumors), or intratumor heterogeneity (within the same tumor tissues). To study micro- or molecular heterogeneity of breast cancer, we established cell-derived clones using CR technology A. Nine cThe heterogeneity found within the normal breast can impact the characterization of cancer stem cells. Nakshatri and colleagues  employedThis result suggests that CR technology may serve as a biological method to study heterogeneity of breast cancer from patients’ specimens, especially minimized samples from advanced breast cancer patients.The CR system has shown great promise in breast cancer research, but it is important to acknowledge and address its limitations. One such limitation is that the CR method lacks the inclusion of essential stromal components, including matrix elements, vascular immune cells, and endothelial cells. This limitation hinders the comprehensive analysis of how stromal cells influence tumor cell growth and how tumor cells respond to drugs . AnotherThe development of the CR method offers encouraging opportunities for studying breast cancer . Cell cu


Maintenance of normal cardiac rhythm requires coordinated activity of ion channels and transporters that allow well-ordered propagation of electrical impulses across the myocardium. Disruptions in this orderly process provoke cardiac arrhythmias that may be lethal in some patients. Risk of common acquired arrhythmias is increased markedly when structural heart disease caused by myocardial infarction (due to fibrotic scar formation) or left ventricular dysfunction is present. Genetic polymorphisms influence structure or excitability of the myocardial substrate, which increases vulnerability or risk of arrhythmias in patients. Similarly, genetic polymorphisms of drug-metabolizing enzymes give rise to distinct subgroups within the population that affect specific drug biotransformation reactions. Nonetheless, identification of triggers involved in initiation or maintenance of cardiac arrhythmias remains a major challenge. Herein, we provide an overview of knowledge regarding physiopathology of inherited and acquired cardiac arrhythmias along with a summary of treatments (pharmacologic or non-pharmacologic) used to limit their effect on morbidity and potential mortality. Improved understanding of molecular and cellular aspects of arrhythmogenesis and more epidemiologic studies  are crucial for development of novel treatments and for management of cardiac arrhythmias and their consequences in patients, as their incidence is increasing worldwide. The original description of sudden cardiac death in seemingly healthy patients who frequently experience severe fainting spells is attributed to Hippocrates ; variousIn clinical practice, atrial fibrillation  is a pervasive cardiac arrhythmia, principally brought about by structural and electrophysiological alterations in atrial tissues. It can be encountered in the absence of underlying heart disease but is more frequently seen in connection with mitral valve disease, heart failure, ischemic heart disease and hypertension ,4. EarlyWhile ventricular arrhythmias are, for the most part, catastrophic and require immediate attention, atrial fibrillation is usually asymptomatic, undetected and self-terminating. However, over time, atrial fibrillation can evolve to a chronic stage , which complicates clinical treatments. In other words, contributory mechanisms as well as triggers change as the disease progresses ,6. The pClinical and basic science studies have enabled development of clinical strategies to improve quality of life in patients. Herein, we examine experimental and clinical advances that are central to clinical treatment of cardiac arrhythmias. For this review, we searched English-language clinical and basic science reports using the PubMed and Google Scholar platforms with the search terms cardiac arrhythmias, ischemic heart disease, electrophysiology, intrinsic cardiac nervous system, pharmacological treatments, implantable cardioverter defibrillator, catheter ablation, ischemic preconditioning, and combinations thereof.Cardiac function relies on rhythmic contraction coordinated by specialized cardiac pacemaker cells in mammalian hearts. A well-established electrical conduction system  coordinMammalian cardiomyocytes express a diversity of voltage-gated ion channel pore-forming subunits, which contribute to formation of inward and outward currents that shape waveforms of action potentials and influence both automaticity and refractoriness. The interplay between all of the ionic currents profoundly affects ventricular action potential waveforms. Insights into these relationships have been provided through molecular genetics studies.In pacemaker cells (distinctive due to properties of automaticity) of the sinoatrial and atrioventricular nodes, atria and the His–Purkinje systems, voltage and calcium dependent mechanisms are involved . NormallIn the absence of a vulnerable myocardial substrate and an appropriate trigger, electrical conduction in the heart is reasonably without incident. However, alteration of cellular and electrophysiological properties  within the myocardium substantially increases the potential for cardiac arrhythmias. Marked deceleration of early repolarization and acceleration of late repolarization caused by changes in current expression result in atrial fibrillation; molecular changes that may drive these outcomes include 1—augmented inward-rectified potassium current activity, and 2—simultaneous reduction in L-type calcium current activity . RemediaElectrical remodeling  is associated with ion channel gene mutations but is most important within the context of structural myocardial disease. In the failing heart, electrical remodeling increases susceptibility to both atrial and ventricular arrhythmias ,25. Dist2+ cycling may be important [Experimental models to evaluate cardiac cell electrophysiology and changes in the time and voltage dependence as well as the time course of ionic currents that underlie the action potential have been available since they were initially reported by Professor Noble in 1962  ; numeroMultiple microRNAs play a fundamental role in regulating key components  of electrical conduction; impairment of any of these components can lead to development of atrial fibrillation (cf. review article ). Long nEpigenetics (changes in gene expression that occur without changes in DNA sequence ) examineAcute obstruction of a coronary vessel produces profound pathological changes in cardiomyocytes (within the area of no blood flow or anatomic area at risk) due to abrupt stoppage of biochemical and metabolic pathways. Reduced oxygen delivery halts oxidative phosphorylation, depletion of intracellular energy phosphate stores and inhibition of myocyte contractile function. Ischemic heart disease is a major contributor to cardiac arrhythmias, which can be life threatening in patients . IschemiTimely opening of an infarct-related artery is essential for the salvage of viable cardiomyocytes in the anatomic area at risk. While restoration of blood flow to the vascular bed of an infarct-related artery using percutaneous coronary interventions or thrombolytic agents delays necrosis, this may be a mixed blessing as further cardiomyocyte damage may occur to reversibly injured myocytes in the area at risk  . A letha+ currents  and altered handling of intracellular calcium [+ current downregulation is a reduced repolarization reserve; as a result, ventricular myocardium is more susceptible to early afterdepolarizations and functional reentry. Repolarization reserve was first introduced in 1998 [KrI) will not ordinarily lead to failure of repolarization  . The pre calcium . An impo in 1998 ; this cod Baczko  for furt2+ handling. Mechanisms such as Ca2+-mediated inactivation of L-type Ca2+ channels, activation of Ca2+-sensitive transporters and the Na+-Ca2+ exchanger all link intracellular Ca2+ homeostasis and ventricular action potentials. Alterations in Na+ currents and reduced current density also impact conduction in tissues that are adjacent to non-infarcted myocardium in the non-ischemic risk zone [Altered ventricular mechanics and heightened electrical instability in failing myocardium are triggered by irregularities in intracellular Caisk zone ,79,80. Tisk zone ,82; abnoisk zone . Reducedisk zone ,85. The isk zone ,87. In aisk zone  or alterisk zone .The contribution of inflammation as a cause of cardiac arrhythmias is largely overlooked; however, its role in the development of atrial fibrillation is increasingly apparent, as evidenced by the observed acute increase in inflammatory proteins ,91,92 inAn unanticipated emergence of cardiac arrhythmias in patients with COVID-19 has been described in recent studies ,99,100; A pathological link between dietary disorders  and cardiac dysfunction has been suggested. Under normal circumstances, the heart uses free fatty acids as an energy source via a regulated equilibrium between cardiac lipid uptake and oxidation. Metabolic disorders produce a situation where lipid levels exceed storage capacity of adipocytes, which then leads to intracellular accumulation of lipid droplets (with attendant disruption of cardiac function). Myocardial lipid accumulation generally impairs fatty acid metabolism and inflammation and increases vulnerability to sustained or even fatal arrhythmias ,103,104;+ channels). They also affect action potential and effective refractory period duration and thereby influence automaticity. Class II medications  act by blunting sympathetic activity, resulting in a reduced rate of the initial depolarization of the action potential, which mitigates automaticity and conduction velocity [The Vaughan Williams classification system cf.  is widelvelocity . The usevelocity ; howevervelocity ,114. On velocity ,116,117.velocity ,119,120.velocity ,122. Altvelocity ) and idiNa-L)-blocking effect, also acts in a manner similar to amiodarone  to reduce recurrence of arrhythmias [Na, which reduces excitability and leads to prolongation of the end-refractory period (causing reduced activation of the atria) [Na inhibition by ranolazine in the management of AF has not been established. Several clinical trials  have reported variable findings with respect to risk reduction for arrhythmias with ranolazine [Some pharmaceuticals outside the Vaughan Williams classification system are notable for their anti-arrhythmic actions. For example, ranolazine, primarily used as an antianginal medication with its late sodium channel  . Howevernolazine ,128.+/K+ ATPase  and enhanced contractility , thereby lowering conduction velocity and increasing the effective refractory period [Another antianginal drug, ivabradine (mixed sodium–potassium current blocker), unlike beta-blockers, reduces heart rate without affecting other aspects of cardiac function, such as inotropy . That bey period . Howevery period ,137.While clinical use of pharmacological agents to limit cardiac arrhythmias is the norm, significant cardiac and extracardiac  side effects have also been described, the most important being their potential proarrhythmic properties in patients with structural heart disease . While cFirst-order treatment against cardiac arrhythmias in patients is principally accomplished using antiarrhythmic drugs. However, evidence of the overall efficacy of pharmacotherapy is incomplete. This has spurred development of interventions such as implantable electronic pacemakers, cardioverter defibrillators and catheter ablation.Cardiac pacing  was introduced clinically in the 1930s cf. . ElectroImplantable cardioverter defibrillators were initially used more than 30 years ago in patients recovering from near-fatal ventricular fibrillation and syncope with documented sustained ventricular tachycardia, with or without compromised left ventricular ejection fraction (<40%). Survival, after a two year follow-up period, was significantly greater in these patients compared to pharmacologic treatment . SmallerRetrospective clinical findings suggest that ablation is considerably more effective than conventional pharmacotherapy for treatment of cardiac arrhythmias ,156. RecExtrinsic (vagus nerve) and intrinsic (network of intracardiac ganglia and interconnecting neurons) components comprise the cardiac autonomic nervous system, which regulates heart rate and cardiac output in response to varying physiologic states . The extPotent, non-pharmacologic protective interventions for lethal ischemia–reperfusion-injury-mediated arrhythmias have emerged in experimental and clinical studies. Ischemic conditioning consists of brief episodes of repeated arterial occlusion/reperfusion carried out prior to a longer episode of arterial occlusion  and has Despite the many thousands of published studies that report the considerable benefits of ischemic conditioning against ischemic injury, translation to clinical practice remains a particular challenge, in part due to a limited time frame during which potential protective mechanisms can be solicited as well as the random nature of acute myocardial disease . Whether ischemic conditioning can abolish or merely delay the onset of ischemia or reperfusion-induced cardiac arrhythmias remains to be established—the same question persists with regard to structural myocardial damage post-ischemia. Nonetheless, the use of post- or remote ischemic conditioning cf.  in patieA more relevant intervention with clinical potential, remote ischemic conditioning , has been used to limit myocardial injury during cardiac surgery but might also be applied to limit arrhythmogenesis. To date, findings for this intervention in clinical studies remain ambiguous. Significant protection against new onset atrial fibrillation has been reported in patients undergoing cardiac surgery ,181; howThe prevalence of cardiac arrhythmias and their consequences is increasing worldwide and may be explained by improved diagnostic tools and detection strategies available to clinicians and health care professionals. Worldwide projections are that cardiac arrhythmias affect almost two percent of the global population and are associated with substantial socioeconomic burden. This review article presents recent findings regarding the pathogenesis of cardiac arrhythmias as well as different strategies for their clinical management. Treatment for arrhythmia depends on the underlying cause. Some cases require medication, while others require more invasive procedures such as electrical cardioversion, catheter ablation or implantation of a pacemaker or defibrillator. The ultimate goal of treatment is to restore normal sinus rhythm, so it is imperative that the processes associated with electrical and structural modeling that perpetuate cardiac arrhythmias are reversed. However, it is increasingly clear that pharmaceuticals alone are limited with regard to efficacy for treatment of cardiac arrhythmias. As a result, considerable efforts are underway to find relevant alternatives; combined therapy using pharmacologic and non-pharmacologic interventions should not be excluded.The identification of risk factors responsible for the pathogenesis of cardiac arrhythmias needs to be addressed. Increasing focus on sex and gender differences is also necessary with regard to the pathogenesis of cardiac arrhythmias ,192,193;