Mobile DNA最新文献

{"title":"Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element.","authors":"Birgit Henrich,&nbsp;Stephanie Hammerlage,&nbsp;Sebastian Scharf,&nbsp;Diana Haberhausen,&nbsp;Ursula Fürnkranz,&nbsp;Karl Köhrer,&nbsp;Lena Peitzmann,&nbsp;Pier Luigi Fiori,&nbsp;Joachim Spergser,&nbsp;Klaus Pfeffer,&nbsp;Alexander T Dilthey","doi":"10.1186/s13100-020-00225-9","DOIUrl":"https://doi.org/10.1186/s13100-020-00225-9","url":null,"abstract":"<p><strong>Background: </strong>Mobile genetic elements are found in genomes throughout the microbial world, mediating genome plasticity and important prokaryotic phenotypes. Even the cell wall-less mycoplasmas, which are known to harbour a minimal set of genes, seem to accumulate mobile genetic elements. In Mycoplasma hominis, a facultative pathogen of the human urogenital tract and an inherently very heterogeneous species, four different MGE-classes had been detected until now: insertion sequence ISMhom-1, prophage MHoV-1, a tetracycline resistance mediating transposon, and ICEHo, a species-specific variant of a mycoplasma integrative and conjugative element encoding a T4SS secretion system (termed MICE).</p><p><strong>Results: </strong>To characterize the prevalence of these MGEs, genomes of 23 M. hominis isolates were assembled using whole genome sequencing and bioinformatically analysed for the presence of mobile genetic elements. In addition to the previously described MGEs, a new ICEHo variant was found, which we designate ICEHo-II. Of 15 ICEHo-II genes, five are common MICE genes; eight are unique to ICEHo-II; and two represent a duplication of a gene also present in ICEHo-I. In 150 M. hominis isolates and based on a screening PCR, prevalence of ICEHo-I was 40.7%; of ICEHo-II, 28.7%; and of both elements, 15.3%. Activity of ICEHo-I and -II was demonstrated by detection of circularized extrachromosomal forms of the elements through PCR and subsequent Sanger sequencing.</p><p><strong>Conclusions: </strong>Nanopore sequencing enabled the identification of mobile genetic elements and of ICEHo-II, a novel MICE element of M. hominis, whose phenotypic impact and potential impact on pathogenicity can now be elucidated.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 1","pages":"30"},"PeriodicalIF":4.9,"publicationDate":"2020-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00225-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38349909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains.","authors":"Mahoko Takahashi Ueda,&nbsp;Kirill Kryukov,&nbsp;Satomi Mitsuhashi,&nbsp;Hiroaki Mitsuhashi,&nbsp;Tadashi Imanishi,&nbsp;So Nakagawa","doi":"10.1186/s13100-020-00224-w","DOIUrl":"https://doi.org/10.1186/s13100-020-00224-w","url":null,"abstract":"<p><strong>Background: </strong>Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes.</p><p><strong>Results: </strong>We investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (<i>gag</i>, <i>pro</i>, <i>pol</i>, and <i>env</i>) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (~ 0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences showed bimodal distributions, suggesting that a large proportion of ERV-ORFs either recently, or anciently, inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify candidates for ERV-derived genes, we estimated the ratio of non-synonymous to synonymous substitution rates (<i>dN/dS</i>) for ERV-ORFs in human and non-human mammalian pairs, and found that approximately 42% of the ERV-ORFs showed <i>dN/dS</i> < 1. Further, using functional genomics data including transcriptome sequencing, we determined that approximately 9.7% of these selected ERV-ORFs exhibited transcriptional potential.</p><p><strong>Conclusions: </strong>These results suggest that purifying selection operates on a certain portion of ERV-ORFs, some of which may correspond to uncharacterized functional genes hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"29"},"PeriodicalIF":4.9,"publicationDate":"2020-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00224-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38409424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Dfam community resource of transposable element families, sequence models, and genome annotations","authors":"Jessica M. Storer, R. Hubley, Jeb Rosen, T. Wheeler, A. Smit","doi":"10.21203/rs.3.rs-76062/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-76062/v1","url":null,"abstract":"Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam ( https://dfam.org ) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2020-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49632692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Twenty years of transposable element analysis in the <i>Arabidopsis thaliana</i> genome.","authors":"Hadi Quesneville","doi":"10.1186/s13100-020-00223-x","DOIUrl":"https://doi.org/10.1186/s13100-020-00223-x","url":null,"abstract":"<p><p>Transposable elements (TEs) are mobile repetitive DNA sequences shown to be major drivers of genome evolution. As the first plant to have its genome sequenced and analyzed at the genomic scale, <i>Arabidopsis thaliana</i> has largely contributed to our TE knowledge. The present report describes 20 years of accumulated TE knowledge gained through the study of the <i>Arabidopsis</i> genome and covers the known TE families, their relative abundance, and their genomic distribution. It presents our knowledge of the different TE family activities, mobility, population and long-term evolutionary dynamics. Finally, the role of TE as substrates for new genes and their impact on gene expression is illustrated through a few selected demonstrative cases. Promising future directions for TE studies in this species conclude the review.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"28"},"PeriodicalIF":4.9,"publicationDate":"2020-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00223-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38218736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of <i>pogo</i>, a separate superfamily of <i>IS630-Tc1-mariner</i> transposons, revealing recurrent domestication events in vertebrates.","authors":"Bo Gao,&nbsp;Yali Wang,&nbsp;Mohamed Diaby,&nbsp;Wencheng Zong,&nbsp;Dan Shen,&nbsp;Saisai Wang,&nbsp;Cai Chen,&nbsp;Xiaoyan Wang,&nbsp;Chengyi Song","doi":"10.1186/s13100-020-00220-0","DOIUrl":"10.1186/s13100-020-00220-0","url":null,"abstract":"<p><strong>Background: </strong><i>Tc1/mariner</i> and <i>Zator</i>, as two superfamilies of <i>IS630-Tc1</i>-<i>mariner</i> (<i>ITm</i>) group, have been well-defined. However, the molecular evolution and domestication of <i>pogo</i> transposons, once designated as an important family of the <i>Tc1/mariner</i> superfamily, are still poorly understood.</p><p><strong>Results: </strong>Here, phylogenetic analysis show that <i>pogo</i> transposases, together with <i>Tc1/mariner</i>, DD34E/<i>Gambol</i>, and <i>Zator</i> transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of <i>ITm</i> group. The <i>pogo</i> superfamily represents high diversity with six distinct families (<i>Passer</i>, <i>Tigger</i>, <i>pogoR</i>, <i>Lemi</i>, <i>Mover</i>, and <i>Fot/Fot-like</i>) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals-even mammals-and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix-turn-helix protein (JRK), JRK like (JRKL), <i>pogo</i> transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and <i>Tigger</i> transposable element-derived 2 to 7 (TIGD2-7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29-56D) were observed for <i>pogo</i> transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains.</p><p><strong>Conclusions: </strong>This is the first report to systematically reveal the evolutionary profiles of the <i>pogo</i> transposons, suggesting that <i>pogo</i> and <i>Tc1/Mariner</i> are two separate superfamilies of <i>ITm</i> group, and demonstrating the repeated domestications of <i>pogo</i> in vertebrates. These data indicate that <i>pogo</i> transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of <i>pogo</i> transposons and updates the classification of <i>ITm</i> group.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"25"},"PeriodicalIF":4.9,"publicationDate":"2020-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00220-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38218735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA.","authors":"Annette Damert","doi":"10.1186/s13100-020-00222-y","DOIUrl":"https://doi.org/10.1186/s13100-020-00222-y","url":null,"abstract":"<p><strong>Background: </strong>Non-autonomous VNTR (Variable Number of Tandem Repeats) composite retrotransposons - SVA (SINE-R-VNTR-<i>Alu</i>) and LAVA (L1-<i>Alu</i>-VNTR-<i>Alu</i>) - are specific to hominoid primates. SVA expanded in great apes, LAVA in gibbon. Both SVA and LAVA have been shown to be mobilized by the autonomous LINE-1 (L1)-encoded protein machinery in a cell-based assay in <i>trans</i>. The efficiency of human SVA retrotransposition in vitro has, however, been considerably lower than would be expected based on recent pedigree-based in vivo estimates. The VNTR composite elements across hominoids - gibbon LAVA, orangutan SVA_A descendants and hominine SVA_D descendants - display characteristic structures of the 5' <i>Alu</i>-like domain and the VNTR. Different partner L1 subfamilies are currently active in each of the lineages. The possibility that the lineage-specific types of VNTR composites evolved in response to evolutionary changes in their autonomous partners, particularly in the nucleic acid binding L1 ORF1-encoded protein, has not been addressed.</p><p><strong>Results: </strong>Here I report the identification and functional characterization of a highly active human SVA element using an improved <i>mneo</i> retrotransposition reporter cassette. The modified cassette (<i>mneoM</i>) minimizes splicing between the VNTR of human SVAs and the neomycin phosphotransferase stop codon. SVA deletion analysis provides evidence that key elements determining its mobilization efficiency reside in the VNTR and 5' hexameric repeats. Simultaneous removal of the 5' hexameric repeats and part of the VNTR has an additive negative effect on mobilization rates. Taking advantage of the modified reporter cassette that facilitates robust cross-species comparison of SVA/LAVA retrotransposition, I show that the ORF1-encoded proteins of the L1 subfamilies currently active in gibbon, orangutan and human do not display substrate preference for gibbon LAVA versus orangutan SVA versus human SVA. Finally, I demonstrate that an orangutan-derived ORF1p supports only limited retrotransposition of SVA/LAVA in <i>trans</i>, despite being fully functional in L1 mobilization in <i>cis</i>.</p><p><strong>Conclusions: </strong>Overall, the analysis confirms SVA as a highly active human retrotransposon and preferred substrate of the L1-encoded protein machinery. Based on the results obtained in human cells coevolution of L1 ORF1p and VNTR composites does not appear very likely. The changes in orangutan L1 ORF1p that markedly reduce its mobilization capacity in <i>trans</i> might explain the different SVA insertion rates in the orangutan and hominine lineages, respectively.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"27"},"PeriodicalIF":4.9,"publicationDate":"2020-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00222-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38169547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of <i>E. coli</i>.","authors":"David M Walker,&nbsp;Rasika M Harshey","doi":"10.1186/s13100-020-00217-9","DOIUrl":"https://doi.org/10.1186/s13100-020-00217-9","url":null,"abstract":"<p><strong>Background: </strong>The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the <i>E. coli</i> genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (<i>cis</i>-immunity) as well as the entire ~ 37 kb genome of Mu (Mu genome immunity). Paradoxically, MuB is responsible for <i>cis</i>-immunity and is also implicated in Mu genome immunity, but via different mechanisms. This study was undertaken to dissect the role of MuB in target choice in vivo.</p><p><strong>Results: </strong>We tracked Mu transposition from six different starting locations on the <i>E. coli</i> genome, in the presence and absence of MuB. The data reveal that Mu's ability to sample the entire genome during a single hop in a clonal population is independent of MuB, and that MuB is responsible for <i>cis</i>-immunity, plays a minor role in Mu genome immunity, and facilitates insertions into transcriptionally active regions. Unexpectedly, transposition patterns in the absence of MuB have helped extend the boundaries of the insular Ter segment of the <i>E. coli</i> genome.</p><p><strong>Conclusions: </strong>The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"26"},"PeriodicalIF":4.9,"publicationDate":"2020-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00217-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38159010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IS<i>982</i> and kin: new insights into an old IS family.","authors":"Nancy Fayad, Mireille Kallassy Awad, Jacques Mahillon","doi":"10.1186/s13100-020-00221-z","DOIUrl":"10.1186/s13100-020-00221-z","url":null,"abstract":"<p><p>Insertion sequences (IS) are ubiquitous transposable elements with a very simple organization: two inverted repeats flanking a transposase coding gene. IS<i>982</i> is one of 26 insertion sequence families known so far. With 70 registered members in the ISFinder database, this family remains somewhat unexplored, despite the association of many of its members with important features such as antibiotic resistance. IS<i>982</i> has a fairly simple organization with a mean length of ca. 1 Kb, two inverted repeats with conserved 5' AC 3' ends flanking a transposase coding gene and direct repeats of variable lengths. Its transposase has a RNAse-H like chemistry with an atypical DDE motif. In this study, we first highlight the current knowledge on the IS<i>982</i> family by dissecting its registered members and their characteristics. Secondly, we bring new insights into this old, yet uncharted IS family, by exploring its registered elements, as well as the genomic and proteomic databases of bacterial and archaeal strains. This probing showed that the presence and distribution of this family goes far beyond the clear-cut registry of ISFinder database.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"24"},"PeriodicalIF":4.9,"publicationDate":"2020-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38139618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transposable elements in <i>Drosophila</i>.","authors":"Vincent Mérel, Matthieu Boulesteix, Marie Fablet, Cristina Vieira","doi":"10.1186/s13100-020-00213-z","DOIUrl":"10.1186/s13100-020-00213-z","url":null,"abstract":"<p><p><i>Drosophila</i> has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. <i>Drosophila</i> has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of <i>Drosophila</i> with a historical hindsight as well as recent discoveries in the field.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"23"},"PeriodicalIF":4.9,"publicationDate":"2020-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38128714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data.","authors":"Andrew S Mason,&nbsp;Ashlee R Lund,&nbsp;Paul M Hocking,&nbsp;Janet E Fulton,&nbsp;David W Burt","doi":"10.1186/s13100-020-00216-w","DOIUrl":"https://doi.org/10.1186/s13100-020-00216-w","url":null,"abstract":"<p><strong>Background: </strong>Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants.</p><p><strong>Results: </strong>We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes.</p><p><strong>Conclusions: </strong>obsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"22"},"PeriodicalIF":4.9,"publicationDate":"2020-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00216-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38112548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}