{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T18:14:29Z","timestamp":1790619269206,"version":"4.1.0"},"reference-count":53,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2023,3,9]],"date-time":"2023-03-09T00:00:00Z","timestamp":1678320000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004901","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004901","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100007374","name":"Universidade Federal de Minas Gerais","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100007374","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n               <jats:title>Background<\/jats:title>\n               <jats:p><jats:italic>Corynebacterium silvaticum<\/jats:italic> is a pathogenic, gram-positive bacterial species that causes caseous lymphadenitis in wild boars, domestic pigs and roe deer in Western Europe. It can affect animal production and cause zoonosis. Genome analysis has suggested that one strain from Portugal and one from Austria could probably produce the diphtheria toxin (DT), which inhibits protein synthesis and can cause death.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Methods<\/jats:title>\n               <jats:p>To further investigate the species genetic diversity and probable production of DT by Portuguese strains, eight isolates from this country were sequenced and compared to 38 public ones.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Results<\/jats:title>\n               <jats:p>Strains from Portugal are monophyletic, nearly identical, form a unique cluster and have 27 out of 36 known <jats:italic>Corynebacterium<\/jats:italic> virulence or niche factors. All of them lack a frameshift in the <jats:italic>tox<\/jats:italic> gene and were suggested to produce DT. A phylogenetic analysis shows that the species has diverged into two clades. Clade 1 is composed of strains that were suggested to have the ability to produce DT, represented by the monophyletic strains from Portugal and strain 05-13 from Austria. Clade 2 is composed of strains unable to produce DT due to a frameshifted <jats:italic>tox<\/jats:italic> gene. The second clade is represented by strains from Austria, Germany and Switzerland. Ten genome clusters were detected, in which strains from Germany are the most diverse. Strains from Portugal belong to an exclusive cluster. The pangenome has 2,961 proteins and is nearly closed (<jats:italic>\u03b1<\/jats:italic>\u00a0=\u00a00.968). Exclusive genes shared by clusters 1 and 2, and Portuguese strains are probably not related to disease manifestation as they share the same host but could play a role in their extra-host environmental adaptation. These results show the potential of the species to cause zoonosis, possibly diphtheria. The identified clusters, exclusively shaded genes, and exclusive STs identified in Portugal could be applied in the identification and epidemiology of the species.<\/jats:p>\n            <\/jats:sec>","DOI":"10.7717\/peerj.14895","type":"journal-article","created":{"date-parts":[[2023,3,9]],"date-time":"2023-03-09T09:31:04Z","timestamp":1678354264000},"page":"e14895","source":"Crossref","is-referenced-by-count":10,"title":["Analysis of <i>Corynebacterium silvaticum<\/i> genomes from Portugal reveals a single cluster and a clade suggested to produce diphtheria toxin"],"prefix":"10.7717","volume":"11","author":[{"given":"Marcus Vinicius Canario","family":"Viana","sequence":"first","affiliation":[{"name":"Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Henrique","family":"Galdino","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, State University of Southwest of Bahia, Jequi\u00e9, Bahia, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo","family":"Profeta","sequence":"additional","affiliation":[{"name":"Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuela","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu\u00eds","family":"Tavares","sequence":"additional","affiliation":[{"name":"Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siomar","family":"de Castro Soares","sequence":"additional","affiliation":[{"name":"Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Tri\u00e2ngulo Mineiro, Uberaba, Minas Gerais, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paulo","family":"Carneiro","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, State University of Southwest of Bahia, Jequi\u00e9, Bahia, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice Rebecca","family":"Wattam","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute, University of Virginia, Charlottesville, VA, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasco","family":"Azevedo","sequence":"additional","affiliation":[{"name":"Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4443","published-online":{"date-parts":[[2023,3,9]]},"reference":[{"key":"10.7717\/peerj.14895\/ref-1","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST ring image generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"10.7717\/peerj.14895\/ref-2","article-title":"FASTQC a quality control tool for high throughput sequence data","author":"Andrews","year":"2015"},{"key":"10.7717\/peerj.14895\/ref-3","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic acids research"},{"key":"10.7717\/peerj.14895\/ref-4","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.resmic.2020.02.003","article-title":"Corynebacterium rouxii sp. nov. a novel member of the diphtheriae species complex","volume":"171","author":"Badell","year":"2020","journal-title":"Research in Microbiology"},{"key":"10.7717\/peerj.14895\/ref-5","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"Journal of Computational Biology"},{"key":"10.7717\/peerj.14895\/ref-6","doi-asserted-by":"publisher","first-page":"D36","DOI":"10.1093\/nar\/gks1195","article-title":"GenBank","volume":"41","author":"Benson","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"10.7717\/peerj.14895\/ref-7","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-007-7624-1_9","article-title":"Detection methods for laboratory diagnosis of diphtheria","volume-title":"Corynebacterium diphtheriae and related toxigenic species","author":"Berger","year":"2014"},{"key":"10.7717\/peerj.14895\/ref-8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/9781118960608","volume-title":"Corynebacterium","author":"Bernard","year":"2015"},{"key":"10.7717\/peerj.14895\/ref-9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/srep08365","article-title":"RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Scientific Reports"},{"key":"10.7717\/peerj.14895\/ref-10","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"10.7717\/peerj.14895\/ref-11","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"10.7717\/peerj.14895\/ref-12","doi-asserted-by":"publisher","first-page":"2672","DOI":"10.1093\/bioinformatics\/btn529","article-title":"Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database","volume":"24","author":"Carver","year":"2008","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj.14895\/ref-13","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","article-title":"Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data","volume":"28","author":"Carver","year":"2012","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj.14895\/ref-14","doi-asserted-by":"publisher","first-page":"W246","DOI":"10.1093\/NAR\/GKY425","article-title":"CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Research"},{"key":"10.7717\/peerj.14895\/ref-15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12866-019-1402-1","article-title":"NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission","volume":"19","author":"Dangel","year":"2019","journal-title":"BMC Microbiology"},{"issue":"6","key":"10.7717\/peerj.14895\/ref-16","doi-asserted-by":"publisher","first-page":"3614","DOI":"10.1099\/ijsem.0.004195","article-title":"Corynebacterium silvaticum sp. nov. a unique group of NTTB corynebacteria in wild boar and roe deer","volume":"70","author":"Dangel","year":"2020","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"10.7717\/peerj.14895\/ref-17","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1051\/vetres:2005056","article-title":"Corynebacterium pseudotuberculosis: microbiology, biochemical properties, pathogenesis and molecular studies of virulence","volume":"37","author":"Dorella","year":"2006","journal-title":"Veterinary Research"},{"key":"10.7717\/peerj.14895\/ref-18","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"10.7717\/peerj.14895\/ref-19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biology"},{"key":"10.7717\/peerj.14895\/ref-20","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/1751-0473-6-11","article-title":"CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes","volume":"6","author":"Galardini","year":"2011","journal-title":"Source Code for Biology and Medicine"},{"key":"10.7717\/peerj.14895\/ref-21","doi-asserted-by":"publisher","first-page":"34963","DOI":"10.1038\/srep34963","article-title":"GFinisher: a new strategy to refine and finish bacterial genome assemblies","volume":"6","author":"Guizelini","year":"2016","journal-title":"Scientific Reports"},{"key":"10.7717\/peerj.14895\/ref-22","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj.14895\/ref-23","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1101\/gr.072033.107","article-title":"De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer","volume":"18","author":"Hernandez","year":"2008","journal-title":"Genome Research"},{"key":"10.7717\/peerj.14895\/ref-24","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nature Communications"},{"key":"10.7717\/peerj.14895\/ref-25","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nature Methods"},{"key":"10.7717\/peerj.14895\/ref-26","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"Journal of Clinical Microbiology"},{"key":"10.7717\/peerj.14895\/ref-27","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1101\/gr.241455.118","article-title":"Fast and flexible bacterial genomic epidemiology with PopPUNK","volume":"29","author":"Lees","year":"2019","journal-title":"Genome Research"},{"key":"10.7717\/peerj.14895\/ref-28","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj.14895\/ref-29","doi-asserted-by":"publisher","first-page":"2182","DOI":"10.1038\/s41467-019-10210-3","article-title":"TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy","volume":"10","author":"Meier-Kolthoff","year":"2019","journal-title":"Nature Communications"},{"key":"10.7717\/peerj.14895\/ref-30","doi-asserted-by":"publisher","first-page":"3549","DOI":"10.3390\/ijms22073549","article-title":"Newly isolated animal pathogen Corynebacterium silvaticum is cytotoxic to human epithelial cells","volume":"22","author":"M\u00f6ller","year":"2021","journal-title":"International Journal of Molecular Sciences"},{"key":"10.7717\/peerj.14895\/ref-31","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1007\/s10482-020-01430-5","article-title":"Phylogenomic characterisation of a novel corynebacterial species pathogenic to animals","volume":"113","author":"M\u00f6ller","year":"2020","journal-title":"Antonie van Leeuwenhoek"},{"key":"10.7717\/peerj.14895\/ref-32","doi-asserted-by":"publisher","DOI":"10.3390\/proteomes8030019","article-title":"Cellular and extracellular proteome of the animal pathogen Corynebacterium silvaticum, a close relative of zoonotic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis","volume":"8","author":"M\u00f6ller","year":"2020","journal-title":"Proteomes"},{"key":"10.7717\/peerj.14895\/ref-33","doi-asserted-by":"publisher","first-page":"4713","DOI":"10.1128\/JCM.40.12.4713-4719.2002","article-title":"Development of a real-time fluorescence PCR assay for rapid detection of the diphtheria toxin gene","volume":"40","author":"Mothershed","year":"2002","journal-title":"Journal of Clinical Microbiology"},{"key":"10.7717\/peerj.14895\/ref-34","doi-asserted-by":"publisher","first-page":"294","DOI":"10.3390\/toxins3030294","article-title":"Mechanism of diphtheria toxin catalytic domain delivery to the eukaryotic cell cytosol and the cellular factors that directly participate in the process","volume":"3","author":"Murphy","year":"2011","journal-title":"Toxins"},{"key":"10.7717\/peerj.14895\/ref-35","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1093\/BIOINFORMATICS\/BTS091","article-title":"Unipro UGENE: a unified bioinformatics toolkit","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj.14895\/ref-36","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1186\/s12917-014-0218-3","article-title":"First report of Corynebacterium pseudotuberculosis from caseous lymphadenitis lesions in Black Alentejano pig (Sus scrofa domesticus)","volume":"10","author":"Oliveira","year":"2014","journal-title":"BMC Veterinary Research"},{"issue":"D1","key":"10.7717\/peerj.14895\/ref-37","doi-asserted-by":"publisher","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR","volume":"51","author":"Olson","year":"2022","journal-title":"Nucleic Acids Research"},{"key":"10.7717\/peerj.14895\/ref-38","doi-asserted-by":"publisher","first-page":"108399","DOI":"10.1016\/j.vetmic.2019.108399","article-title":"Reliable differentiation of a non-toxigenic tox gene-bearing Corynebacterium ulcerans variant frequently isolated from game animals using MALDI-TOF MS","volume":"237","author":"Rau","year":"2019","journal-title":"Veterinary Microbiology"},{"key":"10.7717\/peerj.14895\/ref-39","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1111\/mmi.13172","article-title":"A thiol-disulfide oxidoreductase of the Gram-positive pathogen Corynebacterium diphtheriae is essential for viability, pilus assembly, toxin production and virulence","volume":"98","author":"Reardon-Robinson","year":"2015","journal-title":"Molecular Microbiology"},{"key":"10.7717\/peerj.14895\/ref-40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/mra.00946-20","article-title":"Draft genome sequences of six Corynebacterium ulcerans strains isolated from humans and animals in Austria, 2013 to 2019","volume":"9","author":"Schaeffer","year":"2020","journal-title":"Microbiology Resource Announcements"},{"key":"10.7717\/peerj.14895\/ref-41","doi-asserted-by":"publisher","first-page":"2822","DOI":"10.1128\/JCM.01010-08","article-title":"Detection of toxigenic Corynebacterium diphtheriae and Corynebacterium ulcerans strains by a novel real-time PCR","volume":"46","author":"Schuhegger","year":"2008","journal-title":"Journal of Clinical Microbiology"},{"key":"10.7717\/peerj.14895\/ref-42","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Research"},{"key":"10.7717\/peerj.14895\/ref-43","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.jbiotec.2015.09.008","article-title":"GIPSy: genomic island prediction software","volume":"232","author":"Soares","year":"2016","journal-title":"Journal of Biotechnology"},{"key":"10.7717\/peerj.14895\/ref-44","doi-asserted-by":"publisher","first-page":"fnv185","DOI":"10.1093\/femsle\/fnv185","article-title":"Molecular armory or niche factors: virulence determinants of Corynebacterium species","volume":"67","author":"Tauch","year":"2015","journal-title":"FEMS Microbiology Letters"},{"key":"10.7717\/peerj.14895\/ref-45","doi-asserted-by":"publisher","first-page":"4671","DOI":"10.1128\/JB.187.13.4671-4682.2005","article-title":"Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora","volume":"187","author":"Tauch","year":"2005","journal-title":"Journal of Bacteriology"},{"key":"10.7717\/peerj.14895\/ref-46","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1186\/1471-2164-12-383","article-title":"Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors","volume":"12","author":"Trost","year":"2011","journal-title":"BMC Genomics"},{"key":"10.7717\/peerj.14895\/ref-47","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1186\/1471-2164-11-728","article-title":"The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence","volume":"11","author":"Trost","year":"2010","journal-title":"BMC Genomics"},{"key":"10.7717\/peerj.14895\/ref-48","doi-asserted-by":"publisher","first-page":"e0176347","DOI":"10.1371\/journal.pone.0176347","article-title":"Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo","volume":"12","author":"Viana","year":"2017","journal-title":"PLOS ONE"},{"key":"10.7717\/peerj.14895\/ref-49","doi-asserted-by":"publisher","first-page":"e0244210","DOI":"10.1371\/journal.pone.0244210","article-title":"Taxonomic classification of strain PO100\/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum","volume":"15","author":"Viana","year":"2020","journal-title":"PLOS ONE"},{"key":"10.7717\/peerj.14895\/ref-50","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2013a multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj.14895\/ref-51","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1099\/mic.0.000820","article-title":"Beyond diphtheria toxin: cytotoxic proteins of Corynebacterium ulcerans and Corynebacterium diphtheriae","volume":"165","author":"Weerasekera","year":"2019","journal-title":"Microbiology"},{"key":"10.7717\/peerj.14895\/ref-52","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLOS Computational Biology"},{"key":"10.7717\/peerj.14895\/ref-53","doi-asserted-by":"publisher","first-page":"3340","DOI":"10.1093\/bioinformatics\/btx433","article-title":"ISEScan: automated identification of insertion sequence elements in prokaryotic genomes","volume":"33","author":"Xie","year":"2017","journal-title":"Bioinformatics"}],"container-title":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/14895.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/14895.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/14895.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/14895.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,9]],"date-time":"2023-03-09T09:31:16Z","timestamp":1678354276000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/14895"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,9]]},"references-count":53,"alternative-id":["10.7717\/peerj.14895"],"URL":"https:\/\/doi.org\/10.7717\/peerj.14895","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2167-8359"],"issn-type":[{"value":"2167-8359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,9]]},"article-number":"e14895"}}