{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T14:25:53Z","timestamp":1770647153165,"version":"3.49.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,12,24]],"date-time":"2021-12-24T00:00:00Z","timestamp":1640304000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Strategic Priority Research Program of Chinese Academy of Sciences","award":["XDB31000000"],"award-info":[{"award-number":["XDB31000000"]}]},{"name":"Second Tibetan Plateau Scientific Expedition and Research Program","award":["2019QZKK0501"],"award-info":[{"award-number":["2019QZKK0501"]}]},{"name":"International Partnership Program of Chinese Academy of Sciences","award":["151751KYSB20190024"],"award-info":[{"award-number":["151751KYSB20190024"]}]},{"name":"Key Research Program of Frontier Sciences","award":["QYZDB-SSW-SMC058"],"award-info":[{"award-number":["QYZDB-SSW-SMC058"]}]},{"name":"Sichuan Science and Technology Program","award":["2021JDJQ0002"],"award-info":[{"award-number":["2021JDJQ0002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Advances in next-generation sequencing (NGS) technologies have led to an exponential increase in the number of whole genome sequences (WGS) in databases. This wealth of WGS data has greatly facilitated the recovery of full mitochondrial genomes (mitogenomes), which are vital for phylogenetic, evolutionary and ecological studies. Unfortunately, most existing software cannot easily assemble mitogenome reference sequences conveniently or efficiently. Therefore, we developed a seed-free de novo assembly tool, MEANGS, which applies the trie-search method to extend contigs from self-discovery seeds and assemble a mitogenome from animal WGS data. We then used data from 16 species with different qualities to compare the performance of MEANGS with three other available programs. MEANGS exhibited the best overall performance since it was the only one that completed all tests, and it assembled full or partial mitogenomes for all of the tested samples while the others failed. Furthermore, MEANGS selects superior assembly sequences and annotates protein-coding genes. Thus, MEANGS can be one of the most efficient software for generating high-quality mitogenomes so far, the further use of it will benefit the study on mitogenome based on whole genome NGS data. MEANGS is available at https:\/\/github.com\/YanCCscu\/meangs.<\/jats:p>","DOI":"10.1093\/bib\/bbab538","type":"journal-article","created":{"date-parts":[[2021,11,24]],"date-time":"2021-11-24T12:11:35Z","timestamp":1637755895000},"source":"Crossref","is-referenced-by-count":19,"title":["MEANGS: an efficient seed-free tool for <i>de novo<\/i> assembling animal mitochondrial genome using whole genome NGS data"],"prefix":"10.1093","volume":"23","author":[{"given":"Meng-Huan","family":"Song","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaochao","family":"Yan","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1799-194X","authenticated-orcid":false,"given":"Jia-Tang","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,12,24]]},"reference":[{"key":"2022012000333845600_ref1","first-page":"798","article-title":"Molecular markers, natural history and evolution","volume":"58","author":"Avise","year":"1995","journal-title":"J Wildl Manage"},{"key":"2022012000333845600_ref2","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1046\/j.1365-294x.1998.00391.x","article-title":"The history and purview of phylogeography: a personal reflection","volume":"7","author":"Avise","year":"1998","journal-title":"Mol Ecol"},{"key":"2022012000333845600_ref3","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1146\/annurev.es.18.110187.002421","article-title":"Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics","volume":"18","author":"Avise","year":"1987","journal-title":"Annu Rev Ecol Evol Syst"},{"key":"2022012000333845600_ref4","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.tig.2007.02.001","article-title":"DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics","volume":"23","author":"Hajibabaei","year":"2007","journal-title":"Trends Genet"},{"key":"2022012000333845600_ref5","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1093\/molbev\/msz051","article-title":"Mitochondrial genomics reveals shared Phylogeographic patterns and demographic history among three periodical cicada species groups","volume":"36","author":"Du","year":"2019","journal-title":"Mol Biol Evol"},{"key":"2022012000333845600_ref6","doi-asserted-by":"crossref","first-page":"e9255","DOI":"10.1371\/journal.pone.0009255","article-title":"A complete mitochondrial genome sequence from a Mesolithic wild aurochs (Bos primigenius)","volume":"5","author":"Edwards","year":"2010","journal-title":"PLoS One"},{"key":"2022012000333845600_ref7","doi-asserted-by":"crossref","first-page":"5053","DOI":"10.1073\/pnas.0914266107","article-title":"Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear","volume":"107","author":"Lindqvist","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022012000333845600_ref8","doi-asserted-by":"crossref","first-page":"e73","DOI":"10.1371\/journal.pbio.0040073","article-title":"Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius","volume":"4","author":"Rogaev","year":"2006","journal-title":"PLoS Biol"},{"key":"2022012000333845600_ref9","doi-asserted-by":"crossref","first-page":"e2201","DOI":"10.1371\/journal.pone.0002201","article-title":"Adaptive evolution and functional redesign of core metabolic proteins in snakes","volume":"3","author":"Castoe","year":"2008","journal-title":"PLoS One"},{"key":"2022012000333845600_ref10","doi-asserted-by":"crossref","first-page":"8986","DOI":"10.1073\/pnas.0900233106","article-title":"Evidence for an ancient adaptive episode of convergent molecular evolution","volume":"106","author":"Castoe","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022012000333845600_ref11","first-page":"e18","article-title":"NOVOPlasty: de novo assembly of organelle genomes from whole genome data","volume":"45","author":"Dierckxsens","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2022012000333845600_ref12","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1093\/genetics\/131.2.397","article-title":"A novel mitochondrial genome organization for the blue mussel, Mytilus edulis","volume":"131","author":"Hoffmann","year":"1992","journal-title":"Genetics"},{"key":"2022012000333845600_ref13","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1002\/jcp.1041360316","article-title":"Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells","volume":"136","author":"Robin","year":"1988","journal-title":"J Cell Physiol"},{"key":"2022012000333845600_ref14","doi-asserted-by":"crossref","first-page":"e129","DOI":"10.1093\/nar\/gkt371","article-title":"Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads \u2013 a baiting and iterative mapping approach","volume":"41","author":"Hahn","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2022012000333845600_ref15","article-title":"Assembly by reduced complexity (ARC): a hybrid approach for targeted assembly of homologous sequences","volume":"014662","author":"Hunter","year":"2015","journal-title":"Biorxiv"},{"key":"2022012000333845600_ref16","doi-asserted-by":"crossref","first-page":"e63","DOI":"10.1093\/nar\/gkz173","article-title":"MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization","volume":"47","author":"Meng","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022012000333845600_ref17","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1186\/s12859-017-1927-y","article-title":"Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data","volume":"18","author":"Al-Nakeeb","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2022012000333845600_ref18","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1093\/bioinformatics\/btr076","article-title":"Improving SNP discovery by base alignment quality","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2022012000333845600_ref19","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1093\/bioinformatics\/btl629","article-title":"Assembling millions of short DNA sequences using SSAKE","volume":"23","author":"Warren","year":"2007","journal-title":"Bioinformatics"},{"key":"2022012000333845600_ref20","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gks1195","article-title":"GenBank","volume":"41","author":"Benson","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2022012000333845600_ref21","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2022012000333845600_ref22","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"Oleary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2022012000333845600_ref23","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2022012000333845600_ref24","doi-asserted-by":"crossref","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":"2022012000333845600_ref25","doi-asserted-by":"crossref","first-page":"2487","DOI":"10.1093\/bioinformatics\/btt403","article-title":"Nhmmer: DNA homology search with profile HMMs","volume":"19","author":"Wheeler","year":"2013","journal-title":"Bioinformatics"},{"key":"2022012000333845600_ref26","first-page":"1870","article-title":"MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"7","author":"Sudhir","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2022012000333845600_ref27","doi-asserted-by":"crossref","first-page":"10543","DOI":"10.1093\/nar\/gkz833","article-title":"Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes","volume":"47","author":"Donath","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022012000333845600_ref28","first-page":"47","article-title":"The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?","volume":"15","author":"Smith","year":"2016","journal-title":"Brief Funct Genomics"},{"key":"2022012000333845600_ref29","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/S0968-0004(00)01773-4","article-title":"Organelle genome resources at NCBI","volume":"26","author":"Wolfsberg","year":"2001","journal-title":"Trends Biochem Sci"},{"key":"2022012000333845600_ref30","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1186\/1471-2164-15-691","article-title":"The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization","volume":"15","author":"Xia","year":"2014","journal-title":"BMC Genomics"},{"key":"2022012000333845600_ref31","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1653\/024.097.0407","article-title":"DNA barcoding and elucidation of cryptic diversity in Thrips (Thysanoptera)","volume":"97","author":"Rebijith","year":"2014","journal-title":"Fla Entomol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/1\/bbab538\/42231721\/bbab538.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/1\/bbab538\/42231721\/bbab538.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,20]],"date-time":"2022-01-20T00:51:39Z","timestamp":1642639899000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbab538\/6481918"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,24]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,1,17]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbab538","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1]]},"published":{"date-parts":[[2021,12,24]]},"article-number":"bbab538"}}