{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T04:45:37Z","timestamp":1777005937960,"version":"3.51.4"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,1,30]],"date-time":"2021-01-30T00:00:00Z","timestamp":1611964800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001807","name":"FAPESP","doi-asserted-by":"publisher","award":["2013\/07467-1"],"award-info":[{"award-number":["2013\/07467-1"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"FAPESP","doi-asserted-by":"publisher","award":["2016\/50127-5"],"award-info":[{"award-number":["2016\/50127-5"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"FAPESP","doi-asserted-by":"publisher","award":["2018\/26520-4"],"award-info":[{"award-number":["2018\/26520-4"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Over the past decade, the field of next-generation sequencing (NGS) has seen dramatic advances in methods and a decrease in costs. Consequently, a large expansion of data has been generated by NGS, most of which have originated from RNA-sequencing (RNA-seq) experiments. Because mitochondrial genes are expressed in most eukaryotic cells, mitochondrial mRNA sequences are usually co-sequenced within the target transcriptome, generating data that are commonly underused or discarded. Here, we present MITGARD, an automated pipeline that reliably recovers the mitochondrial genome from RNA-seq data from various sources. The pipeline identifies mitochondrial sequence reads based on a phylogenetically related reference, assembles them into contigs, and extracts a complete mtDNA for the target species.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We demonstrate that MITGARD can reconstruct the mitochondrial genomes of several species throughout the tree of life. We noticed that MITGARD can recover the mitogenomes in different sequencing schemes and even in a scenario of low-sequencing depth. Moreover, we showed that the use of references from congeneric species diverging up to 30 million years ago (MYA) from the target species is sufficient to recover the entire mitogenome, whereas the use of species diverging between 30 and 60 MYA allows the recovery of most mitochondrial genes. Additionally, we provide a case study with original data in which we estimate a phylogenetic tree of snakes from the genus Bothrops, further demonstrating that MITGARD is suitable for use on biodiversity projects. MITGARD is then a valuable tool to obtain high-quality information for studies focusing on the phylogenetic and evolutionary aspects of eukaryotes and provides data for easily identifying a sample using barcoding, and to check for cross-contamination using third-party tools.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bib\/bbaa429","type":"journal-article","created":{"date-parts":[[2020,12,23]],"date-time":"2020-12-23T15:22:30Z","timestamp":1608736950000},"source":"Crossref","is-referenced-by-count":30,"title":["MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data"],"prefix":"10.1093","volume":"22","author":[{"given":"Pedro G","family":"Nachtigall","sequence":"first","affiliation":[{"name":"Laborat\u00f3rio Especial de Toxinologia Aplicada , CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Felipe G","family":"Grazziotin","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Cole\u00e7\u00f5es Zool\u00f3gicas , Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"In\u00e1cio L M","family":"Junqueira-de-Azevedo","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Especial de Toxinologia Aplicada , CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,1,30]]},"reference":[{"key":"2026041420023256000_ref1","doi-asserted-by":"crossref","first-page":"342","DOI":"10.3389\/fevo.2019.00342","article-title":"The mitochondrial genome\u2013on selective constraints and signatures at the organism, cell, and single mitochondrion levels","volume":"7","author":"Shtolz","year":"2019","journal-title":"Front Ecol Evol"},{"key":"2026041420023256000_ref2","article-title":"Barbara K Mable, and Richard G Olmstead","volume-title":"Molecular systematics","author":"Hillis","year":"1996"},{"key":"2026041420023256000_ref3","author":"John","year":"2000"},{"issue":"4","key":"2026041420023256000_ref4","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1111\/j.1523-1739.2006.00372.x","article-title":"Utility of mitochondrial dna barcodes in species conservation","volume":"20","author":"Rubinoff","year":"2006","journal-title":"Conserv Biol"},{"issue":"1","key":"2026041420023256000_ref5","first-page":"1","article-title":"Mitochondrial phylogeography of baboons (papio spp.)\u2013indication for introgressive hybridization?","volume":"9","author":"Dietmar Zinner","year":"2009","journal-title":"BMC Evol Biol"},{"issue":"2","key":"2026041420023256000_ref6","first-page":"101","article-title":"Forensic mitochondria dna analysis: current practice and future potential","volume":"24","author":"Melton","year":"2012","journal-title":"Forensic science review"},{"issue":"5","key":"2026041420023256000_ref7","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1007\/s00227-015-2636-6","article-title":"Stephen a Karl, Rebekah L horn, Andrea M Bernard, James S Lea, Fabio H Hazin, Paulo a Prod\u00f6hl, and Mahmood S Shivji. Global mitochondrial dna phylogeography and population structure of the silky shark, carcharhinus falciformis","volume":"162","author":"Clarke","year":"2015","journal-title":"Mar Biol"},{"issue":"1","key":"2026041420023256000_ref8","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1186\/s12862-016-0735-8","article-title":"Alexander M Weigand, and Markus Pfenninger. Positive selection on panpulmonate mitogenomes provide new clues on adaptations to terrestrial life","volume":"16","author":"Romero","year":"2016","journal-title":"BMC Evol Biol"},{"issue":"5","key":"2026041420023256000_ref9","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1111\/jbi.13542","article-title":"Felipe G Grazziotin, Hussam Zaher, Alan R Lemmon, Emily Moriarty Lemmon, and Christopher L Parkinson. Reticulate evolution in nuclear middle america causes discordance in the phylogeny of palm-pitvipers (viperidae: Bothriechis)","volume":"46","author":"Mason","year":"2019","journal-title":"J Biogeogr"},{"issue":"5","key":"2026041420023256000_ref10","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1016\/j.molcel.2016.01.028","article-title":"The mitochondrial basis of aging","volume":"61","author":"Sun","year":"2016","journal-title":"Mol Cell"},{"key":"2026041420023256000_ref11","author":"Kelvin Yen","year":"2020"},{"key":"2026041420023256000_ref12","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.mito.2016.07.003","article-title":"The rise of mitochondria in medicine","volume":"30","author":"Picard","year":"2016","journal-title":"Mitochondrion"},{"issue":"1","key":"2026041420023256000_ref13","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.biotechadv.2009.11.002","article-title":"Littlewood, and Robin B gasser. 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Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new mitogenomes","volume":"9","year":"2019","journal-title":"Sci Rep"},{"issue":"1","key":"2026041420023256000_ref31","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.gene.2015.08.059","article-title":"Parente. The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of ancistrus spp.(loricariidae)","volume":"573","author":"Moreira","year":"2015","journal-title":"Gene"},{"issue":"4","key":"2026041420023256000_ref32","doi-asserted-by":"crossref","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":"Nat Methods"},{"issue":"8","key":"2026041420023256000_ref33","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber, et al. 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Contamination of clinical specimens with mlv-encoding nucleic acids: implications for xmrv and other candidate human retroviruses","volume":"7","author":"Robert","year":"2010","journal-title":"Retrovirology"},{"key":"2026041420023256000_ref60"},{"key":"2026041420023256000_ref61","first-page":"2","article-title":"Unexpected cross-species contamination in genome sequencing projects","volume":"e675","author":"Merchant","year":"2014","journal-title":"PeerJ"},{"issue":"6","key":"2026041420023256000_ref62","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1261\/rna.044263.114","article-title":"Mining of public sequencing databases supports a non-dietary origin for putative foreign mirnas: underestimated effects of contamination in ngs","volume":"20","author":"Tosar","year":"2014","journal-title":"RNA"},{"key":"2026041420023256000_ref63"},{"issue":"1","key":"2026041420023256000_ref64","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12915-018-0486-7","article-title":"A software tool \u2018croco\u2019detects pervasive cross-species contamination in next generation sequencing data","volume":"16","author":"Simion","year":"2018","journal-title":"BMC Biol"},{"key":"2026041420023256000_ref65"},{"key":"2026041420023256000_ref66"},{"key":"2026041420023256000_ref67"},{"issue":"7","key":"2026041420023256000_ref68","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/s41576-018-0022-1","article-title":"First-line genomic diagnosis of mitochondrial disorders","volume":"19","author":"Lucy Raymond","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2026041420023256000_ref69"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/22\/5\/bbaa429\/40260812\/bbaa429.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/22\/5\/bbaa429\/40260812\/bbaa429.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:03:08Z","timestamp":1776211388000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaa429\/6123950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,1,30]]},"references-count":69,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,9,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaa429","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,9]]},"published":{"date-parts":[[2021,1,30]]},"article-number":"bbaa429"}}