MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data

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dc.contributorCentro de Toxinas, Resposta-imune e Sinalização Celular (CeTICS)pt_BR
dc.contributorLECZ - Laboratório de Coleções Zoológicaspt_BR
dc.contributor.authorNachtigall, Pedro Gabrielpt_BR
dc.contributor.authorGrazziotin, Felipe Gobbipt_BR
dc.contributor.authorJunqueira-de-Azevedo, Inácio de Loiola Meirellespt_BR
dc.date.accessioned2021-02-02T17:40:17Z-
dc.date.available2021-02-02T17:40:17Z-
dc.date.issued2021pt_BR
dc.identifier.citationNachtigall PG, Grazziotin FG, Junqueira-de-Azevedo ILM. MIIGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data. Brief Bioinform. 2021 Jan;in press:1-15. doi:10.1093/bib/bbaa429.pt_BR
dc.identifier.urihttps://repositorio.butantan.gov.br/handle/butantan/3503-
dc.description.abstractMotivation: 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. Results: 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.pt_BR
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)pt_BR
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)pt_BR
dc.format.extent1-15pt_BR
dc.language.isoEnglishpt_BR
dc.relation.ispartofBriefings in Bioinformaticspt_BR
dc.rightsOpen Accesspt_BR
dc.titleMITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq datapt_BR
dc.typeArticlept_BR
dc.identifier.doi10.1093/bib/bbaa429pt_BR
dc.identifier.urlhttps://doi.org/10.1093/bib/bbaa429pt_BR
dc.relation.ispartofabbreviatedBrief Bioinformpt_BR
dc.identifier.citationabntin press, p. 1-15, jan, 2021pt_BR
dc.identifier.citationvancouver2021 Jan;in press:1-15pt_BR
dc.contributor.butantanNachtigall, Pedro Gabriel|:Aluno|:Centro de Toxinas, Resposta-imune e Sinalização Celular (CeTICS)|:PrimeiroAutor|:Autor de correspondênciapt_BR
dc.contributor.butantanGrazziotin, Felipe Gobbi|:Pesquisador:Docente Colaborador PPGTOX|:LECZ - Laboratório de Coleções Zoológicaspt_BR
dc.contributor.butantanJunqueira-de-Azevedo, Inácio de Loiola Meirelles|:PesquisadorDocente Permanente PPGTOX|:Centro de Toxinas, Resposta-imune e Sinalização Celular (CeTICS)pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2013/07467-1pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦2016/50127-5pt_BR
dc.sponsorship.butantanFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)¦¦018/26520-4pt_BR
dc.sponsorship.butantanConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)¦¦pt_BR
dc.identifier.bvsccBR78.1pt_BR
dc.identifier.bvsdbIBProdpt_BR
dc.description.dbindexedYespt_BR
item.openairetypeArticle-
item.fulltextCom Texto completo-
item.grantfulltextembargo_29990101-
item.languageiso639-1English-
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crisitem.author.orcid0000-0001-9896-9722-
crisitem.author.orcid0000-0003-4491-0180-
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