Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Mostra el registre complet Registre parcial de l'ítem

• dc.contributor.author Formenti, Giulio
• dc.contributor.author Vertebrate Genomes Project Consortium
• dc.date.accessioned 2021-06-09T07:37:52Z
• dc.date.available 2021-06-09T07:37:52Z
• dc.date.issued 2021
• dc.description.abstract Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
• dc.format.mimetype application/pdf
• dc.identifier.citation Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O et al. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol. 2021;22(1):120. DOI: 10.1186/s13059-021-02336-9
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-021-02336-9
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/47812
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biol. 2021;22(1):120
• dc.rights © The Author(s). 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data ma
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Assembly
• dc.subject.keyword Duplications
• dc.subject.keyword Long reads
• dc.subject.keyword Mitochondrial DNA
• dc.subject.keyword Repeats
• dc.subject.keyword Sequencing
• dc.subject.keyword Vertebrate
• dc.title Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion