Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

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 p...

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Vydáno v:	Genome Biology Ročník 22; číslo 1; s. 120
Hlavní autoři:	Formenti, Giulio, Rhie, Arang, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Kwak, Woori, Korlach, Jonas, Fungtammasan, Arkarachai, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., Jarvis, Erich D.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London BioMed Central 29.04.2021 Springer Nature B.V BMC
Témata:	Accuracy Animal Genetics and Genomics Animals Assembly automation Bioinformatics Biomedical and Life Sciences Computational Biology - methods Computational Biology - standards Cytochrome Duplications Evolution, Molecular Evolutionary Biology Gene Duplication Genes Genome, Mitochondrial Genomes Genomics Genomics - methods High-Throughput Nucleotide Sequencing Human Genetics Life Sciences Long reads Microbial Genetics and Genomics Mitochondria Mitochondrial DNA mitochondrial genome nanopores Phylogenetics Plant Genetics and Genomics Repetitive Sequences, Nucleic Acid Sequencing species Success Taxonomy Vertebrate Vertebrates Vertebrates - genetics Duplications Long reads Vertebrate Mitochondrial DNA Repeats Sequencing Assembly
ISSN:	1474-760X, 1474-7596, 1474-760X
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Shrnutí:	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.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-021-02336-9