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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Bibliographic Details
Published in:Genome Biology Vol. 22; no. 1; p. 120
Main Authors: 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.
Format: Journal Article
Language:English
Published: London BioMed Central 29.04.2021
Springer Nature B.V
BMC
Subjects:
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
Online Access:Get full text
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Summary: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.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-021-02336-9