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Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Formenti G 1 , Rhie A 2 , Balacco J 3 , Haase B 3 , Mountcastle J 3 , Fedrigo O 3 Show all authors , Brown S 4 , Capodiferro MR 5 , Al-Ajli FO 6 , Ambrosini R 7 , Houde P 8 , Koren S 2 , Oliver K 9 , Smith M 9 , Skelton J 9 , Betteridge E 9 , Dolucan J 9 , Corton C 9 , Bista I 9 , Torrance J 9 , Tracey A 9 , Wood J 9 , Uliano-Silva M 9 , Howe K 9 , McCarthy S 9 , Winkler S 10 , Kwak W 11 , Korlach J 12 , Fungtammasan A 13 , Fordham D 14 , Costa V 14 , Mayes S 14 , Chiara M 15 , Horner DS 15 , Myers E 10 , Durbin R 9 , Achilli A 5 , Braun EL 16 , Phillippy AM 2 , Jarvis ED 17 , Vertebrate Genomes Project Consortium

Affiliations 

  • 1 The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA. gformenti@rockefeller.edu
  • 2 Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
  • 3 The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA
  • 4 Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY, USA
  • 5 Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
  • 6 Monash University Malaysia Genomics Facility, School of Science, Bandar Sunway, Selangor Darul Ehsan, Malaysia
  • 7 Department of Environmental Science and Policy, University of Milan, Milan, Italy
  • 8 Department of Biology, New Mexico State University, Las Cruces, NM, USA
  • 9 Wellcome Sanger Institute, Cambridge, UK
  • 10 Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
  • 11 Hoonygen, Seoul, Korea
  • 12 Pacific Biosciences, Menlo Park, CA, USA
  • 13 DNAnexus Inc., Mountain View, CA, USA
  • 14 Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK
  • 15 Department of Biosciences, University of Milan, Milan, Italy
  • 16 Department of Biology, University of Florida, Gainesville, FL, USA
  • 17 The Vertebrate Genome Lab, Rockefeller University, New York, NY, USA. ejarvis@rockefeller.edu
Genome Biol, 2021 04 29;22(1):120.
PMID: 33910595 DOI: 10.1186/s13059-021-02336-9

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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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