Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
Creators: name: Formenti, Giulio
name: Rhie, Arang
name: Balacco, Jennifer
name: Haase, Bettina
name: Mountcastle, Jacquelyn
name: Fedrigo, Olivier
name: Brown, Samara
name: Capodiferro, Marco Rosario
name: Al-Ajli, Farooq O.
name: Ambrosini, Roberto
name: Houde, Peter
name: Koren, Sergey
name: Oliver, Karen
name: Smith, Michelle
name: Skelton, Jason
name: Betteridge, Emma
name: Dolucan, Jale
name: Corton, Craig
name: Bista, Iliana
name: Torrance, James
name: Tracey, Alan
name: Wood, Jonathan
name: Uliano-Silva, Marcela
name: Howe, Kerstin
name: McCarthy, Shane
name: Winkler, Sylke
name: Kwak, Woori
name: Korlach, Jonas
name: Fungtammasan, Arkarachai
name: Fordham, Daniel
name: Costa, Vania
name: Mayes, Simon
name: Chiara, Matteo
name: Horner, David S.
name: Myers, Eugene
name: Durbin, Richard
name: Achilli, Alessandro
name: Braun, Edward L.
name: Phillippy, Adam M.
name: Jarvis, Erich D.
name: Kirschel, Alexander N. G.
name: Digby, Andrew
name: Veale, Andrew
name: Bronikowski, Anne
name: Murphy, Bob
name: Robertson, Bruce
name: Baker, Clare
name: Mazzoni, Camila
name: Balakrishnan, Christopher
name: Lee, Chul
name: Mead, Daniel
name: Teeling, Emma
name: Aiden, Erez Lieberman
name: Todd, Erica
name: Eichler, Evan
name: Naylor, Gavin J. P.
name: Zhang, Guojie
name: Smith, Jeramiah
name: Wolf, Jochen
name: Touchon, Justin
name: Delmore, Kira
name: Jakobsen, Kjetill
name: Komoroske, Lisa
name: Wilkinson, Mark
name: Genner, Martin
name: Pšenička, Martin
name: Fuxjager, Matthew
name: Stratton, Mike
name: Liedvogel, Miriam
name: Gemmell, Neil
name: Minias, Piotr
name: Dunn, Peter O.
name: Sudmant, Peter
name: Morin, Phil
name: Ayub, Qasim
name: Kraus, Robert
name: Vernes, Sonja
name: Smith, Steve
name: Lama, Tanya
name: Edwards, Taylor
name: Smith, Tim
name: Gilbert, Tom
name: Marques-Bonet, Tomas
name: Einfeldt, Tony
name: Venkatesh, Byrappa
name: Johnson, Warren
name: Warren, Wes
name: Bukhman, Yury
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Research
Mitochondrial DNA
Vertebrate
Assembly
Long reads
Sequencing
Duplications
Repeats

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 (&gt; 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.