TY - JOUR
T1 - Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
AU - Formenti, Giulio
AU - Rhie, Arang
AU - Balacco, Jennifer
AU - Haase, Bettina
AU - Mountcastle, Jacquelyn
AU - Fedrigo, Olivier
AU - Brown, Samara
AU - Capodiferro, Marco Rosario
AU - Al-Ajli, Farooq O.
AU - Ambrosini, Roberto
AU - Houde, Peter
AU - Koren, Sergey
AU - Oliver, Karen
AU - Smith, Michelle
AU - Skelton, Jason
AU - Betteridge, Emma
AU - Dolucan, Jale
AU - Corton, Craig
AU - Bista, Iliana
AU - Torrance, James
AU - Tracey, Alan
AU - Wood, Jonathan
AU - Uliano-Silva, Marcela
AU - Howe, Kerstin
AU - McCarthy, Shane
AU - Winkler, Sylke
AU - Kwak, Woori
AU - Korlach, Jonas
AU - Fungtammasan, Arkarachai
AU - Fordham, Daniel
AU - Costa, Vania
AU - Mayes, Simon
AU - Chiara, Matteo
AU - Horner, David S.
AU - Myers, Eugene
AU - Durbin, Richard
AU - Achilli, Alessandro
AU - Braun, Edward L.
AU - Phillippy, Adam M.
AU - Jarvis, Erich D.
AU - Kirschel, Alexander N.G.
AU - Digby, Andrew
AU - Veale, Andrew
AU - Bronikowski, Anne
AU - Murphy, Bob
AU - Robertson, Bruce
AU - Baker, Clare
AU - Mazzoni, Camila
AU - Balakrishnan, Christopher
AU - Smith, Jeramiah
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - 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.
AB - 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.
KW - Assembly
KW - Duplications
KW - Long reads
KW - Mitochondrial DNA
KW - Repeats
KW - Sequencing
KW - Vertebrate
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U2 - 10.1186/s13059-021-02336-9
DO - 10.1186/s13059-021-02336-9
M3 - Article
C2 - 33910595
AN - SCOPUS:85105004099
SN - 1474-7596
VL - 22
JO - Genome Biology
JF - Genome Biology
IS - 1
M1 - 120
ER -