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.
Publication details
Genome Biology, Volume 22, Article number: 120 (2021)
Published: 29 April 2021
DOI: 10.1186/s13059-021-02336-9
Publication webpage.