The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids

Abstract

The mackerel icefish (Champsocephalus gunnari Lönnberg, 1905) is a ray‐finned fish living in the Southern Ocean around Antarctica. We sequenced the complete mitochondrial (mt) genome of the mackerel icefish and a segment from cytochrome b to the control region (CR) in 32 individuals. The mt genome of the mackerel icefish was rearranged, containing two nicotinamide adenine dinucleotide (reduced form) dehydrogenase subunit 6 (ND6), two tRNAGlu, and two CRs. However, variations in numbers of ND6 and tRNAGlu were observed amongst individuals. These variations included type 1 (containing two ND6 and two tRNAGlu), type 2 (containing one ND6, one incomplete ND6, and one tRNAGlu), and type 3 (containing one ND6 and one tRNAGlu). The gene orders of types 1 and 2, and variations in numbers of ND6 and tRNAGlu were not previously found in any Antarctic notothenioids, whereas type 3 is the same as that of Racovitzia glacialis. Phylogenetic analyses of CR DNA sequences showed that duplicated CRs of the same species formed a monophyletic group, suggesting that duplication of CRs occurred in each species. The frequent duplication of mt genomes in Antarctic notothenioids is an unusual feature in vertebrates. We propose that interspecific hybridization and impairment of mismatch repair might account for the high frequency of gene duplications and rearrangement of mt genomes in Antarctic notothenioids.

A Unique Mitochondrial Gene Block Inversion in Antarctic Trematomin Fishes: A Cautionary Tale

“…As a result there is, in many cases, complete mt genomic data available from only a single individual or at best a very small number of individuals for each species. In contrast, Lin et al (2012) sequenced large regions of the mt genomes of the mackerel icefish ( Champsocephalus gunnari ) from 32 individuals and interestingly found variation in the number of CRs and genes among individuals. Similar studies of the mt genomes from T. borchgrevinki and other trematomins would be important, in order to establish if this finding occurs in other species within the family.…”

Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

“…The mitogenomes of Bovichtus argentinus and Eleginops maclovinus exhibit the VertGO ( Satoh et al 2016 ; Lee-Estevez et al 2019 ) and also in Pseudaphritis urvillii , the sole species of the family Pseudaphritidae, the nad5 - trnF region is arranged as in VertGO (the only structural information available for this species, Zhuang and Cheng 2010 ). In the cryonotothenioid, five mitogenomic arrangements different from VertGO characterize all mitogenomes analyzed to date ( Zhuang and Cheng 2010 ; Lin et al 2012 ; Lee et al 2015a ; Lee et al 2015b ; Oh et al 2016 ; Song et al 2016 ). All rearrangements occur in the nad5 - trnF region ( fig.…”

“…3 ) ( Zhuang and Cheng 2010 ; Lee et al 2015a , 2015b ; Oh et al 2016 ; Song et al 2016 ). A fourth GO (hereafter named ChamGO) was retrieved only in the mitogenome of Champsocephalus gunnari (subfamily Channichthyinae, Lin et al 2012 ). The fifth GO (hereafter named DissoGO) is described in this study for the first time and resulted from the analysis of the mitogenomes of Dissostichus eleginoides and Dissostichus mawsoni (unpublished, but available in GenBank).…”

Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes

“…For all five notothenioids, raw reads were mapped against available mt reference genomes using minimap2 98 . C. gunnari and C. esox were both mapped against C. gunnari (NCBI accession NC_018340) 99 . The C. aceratus and P. georgianus raw reads were mapped to NCBI accessions NC_015654.1 100 and NC_057673.1 41 , respectively, T. borchgrevinki was mapped against NCBI accession KU951144.1 55 .…”