DOI: 10.5061/dryad.9ghx3ffn0
title: Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes

description: Mitochondrial genomes are known for their compact size and conserved gene
 order, however, recent studies employing long-read sequencing technologies
 have revealed the presence of atypical mitogenomes in some species. In
 this study, we assembled and annotated the mitogenomes of five Antarctic
 notothenioids, including four icefishes (Champsocephalus gunnari, C. esox,
 Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the
 cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are
 known to harbor some rearrangements in their mt genomes, however the
 extensive duplications in icefishes observed in our study have never been
 reported before. In the icefishes, we observed duplications of the protein
 coding gene ND6, two transfer RNAs, and the control region with different
 copy number variants present within the same individuals and with some ND6
 duplications appearing to follow the canonical
 Duplication-Degeneration-Complementation (DDC) model in C. esox and C.
 gunnari. In addition, using long-read sequencing and k-mer analysis, we
 were able to detect extensive heteroplasmy in C. aceratus and C. esox. We
 also observed a large inversion in the mitogenome of T. borchgrevinki,
 along with the presence of tandem repeats in its control region. This
 study is the first in using long-read sequencing to assemble and identify
 structural variants and heteroplasmy in notothenioid mitogenomes and
 signifies the importance of long-reads in resolving complex mitochondrial
 architectures. Identification of such wide-ranging structural variants in
 the mitogenomes of these fishes could provide insight into the genetic
 basis of the atypical icefish mitochondrial physiology and more generally
 may provide insights about their potential role in cold adaptation.
description: The tissue sampling for <em>C. gunnari, C. esox, and T.
 borchgrevinki </em>were collected and sequenced using PacBio Sequel
 II instruments. The raw read data for <em>C. gunnari</em>
 (SRR20140461, SRR20140462), <em>C. esox</em>
 (SRR20115482, SRR20115483), and <em>T. borchgrevinki</em> is
 available under BioProjects PRJNA857989 and PRJNA907802 respectively.
 For <em>C.</em> <em>aceratus
 and P. georgianus</em> the available PacBio rawread data was
 downloaded from PRJNA420419 and PRJEB19273 respectively. The reads
 aligning to mt reference genomes were extracted using minimap2 and after
 read correction from Canu 1.8, the reads were assembled using Flye
 assembler. The resulting genome assemblies were annotated using Mitos2
 and tRNAscan-SE 2.0 along with manual confirmation of
 annotations.
description: The mitochondrial genome assembly files are in FASTA format
 (.fasta). The annotation of the sequences is in GFF format (.gff). Both
 FASTA and GFF are text-based and can be opened in any text editor, both in
 the command line and/or graphical applications. See links for a
 description of the FASTA (http://www.ncbi.nlm.nih.gov/blast/fasta.shtml) and GFF (https://useast.ensembl.org/info/website/upload/gff.html) file format specifications.
description: # Data for "Novel mitochondrial genome rearrangements including
 duplications and extensive heteroplasmy could underlie temperature
 adaptations in Antarctic Notothenioid Fishes" Minhas BF, Beck EA,
 Cheng CC-H, Catchen, JM. (2022). **Novel mitochondrial genome
 rearrangements including duplications and extensive heteroplasmy in
 Antarctic Notothenioid Fishes** *bioRxiv* 2022.09.19.508608; doi:
 # Species ### Blackfin
 icefish Mitochondrial genome assembly and annotation for the
 white-blooded, Antarctic blackfin icefish (*Chaenocephalus aceratus*). Mt
 genome shows 3 tandemly duplicated *ND6* copies and evidence of
 heteroplasmy. ### Pike Icefish Mitochondrial genome assembly and
 annotation for the white-blooded, secondarily temperate pike icefish
 (*Champsocephalus aceratus*). Mt genome shows 4 tandemly duplicated *ND6*
 copies and evidence of heteroplasmy. ### Mackerel icefish Mitochondrial
 genome assembly and annotation for the white-blooded, Antarctic mackerel
 icefish (*Champsocephalus gunnari*). Mt genome shows 4 tandemly duplicated
 *ND6* copies (2 complete and 2 truncated copies). ### South Georgia
 icefish Mitochondrial genome assembly and annotation for the
 white-blooded, Antarctic South Georgia icefish icefish
 (*Pseudochaenichthys georgianus*). Mt genome shows 2 tandemly duplicated
 *ND6* copies. ### Bald rockcod Mitochondrial genome assembly and
 annotation for the red-blooded, Antarctic bald rockcod (*Trematomus
 borchgrevinki*). Mt genome shows an inversion spanning several genes. ##
 Files | File | Description | | -------------------------- |
 -------------------------------------------------------------------- | |
 `C_aceratus_mt.fasta` | Mitochondrial genome assembly for *C. aceratus* in
 FASTA format | | `C_aceratus_mt.gff` | Mitochondrial genome annotation for
 *C. aceratus* in GFF format | | `C_esox_mt.fasta` | Mitochondrial genome
 assembly for *C. esox* in FASTA format | | `C_esox_mt.gff` | Mitochondrial
 genome annotation for *C. esox* in GFF format | | `C_gunnari_mt.fasta` |
 Mitochondrial genome assembly for *C. gunnari* in FASTA format | |
 `C_gunnari_mt.gff` | Mitochondrial genome annotation for *C. gunnari* in
 GFF format | | `P_georgianus_mt.fasta` | Mitochondrial genome assembly for
 *P. georgianus* in FASTA format | | `P_georgianus_mt.gff` | Mitochondrial
 genome annotation for *P. georgianus* in GFF format | |
 `T_borchgrevinki_mt.fasta` | Mitochondrial genome assembly for *T.
 borchgrevinki* in FASTA format | | `T_borchgrevinki_mt.gff` |
 Mitochondrial genome annotation for *T. borchgrevinki* in GFF format | ##
 Author **Bushra Fazal Minhas**\ Informatics Program\ University of
 Illinois at Urbana-Champaign\