DOI: 10.5061/dryad.h44j0zpv7
title: Data from: The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki

description: The Antarctic bald notothen, Trematomus borchgrevinki (Notothenioidae)
 occupies a high latitude, ice-laden environment and represents an extreme
 example of cold-specialization among fishes. We present the first, high
 quality, long-read genome of a female T. borchgrevinki genome comprised of
 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in
 length. The total length of the genome 935.13 Mbp, composed of 2,095
 scaffolds, with a scaffold N50 of 42.80 Mbp. Annotation yielded 22,567
 protein coding genes while 54.75% of the genome was occupied by repetitive
 elements; an analysis of repeats demonstrated that an expansion occurred
 in recent time. Conserved synteny analysis revealed that the genome
 architecture of T. borchgrevinki is largely maintained with other members
 of the notothenioid clade, although several significant translocations and
 inversions are present, including the fusion of orthologous chromosomes 8
 and 11 into a single element. This genome will serve as a cold-specialized
 model for comparisons to other members of the notothenioid adaptive
 radiation.
description: A female <em>T. borchgrevinki</em> individual was
 sampled from McMurdo Sound, Antarctica (77.5°S, 165°E). The fish was
 caught by hook and line through holes drilled through annual sea ice and
 transported back to the aquarium facility at McMurdo Station. The fish was
 anesthetized and tissues were dissected on ice, flash frozen in liquid
 nitrogen and stored in a -80<sup>o</sup>C freezer until use.
 High molecular weight (HMW) DNA was prepared from frozen muscle using the
 Nanobind HMW Tissue DNA Kit following vendor instructions. 
 PacBio continuous long read (CLR) library preparation and
 sequencing were carried out at the University of Oregon Genomics &
 Cell Characterization Core Facility. The HMW DNA was lightly sheared at
 ~75 Kbp target length for library construction using PacBio SMRTbell
 Express Template Prep Kit 2.0. The resulting library was selected for
 inserts approximately greater than 25 Kbp with the BluePippin (Sage
 Science) and sequenced on one SMRT cell 8M on Sequel II for 30 hours of
 data capture. A Hi-C library was constructed from liver
 DNA of the same <em>T. borchgrevinki</em> individual by Phase
 Genomics, Inc. using their Proximo Hi-C kit and then sequenced on an
 Illumina NovaSeq6000 machine to generate 2x150bp paired-end
 reads. Raw CLR long-reads were filtered with ycard and
 fpa and then assembled with the Flye assembler. The resulting assembled
 contigs were then scaffolded with Juicer and manually curated via
 conserved synteny analysis. Genes were annotated using the Braker3
 pipeline and functions were assigned using the Interproscan pipeline. Gene
 names were assigned based on orthology to the zebrafish (<em>Danio
 rerio</em>) genome.
description: # The genome of the cryopelagic Antarctic bald notothen, Trematomus
 borchgrevinki
 [https://doi.org/10.5061/dryad.h44j0zpv7](https://doi.org/10.5061/dryad.h44j0zpv7) This dataset contains the genome assembly and associated annotation for the Antarctic bald notothen, *Trematomus borchgrevinki*. It is associated with the following publication: Niraj Rayamajhi, Angel G. Rivera-Colón, Bushra Fazal Minhas, C.-H. Christina Cheng, Julian M. Catchen. (2024) The genome of the cryopelagic Antarctic bald notothen, *Trematomus borchgrevinki*. ## Description of the data and file structure | File | Description | | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | `tbor.fa.gz` | Genome assembly in FASTA format. File contains 2,094 sequences, including 23 chromosome-scale scaffolds. Total genome length of 935.13 Megabasepairs (Mbp) and a scaffold N50 of 42.8 Mbp. | | `tbor.agp.gz` | Assembly structure file in AGP format. | | `tbor.gtf.gz` | Genome annotation in GTF format. | | `tbor.afgp.gtf` | Manual genome annotation of AFGP genes in GTF format. | | `tbor.cds.fa.gz` | CDS for all annotated protein-coding genes in FASTA format. | | `tbor.protein.fa.gz` | Amino acid sequences for all annotated protein-coding genes in FASTA format. | ## Sharing/Access information A version of this data is also available on NCBI under BioProject `PRJNA907802`. Raw PacBio and Hi-C reads can be also found in the NCBI Sequence Read Archive under accessions `SRX18476836` and `SRX24931301`, respectively.