The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki

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.

Methods
A female T. borchgrevinki 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 -80oC 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 T. borchgrevinki 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 (Danio rerio) genome.