Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies

Euna Jo,Hyun Park,Tae-Jin Oh,Jeong-Hoon Kim,So-Ra Han,Steven J Parker,Eunkyung Choi,Seung Jae Lee,Jinmu Kim

doi:10.3390/d13120668

Abstract

Trematomus species (suborder Notothenioidei; family Nototheniidae) are widely distributed in the southern oceans near Antarctica. There are 11 recognized species in the genus Trematomus, and notothenioids are known to have high chromosomal diversity (2n = 24–58) because of relatively recent and rapid adaptive radiation. Herein, we report the chromosomal-level genome assembly of T. loennbergii, the first characterized genome representative of the genus Trematomus. The final genome assembly of T. loennbergii was obtained using a Pacific Biosciences long-read sequencing platform and high-throughput chromosome conformation capture technology. Twenty-three chromosomal-level scaffolds were assembled to 940 Mb in total size, with a longest contig size of 48.5 Mb and contig N50 length of 24.7 Mb. The genome contained 42.03% repeat sequences, and a total of 24,525 protein-coding genes were annotated. We produced a high-quality genome assembly of T. loennbergii. Our results provide a first reference genome for the genus Trematomus and will serve as a basis for studying the molecular taxonomy and evolution of Antarctic fish.

Highlights

IntroductionPublisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations
Genus Trematomus belongs to the suborder Notothenioidei, the dominant fish fauna distributed in the Southern Ocean around Antarctica
Notothenioids are adapted to low temperatures to protect them from cold stress, and they have been found to contain antifreeze glycoproteins (AFGPs) and lack a heat-shock response (HSR) [1,2,3,4]

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Genus Trematomus belongs to the suborder Notothenioidei, the dominant fish fauna distributed in the Southern Ocean around Antarctica. Notothenioids are adapted to low temperatures to protect them from cold stress, and they have been found to contain antifreeze glycoproteins (AFGPs) and lack a heat-shock response (HSR) [1,2,3,4]. Some notothenioid species lost myoglobin and/or hemoglobin during adaptation to cold water [1,5,6]. There are 11 recognized species in the genus Trematomus [7], some species are deemed to be taxonomically problematic.

Methods

Results

Conclusion