Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti

Jinmu Kim, Seung Jae Lee, Euna Jo, Eunkyung Choi, Minjoo Cho, Soyun Choi, Jeong Hoon Kim, Hyun Park

Research output: Contribution to journalArticlepeer-review

Abstract

The crocodile icefish, Chionobathyscus dewitti, belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers.

Original languageEnglish
Article number2598
JournalAnimals
Volume12
Issue number19
DOIs
Publication statusPublished - 2022 Oct

Bibliographical note

Publisher Copyright:
© 2022 by the authors.

Keywords

  • Chionobathyscus dewitti
  • crocodile icefish
  • GenomeScope
  • Illumina Novaseq 6000
  • Jellyfish
  • K-value
  • microsatellite

ASJC Scopus subject areas

  • Animal Science and Zoology
  • General Veterinary

Fingerprint

Dive into the research topics of 'Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti'. Together they form a unique fingerprint.

Cite this