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

• Published in: Animals
• Main Authors: Kim, Jinmu, Lee, Seung-Jae, Jo, Euna, Choi, Eunkyung, Cho, Minjoo, Choi, Soyun, Kim, Jeong-Hoon, Park, Hyun
• Format: Text
• Language: English
• Published: MDPI 2022
• Subjects: Article; Antarctic; Southern Ocean; Antarc*; Icefish
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558526/; https://doi.org/10.3390/ani12192598

SIMPLE SUMMARY: Crocodile icefish inhabit the deep sea around the Southern Ocean and belong to the family Channichthyidae. The species lacks hemoglobin and has evolved an antifreeze protein, unlike other teleosts. In this study, the whole-genome survey and microsatellite motifs were analyzed, which provide relevant information on genetic diversity, population genetics, and the genomic study of crocodile icefish. 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.