A first genome survey and genomic ssr marker analysis of trematomus loennbergii regan, 1913

Eunkyung Choi, Sun Hee Kim, Seung Jae Lee, Euna Jo, Jinmu Kim, Jeong Hoon Kim, Steven J. Parker, Young Min Chi, Hyun Park

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

Trematomus loennbergii Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.

Original languageEnglish
Article number3186
JournalAnimals
Volume11
Issue number11
DOIs
Publication statusPublished - 2021 Nov

Keywords

  • Illumina
  • Microsatellite
  • Repeat motif
  • SSR
  • Scaly rockcod
  • Trematomus loennbergii

ASJC Scopus subject areas

  • Animal Science and Zoology
  • veterinary(all)

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