A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913

Abstract

Simple Summary: The scaly rockcod (Trematomus loennbergii) is distributed in the Antarctic Ocean and this area is isolated by the Antarctic Circumpolar Current. It is important region to study evolutionary diversity. Trematomus is the main genus, having 11 species, and their habit distribution is well known. However, their genetic and genomic information is not studied. In addition, some species have similar morphology. In this study, a genome survey of T. loennbergii and microsatellite motif analysis were conducted to obtain genomic profile. The fundamental data such as genome size, heterozygosity ratio, duplication ration and microsatellite motifs were obtained. These data will provide a foundation for further whole-genome sequencing and the development of new molecular markers of T. loennbergii.

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.