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

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.

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.

The complete mitochondrial genome of Trematomus loennbergii (Perciformes, Nototheniidae)

The complete mitochondrial genome of Trematomus loennbergii was studied using NGS technology with PacBio platform. The mitochondrial genome size was 19,374bp and it had 13 protein-coding genes, 22 tRNAs and 2 rRNAs. There were 4 types of stop codons which were TAA, TAG, AGG and T(AA) but start codon type was only one (ATG). The contents of GC were 44.09% and AT contents were 55.91%. To conduct phylogenetic analysis, 12 species in 3 families were used. The result suggested that T. loennbergii was close to Pagothenia borchgrevinki in Nototheniidae. This study would provide a fundamental data for molecular evolution of T. loennbergii.

Persistent organic pollutants in red- and white-blooded High-Antarctic notothenioid fish from the remote Weddell Sea

It has been suggested that High-Antarctic waters, despite their remoteness from human activities, are impacted by anthropogenic pollution, and that the local biota are accumulating the contaminants. At present, no data exist on persistent organic pollutant (POP) body burdens for notothenioid fish inhabiting the High-Antarctic Weddell Sea. We determined the pollutant load in white muscle tissue of red- and white-blooded notothenoids from the Weddell Sea (Trematomus loennbergii and Chionodraco hamatus, respectively), and compared them to our previous measurements of POPs in Low-Antarctic notothenioids. Analytes included various organochlorine pesticides (OCPs), polychlorinated biphenyls (indicator (i) PCBs, dioxine-like (dl) PCBs) and polybrominated diphenyl ethers (PBDEs). The analytical concentrations were converted into 2,3,7,8-TCDD toxic equivalents (TEQs). Compared to T. loennbergii, C. hamatus had lower levels of β-HCH (0.45 vs. 4.5 ng g^-1 lipid weight), and Σ iPCBs (30 vs. 39 ng g^-1 lipid weight), as well as lower levels of Σ PBDEs (131 vs. 261 ng g^-1 fresh weight). POP body burdens and TEQs were mostly similar to those of Low-Antarctic notothenioids analysed previously, and not related to the trophic positions of the species. The variations in POP levels between and within High- and Low-Antarctic notothenioids only marginally corresponded to sampling site, ecological differences or trophic levels of the species, and might rather be related to metabolism or age effects. The present findings suggest that fishes of High-Antarctic waters, although this area is more remote and less influenced by local human activities, do not show lower POP body burdens than fishes from Low-Antarctic waters.