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

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.

Genome characterization and comparative analysis among three swimming crab species

“…In this study, high heterozygosity was detected in all three crab species (>1.2%). The genome heterozygosity is generally high (ranging from 1% to 4%) for most crabs and bivalves according to the existing records (Cai et al, 2019;Bachvaroff et al, 2021;Penaloza et al, 2021;Tang et al, 2021), compared to fish genome with usually lower than 0.5% (Chen et al, 2020;Xu et al, 2020;Choi et al, 2021).…”

Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis)

“…Regarding the tetranucleoti nucleotide motifs, the most frequent motifs were ACAG/CTGT AGAGG/CCTCT (32.37%), respectively (Table 4). To compare the microsat Patagonian moray cod with other species, the microsatellite motif analysis matomus loennbergii and Pogonophryne albipinna were used [22,23]. When Len, estimated total genome length; Uniq, unique portion of the genome (not repetitive); Het, heterozygosity rate; Kcov, mean K-mer coverage for the heterozygous bases; Err, error rate; Dup, duplication rate.…”

“…Regarding the tetranucleotide and pentanucleotide motifs, the most frequent motifs were ACAG/CTGT (27.78%) and AGAGG/CCTCT (32.37%), respectively (Table 4). To compare the microsatellite motifs of Patagonian moray cod with other species, the microsatellite motif analysis results of Trematomus loennbergii and Pogonophryne albipinna were used [22,23]. When comparing the number of microsatellites, Patagonian moray cod had the most SSRs, and there was no significant difference in the number of SSRs between T. loennbergii and P. albipinna.…”

A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment

“…Genome survey sequencing (GSS) using next-generation sequencing is currently an important and cost-effective approach to evaluate genome information such as genome size, GC content, heterozygosity and repeat content, as well as developing molecular markers (Li et al ., 2019; Baeza, 2020, 2021; Baeza et al , 2022; Choi et al ., 2021). In the present study, we aimed to estimate the genomic characteristics of S. leurokolos through GSS, identify repetitive elements in the nuclear genome and assemble a complete mitochondrial genome.…”