Polymorphic microsatellite markers in the false kelpfish Sebastiscus marmoratus: isolation, characterization, and cross-species amplification

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.