Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

• Published in: Bioscience reports Vol. 40; no. 2
• Main Authors: Xu, Sheng-Yong, Song, Na, Xiao, Shi-Jun, Gao, Tian-Xiang
• Format: Journal Article
• Language: English
• Published: England Portland Press Ltd 28.02.2020
• Subjects: Animals; Fishes - genetics; Genetic Markers; Genomics; High-Throughput Nucleotide Sequencing; Male; Microsatellite Repeats; Whole Genome Sequencing; Zoology & Marine Biology; genome size; marbled rockfish; microsatellite marker; genome survey
• ISSN: 0144-8463; 1573-4935
• DOI: 10.1042/BSR20192252

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.