Genome survey of Siganus oramin: Identification and development of genome-wide microsatellite markers

Abstract

The rabbitfish Siganus oramin has high economic value and is farmed widely in net cages and offshore ponds in China. S. oramin is popular due to its rapid growth and good meat quality. A genome survey of S. oramin was carried out using next-generation sequencing. About 71.79 Gb of high-quality sequence data were generated. The genome size was estimated to be 447.63 Mb with 17-mer frequency distribution. These clean reads were assembled into 2046,655 contigs, which were assembled further into 1167,113 scaffolds with a total length of 643.46 Mb. The guanine-cytosine (GC) content, heterozygosity, and sequence repeat ratio were calculated to be 43.43 %, 0.968 %, and 28.01 %, respectively. A total of 1692,323 simple sequence repeats (SSRs) were identified from the draft genome sequence. Among these SSRs, the dinucleotide repeat type was the most abundant and frequent (74.42 %, 2636.52 Mb), followed by the trinucleotide (17.83 %, 631.65 Mb) and tetranucleotide (5.44 %, 192.72 Mb). The most abundant motif was AC/GT (1085,431 and 2424.84 loci/Mb), followed by AG/CT (147,808, 330.20 loci/Mb). Among 55 SSR markers, 48 showed a clear and reproducible band checked by gel electrophoresis. The cross-species transferability of 29 out of 48 tested loci were successful in Siganus guttatus. Nine polymorphic SSR primers were used to evaluate the genetic diversity of a wild population of S. oramin from Shenzhen (China). This is the first report of genome-wide characterization within this taxon. These data could provide a useful foundation for the whole-genome sequencing of S. oramin and development of new molecular markers for the genes of Siganus species.

Keywords

• Genome survey
• Next-generation sequencing
• Siganus oramin
• Microsatellite