A First Insight into a Draft Genome of Silver Sillago (Sillago sihama) via Genome Survey Sequencing

SIMPLE SUMMARY: Silver sillago (Sillago sihama Forsskål) is distributed alongshore from the Indian Ocean to the West Pacific. Owing to its delicate quality, rich seafood taste, and high nutritional value, S. sihama is an attractive seafood in China. However, the main supply of this fish is from wild capture. The lack of genetic and genomic data for S. sihama has led to limited improvement in its breeding programs. In this study, we conducted a genomic survey of S. sihama using next-generation sequencing technology to investigate its genomic profile. We obtained useful data, such as genome size, sequence repeat ratio, heterozygosity ratio, and the genome sequences, which might accelerate the breeding and culturing programs for S. sihama. ABSTRACT: Sillago sihama has high economic value and is one of the most attractive aquaculture species in China. Despite its economic importance, studies of its genome have barely been performed. In this study, we conducted a first genomic survey of S. sihama using next-generation sequencing (NGS). In total, 45.063 Gb of high-quality sequence data were obtained. For the 17-mer frequency distribution, the genome size was estimated to be 508.50 Mb. The sequence repeat ratio was calculated to be 21.25%, and the heterozygosity ratio was 0.92%. Reads were assembled into 1,009,363 contigs, with a N50 length of 1362 bp, and then into 814,219 scaffolds, with a N50 length of 2173 bp. The average Guanine and Cytosine (GC) content was 45.04%. Dinucleotide repeats (56.55%) were the dominant form of simple sequence repeats (SSR).