Supporting data for "Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants"

The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic disease have generated increasing conservation concern. Here we present a total of 312 gigabases (Gb) of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb which is about 80.5 % of the estimated genome size (0.82 Gb). We observed nucleotide-level heterozygosity within the assembled genome to be 0.986 %. The resulting draft genome assembly comprising 132,607 scaffolds with an N50 value of 10.5 kb contains a total of 21,771 predicted protein-coding genes. We identified 6.6 – 14.5 million heterozygous SNPs in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146.