Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants

Abstract

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 diseases in A. japonicus have generated increasing conservation concern. However, the genomic knowledge base and resources available for researchers to use in managing this natural resource and to establish genetically based breeding systems for sea cucumber aquaculture are still in a nascent stage. A total of 312 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 single nucleotide polymorphisms in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146. We report the first draft genome of A. japonicus and provide a general overview of the genetic variation in the three major color variants of A. japonicus. These data will help provide a comprehensive view of the genetic, physiological, and evolutionary relationships among color variants in A. japonicus, and will be invaluable resources for sea cucumber genomic research.

Evaluation of two independent protocols for the extraction of DNA and RNA from different tissues of sea cucumber Isostichopus badionotus

“…The methodologies currently available will form the basis to boost molecular biology research in I. badionotus; permitting the analysis of genetic diversity, cloning and gene expression, identification of molecular markers, construction of genetic maps and genome sequencing. In other species of sea cucumbers, such as Apostichopus japonicus, the advances in genome sequencing [14] and transcriptome analyses are having a significant impact on the understanding of a diversity of biological mechanisms, such as regeneration, aestivation, and growth [10,15]. These studies will be fundamental to the development of genetic improvement programs in I. badionotus .…”

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

“…japonicus was published that represented only about 80.5% of the estimated genome size (0.82 Gb), with scaffolds N50 value of 10.5 Kb [14]. These data provided an important resource for sea cucumber genomics, but their incompleteness and fragmentation limit applications for research.…”

Molecular mechanisms of fission in echinoderms: Transcriptome analysis

“…According to the data of morphological and biochemical studies, connective tissue of echinoderms contains bundles of collagen fibrils, proteoglycans, and fibrillin microfibrils [ 24 – 28 ]. Recently, the genome of the holothurian Apostichopus japonicus has been sequenced [ 29 , 30 ]; however, no ECM genes in these species have been analyzed. ECM genes of the sea urchin Strongylocentrotus purpuratus are described more in detail.…”