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

Title
Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants
Authors
Jo, JihoonOh, JooseongLee, Hyun-GwanHong, Hyun-HeeLee, Sung-GwonCheon, SeongminKern, Elizabeth M. A.Jin, SoyeongCho, Sung-JinPark, Joong-KiPark, Chungoo
Ewha Authors
박중기
SCOPUS Author ID
박중기scopus
Issue Date
2017
Journal Title
GIGASCIENCE
ISSN
2047-217XJCR Link
Citation
vol. 6, no. 1
Keywords
Sea cucumber genomeApostichopus japonicasColor variantsGenetic variationPopulation genomics
Publisher
OXFORD UNIV PRESS
Indexed
SCIE; SCOPUS WOS
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.
DOI
10.1093/gigascience/giw006
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일반대학원 > 에코과학부 > Journal papers
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