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Comparative transcriptome analysis of three color variants of the sea cucumber Apostichopus japonicus

Title
Comparative transcriptome analysis of three color variants of the sea cucumber Apostichopus japonicus
Authors
Jo, JihoonPark, JongsunLee, Hyun-GwanKern, Elizabeth M. A.Cheon, SeongminJin, SoyeongPark, Joong-KiCho, Sung-JinPark, Chungoo
Ewha Authors
박중기
SCOPUS Author ID
박중기scopus
Issue Date
2016
Journal Title
MARINE GENOMICS
ISSN
1874-7787JCR Link1876-7478JCR Link
Citation
vol. 28, pp. 21 - 24
Keywords
Sea cucumberApostichopus japonicasBody-color variationsTranscriptomeRNA-seq
Publisher
ELSEVIER SCIENCE BV
Indexed
SCIE; SCOPUS WOS scopus
Abstract
The sea cucumber Apostichopus japonicus Selenka 1867 represents an important resource in biomedical research, traditional medicine, and the seafood industry. Much of the commercial value of A. japonicus is determined by dorsal/ventral color variation (red, green, and black), yet the taxonomic relationships between these color variants are not clearly understood. We performed the first comparative analysis of de novo assembled transcriptome data from three color variants of A. japonicus. Using the Illumina platform, we sequenced nearly 177,596,774 clean reads representing a total of 18.2 Gbp of sea cucumber transcriptome. A comparison of over 0.3 million transcript scaffolds against the Uniprot/Swiss-Prot database yielded 8513, 8602, and 8588 positive matches for green, red, and black body color transcriptomes, respectively. Using the Panther gene classification system, we assessed an extensive and diverse set of expressed genes in three color variants and found that (1) among the three color variants of A. japonicus, genes associated with RNA binding protein, oxidoreductase, nucleic acid binding, transferase, and KRAB box transcription factor were most commonly expressed; and (2) the main protein functional classes are differently regulated in all three color variants (extracellular matrix protein and phosphatase for green color, transporter and potassium channel for red color, and G-protein modulator and enzyme modulator for black color). This work will assist in the discovery and annotation of novel genes that play significant morphological and physiological roles in color variants of A. japonicus, and these sequence data will provide a useful set of resources for the rapidly growing sea cucumber aquaculture industry. (C) 2016 Elsevier B.V. All rights reserved.
DOI
10.1016/j.margen.2016.03.009
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일반대학원 > 에코과학부 > Journal papers
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