Comparative transcriptome analysis of three color variants of the sea cucumber Apostichopus japonicus.
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 18.2Gbp 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.
School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea.
Jihoon
J
Jo
InfoBoss, Co. Ltd., 201 room, 134, Gangseo-ro 17-gil, Hwageok-dong, Gangseo-go, Seoul 07766, Republic of Korea.
Jongsun
J
Park
School of Dentistry, Chonnam National University, Gwangju 500-757, Republic of Korea.
Hyun-Gwan
HG
Lee
Division of EcoScience, Ewha Womans University, Seoul 120-750, Republic of Korea.
Elizabeth M A
EMA
Kern
School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea.
Seongmin
S
Cheon
Division of EcoScience, Ewha Womans University, Seoul 120-750, Republic of Korea.
Soyeong
S
Jin
Division of EcoScience, Ewha Womans University, Seoul 120-750, Republic of Korea.
Joong-Ki
JK
Park
Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea.
Sung-Jin
SJ
Cho
School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea. Electronic address: chungoo@jnu.ac.kr.
Chungoo
C
Park
D000818:Animals; D017756:Aquaculture; D020869:Gene Expression Profiling; D010858:Pigmentation; D017422:Sequence Analysis, DNA; D047528:Stichopus / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
Apostichopus japonicas; Body-color variations; RNA-seq; Sea cucumber; Transcriptome