Transcriptome profiling of larvae of the marine medaka Oryzias melastigma by Illumina RNA-seq.
We sequenced the whole transcriptome of the 24h-old larval stage of the marine medaka Oryzias melastigma using Illumina RNA-seq. De novo assembly of 64,914,324 raw reads was performed using Trinity, resulting in 144,953 contigs. TransDecoder found 58,246 candidate coding contigs with homology to other species based on BLAST analysis. Functional gene annotation was performed by GO, KEGG pathway, and COG analyses. We determined an expressed gene catalog for O. melastigma for gene information-based environmental genomic and ecotoxicogenomic research. This information will serve as a resource for elucidating the molecular mechanisms underlying the response of O. melastigma to environmental stresses and chemicals.
Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
Bo-Mi
BM
Kim
National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea.
Beom-Soon
BS
Choi
Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
Hui-Soo
HS
Kim
Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 406-772, South Korea.
Jae-Sung
JS
Rhee
State Key Laboratory on Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.
Doris W T
DW
Au
School of Biological Sciences, University of Hong Kong, Hong Kong SAR, China.
Rudolf S S
RS
Wu
National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea. Electronic address: choii@snu.ac.kr.
Ik-Young
IY
Choi
Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea. Electronic address: jslee2@skku.edu.
Jae-Seong
JS
Lee
D000818:Animals; D029941:Fish Proteins / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation / Q000502:physiology; D007814:Larva / Q000378:metabolism; D021141:Nucleic Acid Amplification Techniques; D009990:Oryzias / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
D029941:Fish Proteins
Ecotoxicogenomics; Larvae; Marine medaka; Oryzias melastigma; RNA-seq; Transcriptome