title: Transcriptome analysis of vertebral bone in the flounder, Paralichthys olivaceus (Teleostei, Pleuronectiformes), using Illumina sequencing.
abstract: The processes underlying vertebral development in teleosts and tetrapods differ markedly in a variety of ways. At present, the molecular basis of teleost vertebral development and growth is poorly understood. Understanding vertebral development at the molecular level is important for aquaculture to prevent vertebral anomalies that can arise from a variety of factors, including excess vitamin A (all-trans retinol, VA) in the diet. To facilitate studies on teloest vertebral development, we performed transcriptome analysis of four month old flounder, Paralichthys olivaceus, vertebrae using next-generation sequencing. Expression profile obtained demonstrates that some members of the hh, bmp, fgf, wnt gene families, and their receptors, hox, pax, sox, dlx and tbx gene families and ntl, which are known to function in notochord and somite development in embryos, are expressed in the vertebrae. It was also showed that in addition to the retinoic acid receptor (Rar), the vertebrae express alcohol dehydrogenase 1 and retinal dehydrogenase 2 which convert VA to all-trans-retinoic acid (RA). The assembled contigs also included cytochrome p450 family members, which inactivate RA, as well as phosphatidylcholine-retinol O-acetyltransferase, which converts VA to all-trans-retinyl ester, a stock form of VA. These data suggest that in teleost vertebrae, expression of various signals and transcription factors which function in the notochord and somite development is maintained until adult stage, and RA metabolism and signaling are active to regulate transcription of RA-responsible genes, such as hedgehog and hox genes. This is the first transcriptome analysis of teleost fish vertebrae.
authors.affiliation: Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.
authors.forename: Harumi
authors.initials: H
authors.lastname: Ibaraki
authors.affiliation: Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Wu
authors.affiliation: National Research Institute of Aquaculture, Farming Biology Division, Fisheries Research Agency, Mie 516-0193, Japan.
authors.forename: Susumu
authors.initials: S
authors.lastname: Uji
authors.affiliation: Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.
authors.forename: Hayato
authors.initials: H
authors.lastname: Yokoi
authors.affiliation: Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.
authors.forename: Yoshifumi
authors.initials: Y
authors.lastname: Sakai
authors.affiliation: Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan. Electronic address: suzukitr@bios.tohoku.ac.jp.
authors.forename: Tohru
authors.initials: T
authors.lastname: Suzuki
mesh_terms: D000818:Animals; D029941:Fish Proteins / Q000235:genetics / Q000378:metabolism; D005432:Flounder / Q000235:genetics*; D005786:Gene Expression Regulation; D005810:Multigene Family; D021141:Nucleic Acid Amplification Techniques / Q000295:instrumentation / Q000379:methods / Q000662:veterinary*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013131:Spine / Q000378:metabolism*; D014157:Transcription Factors; D059467:Transcriptome
chemical_list: D029941:Fish Proteins; D012333:RNA, Messenger; D014157:Transcription Factors
keywords: De novo transcriptome; Flounder; Next generation sequencing; Signaling molecules; Transcription factors; Vertebrae