title: Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes.
abstract: BACKGROUND
  The marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies. However, the lack of genome and transcriptome reference has largely restricted the use of O. melastigma in the assessment of in vivo molecular responses to environmental stresses and the analysis of biological toxicity in the marine environment. Although O. melastigma is believed to be phylogenetically closely related to Oryzias latipes, the divergence between these two species is still largely unknown. Using Illumina high-throughput RNA sequencing followed by de novo assembly and comprehensive gene annotation, we provided transcriptomic resources for the brain, liver, ovary and testis of O. melastigma. We also investigated the possible extent of divergence between O. melastigma and O. latipes at the transcriptome level.
  
  
  RESULTS
  More than 14,000 transcripts across brain, liver, ovary and testis in marine medaka were annotated, of which 5880 transcripts were orthologous between O. melastigma and O. latipes. Tissue-enriched genes were identified in O. melastigma, and Gene Ontology analysis demonstrated the functional specificity of the annotated genes in respective tissue. Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of O. melastigma.
  
  
  CONCLUSIONS
  Orthologous transcripts between O. melastigma and O. latipes, tissue-enriched genes and O. melastigma-enriched transcripts were identified. Genome-wide expression studies of marine medaka require an assembled transcriptome, and this sequencing effort has generated a valuable resource of coding DNA for a non-model species. This transcriptome resource will aid future studies assessing in vivo molecular responses to environmental stresses and those analyzing biological toxicity in the marine environment.
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. balllai@hku.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. balllai@hku.hk.
authors.forename: Keng Po
authors.initials: KP
authors.lastname: Lai
authors.affiliation: School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, SAR, China. marcoli@cuhk.edu.hk.
authors.forename: Jing-Woei
authors.initials: JW
authors.lastname: Li
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. bioywang@hku.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. bioywang@hku.hk.
authors.forename: Simon Yuan
authors.initials: SY
authors.lastname: Wang
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China. jillchiu@hkbu.edu.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. jillchiu@hkbu.edu.hk.
authors.forename: Jill Man-Ying
authors.initials: JM
authors.lastname: Chiu
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. toannatse@yahoo.com.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. toannatse@yahoo.com.hk.
authors.forename: Anna
authors.initials: A
authors.lastname: Tse
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. karenytlau@hotmail.com.|The State Key Laboratory in Marine Pollution, Hong Kong, China. karenytlau@hotmail.com.
authors.forename: Karen
authors.initials: K
authors.lastname: Lau
authors.affiliation: Genome Research Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, 5 Sassoon Road, Pokfulam, Hong Kong, SAR, China. loks@mac.com.
authors.forename: Si
authors.initials: S
authors.lastname: Lok
authors.affiliation: Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, China. bhdwtau@cityu.edu.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. bhdwtau@cityu.edu.hk.
authors.forename: Doris Wai-Ting
authors.initials: DW
authors.lastname: Au
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China. kftse@hkbu.edu.hk.
authors.forename: William Ka-Fai
authors.initials: WK
authors.lastname: Tse
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China. ckcwong@hkbu.edu.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. ckcwong@hkbu.edu.hk.
authors.forename: Chris Kong-Chu
authors.initials: CK
authors.lastname: Wong
authors.affiliation: School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, SAR, China. tf.chan@cuhk.edu.hk.
authors.forename: Ting-Fung
authors.initials: TF
authors.lastname: Chan
authors.affiliation: Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, China. bhrkong@cityu.edu.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. bhrkong@cityu.edu.hk.
authors.forename: Richard Yuen-Chong
authors.initials: RY
authors.lastname: Kong
authors.affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. rudolfwu@hku.hk.|The State Key Laboratory in Marine Pollution, Hong Kong, China. rudolfwu@hku.hk.
authors.forename: Rudolf Shiu-Sun
authors.initials: RS
authors.lastname: Wu
mesh_terms: D000818:Animals; D059001:Aquatic Organisms / Q000235:genetics; D005618:Fresh Water; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D009928:Organ Specificity / Q000235:genetics; D009990:Oryzias / Q000235:genetics*