title: Transcriptome analysis of the Trachinotus ovatus: identification of reproduction, growth and immune-related genes and microsatellite markers.
abstract: BACKGROUND
  The Trachinotus ovatus (Teleostei, Carangidae) is an economically important marine fish species in the world. However, the lack of genomic information regarding this species limits our understanding of the genetics and biological mechanisms in Trachinotus ovatus. In this study, high throughput transcriptome sequencing was used to obtain comprehensive genomic information in Trachinotus ovatus.
  
  
  RESULTS
  Transcriptome sequencing was performed by using Illumina paired-end sequencing technology. The 98,534,862 high quality reads were yielded, and were de novo assembled into 156,094 unigenes with an average sequence length of 1179 bp. Transcriptome annotation revealed that 75,586 and 67,923 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 67,923 unigenes were grouped into 25 Cluster of Orthologous Groups (COG) functional categories, 37,976 unigenes were clustered into 61 Gene Ontology (GO) terms, and 38,172 unigenes were assigned to 275 different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Based on the transcriptome dataset, a large number of unigenes associated with reproduction, growth and immunity were identified. Furthermore, a total number of 38,794 simple sequence repeats (SSRs) were discovered and 16 polymorphic loci were characterized in Trachinotus ovatus.
  
  
  CONCLUSIONS
  The present study is the first transcriptome analysis of a fish species belonging to the genus Trachinotus and provides a valuable genomic resource for novel gene discovery, gene expression and regulation studies, and the identification of genetic markers in Trachinotus ovatus and the other fish of the genus Trachinotus.
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Xie
authors.initials: X
authors.lastname: Zhenzhen
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ling
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Wang
authors.initials: W
authors.lastname: Dengdong
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Chao
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Liu
authors.initials: L
authors.lastname: Qiongyu
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zihao
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Liu
authors.initials: L
authors.lastname: Xiaochun
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Zhang
authors.initials: Z
authors.lastname: Yong
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Li
authors.initials: L
authors.lastname: Shuisheng
authors.affiliation: State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China; College of Ocean, Hainan University, Haikou, Hainan, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Haoran
mesh_terms: D000818:Animals; D005399:Fishes / Q000235:genetics*; D020869:Gene Expression Profiling; D007107:Immune System; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D012098:Reproduction / Q000235:genetics*; D059467:Transcriptome