title: Transcriptomics Analysis of Crassostrea hongkongensis for the Discovery of Reproduction-Related Genes.
abstract: BACKGROUND
  The reproductive mechanisms of mollusk species have been interesting targets in biological research because of the diverse reproductive strategies observed in this phylum. These species have also been studied for the development of fishery technologies in molluscan aquaculture. Although the molecular mechanisms underlying the reproductive process have been well studied in animal models, the relevant information from mollusks remains limited, particularly in species of great commercial interest. Crassostrea hongkongensis is the dominant oyster species that is distributed along the coast of the South China Sea and little genomic information on this species is available. Currently, high-throughput sequencing techniques have been widely used for investigating the basis of physiological processes and facilitating the establishment of adequate genetic selection programs.
  
  
  RESULTS
  The C.hongkongensis transcriptome included a total of 1,595,855 reads, which were generated by 454 sequencing and were assembled into 41,472 contigs using de novo methods. Contigs were clustered into 33,920 isotigs and further grouped into 22,829 isogroups. Approximately 77.6% of the isogroups were successfully annotated by the Nr database. More than 1,910 genes were identified as being related to reproduction. Some key genes involved in germline development, sex determination and differentiation were identified for the first time in C.hongkongensis (nanos, piwi, ATRX, FoxL2, β-catenin, etc.). Gene expression analysis indicated that vasa, nanos, piwi, ATRX, FoxL2, β-catenin and SRD5A1 were highly or specifically expressed in C.hongkongensis gonads. Additionally, 94,056 single nucleotide polymorphisms (SNPs) and 1,699 simple sequence repeats (SSRs) were compiled.
  
  
  CONCLUSIONS
  Our study significantly increased C.hongkongensis genomic information based on transcriptomics analysis. The group of reproduction-related genes identified in the present study constitutes a new tool for research on bivalve reproduction processes. The large group of molecular markers discovered in this study will be useful for population screening and marker assisted selection programs in C.hongkongensis aquaculture.
authors.affiliation: Key Laboratory of Marine Bio-resource Sustainable Utilization, Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Tong
authors.affiliation: Key Laboratory of Marine Bio-resource Sustainable Utilization, Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Marine Bio-resource Sustainable Utilization, Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.
authors.forename: Jiaomei
authors.initials: J
authors.lastname: Huang
authors.affiliation: Key Laboratory of Marine Bio-resource Sustainable Utilization, Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.
authors.forename: Shu
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Marine Bio-resource Sustainable Utilization, Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.
authors.forename: Yuehuan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Marine Bio-resource Sustainable Utilization, Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: Qingyuan Polytechnic, Qingyuan, China.
authors.forename: Jinhui
authors.initials: J
authors.lastname: Chen
authors.affiliation: Key Laboratory of Marine Bio-resource Sustainable Utilization, Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.
authors.forename: Ziniu
authors.initials: Z
authors.lastname: Yu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017756:Aquaculture; D002681:China; D020451:Contig Mapping; D049896:Crassostrea / Q000235:genetics* / Q000502:physiology; D018076:DNA, Complementary / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D017403:In Situ Hybridization; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009865:Oocytes / Q000166:cytology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012098:Reproduction / Q000235:genetics* / Q000502:physiology; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary