title: Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX.
abstract: BACKGROUND
  Despite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus.
  
  
  RESULTS
  Copepodid larvae and adults were used as the basic material for transcriptome sequencing. Using 454 pyrosequencing, a total of 1,470,799 reads were obtained, which were assembled into 56,809 high quality expressed sequence tags. Based on their sequence similarity to known proteins, about 14,000 different genes were identified, including members of all major conserved signaling pathways. Transcripts that were putatively involved with growth, lipid metabolism, molting, and diapause were also identified among these genes. Differentially expressed genes related to several processes were found in C. sinicus copepodid larvae and adults. We detected 284,154 single nucleotide polymorphisms (SNPs) that provide a resource for gene function studies.
  
  
  CONCLUSIONS
  Our data provide the most comprehensive transcriptome resource available for C. sinicus. This resource allowed us to identify genes associated with primary physiological processes and SNPs in coding regions, which facilitated the quantitative analysis of differential gene expression. These data should provide foundation for future genetic and genomic studies of this and related species.
authors.affiliation: Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Ning
authors.forename: Minxiao
authors.initials: M
authors.lastname: Wang
authors.forename: Chaolun
authors.initials: C
authors.lastname: Li
authors.forename: Song
authors.initials: S
authors.lastname: Sun
mesh_terms: D000818:Animals; D001483:Base Sequence; D033342:Copepoda / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D007814:Larva / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D059467:Transcriptome