title: Transcriptome sequencing of Zhikong scallop (Chlamys farreri) and comparative transcriptomic analysis with Yesso scallop (Patinopecten yessoensis).
abstract: BACKGROUND
  Bivalves play an important role in the ecosystems they inhabit and represent an important food source all over the world. So far limited genetic research has focused on this group of animals largely due to the lack of sufficient genetic or genomic resources. Here, we performed de novo transcriptome sequencing to produce the most comprehensive expressed sequence tag resource for Zhikong scallop (Chlamys farreri), and conducted the first transcriptome comparison for scallops.
  
  
  RESULTS
  In a single 454 sequencing run, 1,033,636 reads were produced and then assembled into 26,165 contigs. These contigs were then clustered into 24,437 isotigs and further grouped into 20,056 isogroups. About 47% of the isogroups showed significant matches to known proteins based on sequence similarity. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified through Gene ontology (GO) and KEGG pathway analyses. Transcriptome comparison with Yesso scallop (Patinopecten yessoensis) revealed similar patterns of GO representation. Moreover, 38 putative fast-evolving genes were identified through analyzing the orthologous gene pairs between the two scallop species. More than 46,000 single nucleotide polymorphisms (SNPs) and 350 simple sequence repeats (SSRs) were also detected.
  
  
  CONCLUSIONS
  Our study provides the most comprehensive transcriptomic resource currently available for C. farreri. Based on this resource, we performed the first large-scale transcriptome comparison between the two scallop species, C. farreri and P. yessoensis, and identified a number of putative fast-evolving genes, which may play an important role in scallop speciation and/or local adaptation. A large set of single nucleotide polymorphisms and simple sequence repeats were identified, which are ready for downstream marker development. This transcriptomic resource should lay an important foundation for future genetic or genomic studies on C. farreri.
authors.affiliation: Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Wang
authors.forename: Rui
authors.initials: R
authors.lastname: Hou
authors.forename: Zhenmin
authors.initials: Z
authors.lastname: Bao
authors.forename: Huixia
authors.initials: H
authors.lastname: Du
authors.forename: Yan
authors.initials: Y
authors.lastname: He
authors.forename: Hailin
authors.initials: H
authors.lastname: Su
authors.forename: Yueyue
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xiaoteng
authors.initials: X
authors.lastname: Fu
authors.forename: Wenqian
authors.initials: W
authors.lastname: Jiao
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Lingling
authors.initials: L
authors.lastname: Zhang
authors.forename: Shi
authors.initials: S
authors.lastname: Wang
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Hu
mesh_terms: D000818:Animals; D001483:Base Sequence; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D008297:Male; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D049897:Pectinidae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics*