title: Transcriptomics of in vitro immune-stimulated hemocytes from the Manila clam Ruditapes philippinarum using high-throughput sequencing.
abstract: BACKGROUND
  The Manila clam (Ruditapes philippinarum) is a worldwide cultured bivalve species with important commercial value. Diseases affecting this species can result in large economic losses. Because knowledge of the molecular mechanisms of the immune response in bivalves, especially clams, is scarce and fragmentary, we sequenced RNA from immune-stimulated R. philippinarum hemocytes by 454-pyrosequencing to identify genes involved in their immune defense against infectious diseases.
  
  
  RESULTS
  High-throughput deep sequencing of R. philippinarum using 454 pyrosequencing technology yielded 974,976 high-quality reads with an average read length of 250 bp. The reads were assembled into 51,265 contigs and the 44.7% of the translated nucleotide sequences into protein were annotated successfully. The 35 most frequently found contigs included a large number of immune-related genes, and a more detailed analysis showed the presence of putative members of several immune pathways and processes like the apoptosis, the toll like signaling pathway and the complement cascade. We have found sequences from molecules never described in bivalves before, especially in the complement pathway where almost all the components are present.
  
  
  CONCLUSIONS
  This study represents the first transcriptome analysis using 454-pyrosequencing conducted on R. philippinarum focused on its immune system. Our results will provide a rich source of data to discover and identify new genes, which will serve as a basis for microarray construction and the study of gene expression as well as for the identification of genetic markers. The discovery of new immune sequences was very productive and resulted in a large variety of contigs that may play a role in the defense mechanisms of Ruditapes philippinarum.
authors.affiliation: Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas, Vigo, Spain.
authors.forename: Rebeca
authors.initials: R
authors.lastname: Moreira
authors.forename: Pablo
authors.initials: P
authors.lastname: Balseiro
authors.forename: Josep V
authors.initials: JV
authors.lastname: Planas
authors.forename: Berta
authors.initials: B
authors.lastname: Fuste
authors.forename: Sergi
authors.initials: S
authors.lastname: Beltran
authors.forename: Beatriz
authors.initials: B
authors.lastname: Novoa
authors.forename: Antonio
authors.initials: A
authors.lastname: Figueras
mesh_terms: D000818:Animals; D017209:Apoptosis / Q000235:genetics / Q000276:immunology; D049872:Bivalvia / Q000235:genetics* / Q000276:immunology*; D003167:Complement Activation / Q000235:genetics; D004269:DNA, Bacterial / Q000276:immunology; D020224:Expressed Sequence Tags; D006434:Hemocytes / Q000187:drug effects / Q000276:immunology*; D059014:High-Throughput Nucleotide Sequencing; D007107:Immune System / Q000378:metabolism; D007155:Immunologic Factors / Q000494:pharmacology; D008070:Lipopolysaccharides / Q000494:pharmacology; D058977:Molecular Sequence Annotation; D010457:Peptidoglycan / Q000276:immunology; D011070:Poly I-C / Q000494:pharmacology; D051192:Receptors, Pattern Recognition / Q000235:genetics / Q000276:immunology; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics / Q000276:immunology; D059467:Transcriptome / Q000276:immunology*; D014733:Vibrio / Q000235:genetics / Q000276:immunology
chemical_list: D004269:DNA, Bacterial; D007155:Immunologic Factors; D008070:Lipopolysaccharides; D010457:Peptidoglycan; D051192:Receptors, Pattern Recognition; D011070:Poly I-C