title: mRNA-Seq and microarray development for the Grooved Carpet shell clam, Ruditapes decussatus: a functional approach to unravel host-parasite interaction.
abstract: BACKGROUND
  The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis.
  
  
  RESULTS
  A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed.
  
  
  CONCLUSIONS
  This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.
authors.affiliation: CCMAR- Center of Marine Sciences/University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal. rleite@igc.gulbenkian.pt.
authors.forename: Ricardo B
authors.initials: RB
authors.lastname: Leite
authors.forename: Massimo
authors.initials: M
authors.lastname: Milan
authors.forename: Alessandro
authors.initials: A
authors.lastname: Coppe
authors.forename: Stefania
authors.initials: S
authors.lastname: Bortoluzzi
authors.forename: António
authors.initials: A
authors.lastname: dos Anjos
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Carlos
authors.initials: C
authors.lastname: Saavedra
authors.forename: Tomaso
authors.initials: T
authors.lastname: Patarnello
authors.forename: M Leonor
authors.initials: ML
authors.lastname: Cancela
authors.forename: Luca
authors.initials: L
authors.lastname: Bargelloni
mesh_terms: D056893:Alveolata / Q000502:physiology*; D000595:Amino Acid Sequence; D000818:Animals; D049872:Bivalvia / Q000235:genetics* / Q000469:parasitology; D020451:Contig Mapping; D020224:Expressed Sequence Tags; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006790:Host-Parasite Interactions; D037102:Lectins / Q000737:chemistry; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D037102:Lectins; D012333:RNA, Messenger