Open Access Research article

Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring

Massimo Milan12*, Alessandro Coppe3, Richard Reinhardt4, Leonor M Cancela5, Ricardo B Leite5, Carlos Saavedra6, Claudio Ciofi2, Guido Chelazzi2, Tomaso Patarnello1, Stefania Bortoluzzi3 and Luca Bargelloni1

Author Affiliations

1 Department of Public Health, Comparative Pathology, and Veterinary Hygiene, Faculty of Veterinary Medicine, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy

2 Department of Evolutionary Biology, University of Florence, 50125 Florence, Italy

3 Biology Department, University of Padova, Via G. Colombo 3, I-35131 Padova, Italy

4 Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany

5 CCMAR/University of Algarve, Campus de Gambelas, Faro, Portugal

6 Instituto de Acuicultura de Torre la Sal (IATS), Consejo Superior de Investigaciones Cientificas (CSIC), 12595 Ribera de Cabanes, Castellon, Spain

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BMC Genomics 2011, 12:234  doi:10.1186/1471-2164-12-234

Published: 12 May 2011

Additional files

Additional file 1:

Summary of Blastx (E-value < 10-3) and Blastn (E-value < 10-5) similarity searches on several protein and nucleotide databases for R.philippinarum transcripts annotation.

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Additional file 2:

GO terms associated to R. philippinarum transcripts represented in the microarray using "Generic GO slim" in Blast2GO software. Details about "Biological process", "Molecular function" and "Cellular component" GO terms.

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Additional file 3:

Lists of annotated differentially expressed genes in digestive gland compared to gills. Score, Fold change, q-value and annotation on several protein and nucleotide database were also reported.

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Additional file 4:

List of significant probes identified by SAM analysis by comparison of digestive gland and gills of Manila clam sampled in Alberoni and Marghera. Significant probes in common between both tissue were also reported. Down-regulated genes in Marghera samples are highlighted in green while over expressed genes are highlighted in red. For each transcript, fold change, q-value, annotation and homologs zebrafish Ensembl Gene IDs (ENDARP and ENDARG) are reported.

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Additional file 5:

Sampling site in the Lagoon of Venice. Map of the Venice Lagoon showing Manila clam sampling sites.

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