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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Citation and License

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

Published: 12 May 2011



The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on the development of a transcriptomic platform for global gene expression profiling in the Manila clam.


A normalized cDNA library representing a mixture of adult tissues was sequenced using a ultra high-throughput sequencing technology (Roche 454). A database consisting of 32,606 unique transcripts was constructed, 9,747 (30%) of which could be annotated by similarity. An oligo-DNA microarray platform was designed and applied to profile gene expression of digestive gland and gills. Functional annotation of differentially expressed genes between different tissues was performed by enrichment analysis. Expression of Natural Antisense Transcripts (NAT) analysis was also performed and bi-directional transcription appears a common phenomenon in the R. philippinarum transcriptome. A preliminary study on clam samples collected in a highly polluted area of the Venice Lagoon demonstrated the applicability of genomic tools to environmental monitoring.


The transcriptomic platform developed for the Manila clam confirmed the high level of reproducibility of current microarray technology. Next-generation sequencing provided a good representation of the clam transcriptome. Despite the known limitations in transcript annotation and sequence coverage for non model species, sufficient information was obtained to identify a large set of genes potentially involved in cellular response to environmental stress.