dc.contributor.author	Milan, Massimo
dc.contributor.author	Coppe, Alessandro
dc.contributor.author	Reinhardt, Richard
dc.contributor.author	Cancela, Leonor
dc.contributor.author	Leite, Ricardo
dc.contributor.author	Saavedra, Carlos
dc.contributor.author	Ciofi, Claudio
dc.contributor.author	Chelazzi, Guido
dc.contributor.author	Patarnello, T.
dc.contributor.author	Bortoluzzi, Stefania
dc.contributor.author	Bargelloni, Luca
dc.date.accessioned	2011-06-03T16:03:39Z
dc.date.available	2011-06-03T16:03:39Z
dc.date.issued	2011-05-12
dc.date.updated	2011-06-03T16:03:39Z
dc.description.abstract	Abstract Background 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. Results 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. Conclusions 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.
dc.description.version	Peer Reviewed
dc.identifier.citation	BMC Genomics. 2011 May 12;12(1):234
dc.identifier.doi	http://dx.doi.org/10.1186/1471-2164-12-234
dc.identifier.uri	http://hdl.handle.net/10400.1/210
dc.language.iso	eng
dc.rights.holder	Milan et al.; licensee BioMed Central Ltd.
dc.title	Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring
dc.type	journal article
dspace.entity.type	Publication
person.familyName	Cancela
person.familyName	Leite
person.givenName	M. Leonor
person.givenName	Ricardo
person.identifier	447622
person.identifier.ciencia-id	F115-256E-C84D
person.identifier.orcid	0000-0003-3114-6662
person.identifier.orcid	0000-0002-9622-3895
person.identifier.rid	B-3389-2008
person.identifier.scopus-author-id	8362650900
rcaap.rights	openAccess
rcaap.type	article
relation.isAuthorOfPublication	b9bbfe32-3dfe-4131-ad14-a4394008447f
relation.isAuthorOfPublication	3fb360e0-a481-486e-96ca-af9f6ecd6eb8
relation.isAuthorOfPublication.latestForDiscovery	3fb360e0-a481-486e-96ca-af9f6ecd6eb8

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

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