GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.

Guillaume Riviere,Pierre Boudry,Pascal Favrel,Arnaud Huvet,Christophe Klopp,Nabihoudine Ibouniyamine

doi:10.1186/s12859-015-0833-4

Abstract

BackgroundThe Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database.DescriptionWe assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries.ConclusionsThe GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

Highlights

The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide
The Pacific Oyster, Crassostrea gigas, is a bivalve mollusk that belongs to lophotrochozoans, an under-described phylogenetic group among protostomes despite being the sister clade of ecdysozoans, which encompass insects and nematodes
Knowledge about the physiology of C. gigas is of fundamental, ecological and applied interests, leading to the generation of an important amount of transcriptomic data, as illustrated by the Gigasdatabase expressed-sequenced tags (EST) database [1]. These ESTs have enabled the development of microarrays used in physiological studies notably focusing on reproduction [2, 3], resistance to summer mortality [4,5,6], hypoxia [7], thermal stress [8] or ploïdy [9]

Summary

Conclusions

We assembled 114 RNA-seq libraries, mostly generated aside of the oyster genome project, into a publicly accessible database that includes userfriendly ‘search, browse and retrieve’ online tools, the GigaTON database. Competing interests The authors declare that they have no competing interests. Authors’ contributions GR conceived the study, participated in the database design and testing and wrote the manuscript. CK conceived the database, performed the bioinformatics analyses and contributed to the manuscript writing. IN set up the online resource tools and participated in the database design and testing. AH conceived the study, helped coordinating the work and participated in writing the manuscript. PB contributed to the design and coordination of the study and participated in writing the manuscript. PF coordinated the study and contributed to its design. All authors read and approved the final manuscript

Background

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