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Open Access Highly Accessed Research article

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

Michele Vidotto1*, Alessandro Grapputo1, Elisa Boscari1, Federica Barbisan1, Alessandro Coppe1, Gilberto Grandi2, Abhishek Kumar13 and Leonardo Congiu1

Author Affiliations

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

2 Department of Biology, University of Ferrara, Ferrara, Via L.Borsari 46, I-44100, Italy

3 Abteilung für Botanische Genetik und Molekularbiologie Botanisches, Institut und Botanischer Garten, Christian-Albrechts-Universität, Kiel, Germany

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BMC Genomics 2013, 14:407  doi:10.1186/1471-2164-14-407

Published: 18 June 2013

Abstract

Background

Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The intense fishing pressure on wild stocks to harvest caviar has caused in the last decades a dramatic decline of their distribution and abundance leading the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, the characterization of the genes involved in sex determination could provide relevant information for the selective farming of the more profitable females.

Results

The 454 sequencing of two cDNA libraries from the gonads and brain of one male and one female full-sib A. naccarii, yielded 182,066 and 167,776 reads respectively, which, after strict quality control, were iterative assembled into more than 55,000 high quality ESTs. The average per-base coverage reached by assembling the two libraries was 4X. The multi-step annotation process resulted in 16% successfully annotated sequences with GO terms. We screened the transcriptome for 32 sex-related genes and highlighted 7 genes that are potentially specifically expressed, 5 in male and 2 in females, at the first life stage at which sex is histologically identifiable. In addition we identified 21,791 putative EST-linked SNPs and 5,295 SSRs.

Conclusions

This study represents the first large massive release of sturgeon transcriptome information that we organized into the public database AnaccariiBase, which is freely available at http://compgen.bio.unipd.it/anaccariibase/ webcite. This transcriptomic data represents an important source of information for further studies on sturgeon species. The hundreds of putative EST-linked molecular makers discovered in this study will be invaluable for sturgeon reintroduction and breeding programs.