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

Michele Vidotto,Gilberto Grandi,Abhishek Kumar,Federica Barbisan,Elisa Boscari,Alessandro Coppe,Alessandro Grapputo,Leonardo Congiu

doi:10.1186/1471-2164-14-407

Michele Vidotto, Gilberto Grandi + Show 6 more

Open Access

https://doi.org/10.1186/1471-2164-14-407

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Abstract

BackgroundSturgeons 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.ResultsThe 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.ConclusionsThis 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/. 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.

Highlights

Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest
The present study provides the first insight into the transcriptome of the Adriatic sturgeon, a critically endangered species endemic to the Adriatic Sea
Beside the evolutionary interest of a database obtained from a member of the Chondrostean, certainly applied genetics studies on sturgeons will benefit from this resource

Summary

Introduction

Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. Sturgeons (order: Acipenseriformes, infraclass: Chondrostei) are a very ancient fish group distributed in the Palearctic hemisphere with about 25 species, most of which are considered to be on the brink of extinction [1]. Their conservation importance has led to the inclusion of all the species in the red list of the International Union for the Conservation of Nature (IUCN) and to commercial restrictions under the Convention for International Trading of Endangered Species (CITES). A detailed transcriptome investigation of a polyploid sturgeon species will become crucial to assess the functional reduction of ploidy once the genome will be sequenced or once either the trancriptome of a 120 chromosomes species will be available. The redundant genetic material experiences a functional reduction which can be monitored by analysing the transcribed part of the genome [9]

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