Transcriptomic analysis of the polyploid Adriatic sturgeon (Acipenser naccarii)

Sturgeons are a group of Condrostean fishes with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent a luxury delicacy and are one of the most valuable foods of animal origin. The intense exploitation of wild stocks for the harvesting of caviar caused in the last decades a dramatic decline of their distribution and abundance leading, in 2010, 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, selective farming of females would increase the economical profits and the characterisation of genes involved in sex determination becomes a major issue. The 454 sequencing of four normalised cDNA libraries from gonads and brain of A naccarii and A. stellatus, one male and one female full-sib per species, yielded 182,066 and 167,776 reads for A. naccarii which after a strict quality control were iteratively assembled together, giving more then 55,000 high quality Expressed sequence tags (ESTs). A total of 184,374 and 169,286 raw reads were instead produced for A. stellaus male and female libraries respectively, resulting in 63,606 ESTs after two round assembly. It was estimated the joint assembly of A. naccarii was able to cover about 80% of its total transcripts expressed in both gonad and brain with a mean contigs coverage of 4X. Similarly 86% transcriptome coverage was achieved by assembling both sex specific libraries of A. stellatus, with 3.6X as mean contig coverage. The Multi-step annotation process finally results in 16% and 15% successfully annotated sequences, with GO terms, respectively in A. naccarii and A. stellatus. Both transcriptomes were screened for 32 sex related genes and highlighted 5 and 2 genes that are potentially specifically expressed in A. naccarii male and female, at the first life stage at which sex is histologically identifiable. The screening in A. stellatus is currently at preliminary stage and further filtering steps are required. Both sturgeon transcriptomes were also compared with those of other fish species for which relevant genomic informations were available. Finally, 21,791 putative EST-linked Single Nucleotide Polymorphisms (SNPs) and 5,295 Single Sequence Repeats (SSRs) were identified in A. naccarii, while 15,449 and 5,696 were putatively classified in A. stellatus assembly. This study represents the first characterisation of transcriptomes from two high endangered sturgeon species. Most of the information acquired for A. naccarii were well organised into the public database AnaccariiBase, freely available at http://compgen.bio. unipd.it/anaccariibase/, while the information obtained for A stellatus will be released soon. This study represents a precious source of information for more focussed studies aimed at characterising or comparing genes, deciphering molecular mechanisms or genetic pathways in this group of species, or discovering hundreds of EST-linked markers with several possible applications in sturgeon conservation.