title: Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon.
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/. 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.
authors.affiliation: Department of Biology, University of Padova, Padova, Via G, Colombo 3 I-35131, Italy. michele.vidotto@gmail.com
authors.forename: Michele
authors.initials: M
authors.lastname: Vidotto
authors.forename: Alessandro
authors.initials: A
authors.lastname: Grapputo
authors.forename: Elisa
authors.initials: E
authors.lastname: Boscari
authors.forename: Federica
authors.initials: F
authors.lastname: Barbisan
authors.forename: Alessandro
authors.initials: A
authors.lastname: Coppe
authors.forename: Gilberto
authors.initials: G
authors.lastname: Grandi
authors.forename: Abhishek
authors.initials: A
authors.lastname: Kumar
authors.forename: Leonardo
authors.initials: L
authors.lastname: Congiu
mesh_terms: D000818:Animals; D030562:Databases, Protein; D056727:Endangered Species; D019143:Evolution, Molecular; D005260:Female; D005399:Fishes / Q000235:genetics*; D020869:Gene Expression Profiling; D008297:Male; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D009711:Nucleotides / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D017421:Sequence Analysis; D019849:Sex Determination Processes / Q000235:genetics
chemical_list: D009711:Nucleotides; D022661:RNA, Untranslated