Anaccariibase

The Adriatic Sturgeon (Acipense naccarii) transcriptome database

Sturgeons (order Acipenseriformes, infraclass Chondrostei) are a very ancient fish group, distributed in the Paleartic hemisphere with about 25 species most of which are considered critically endangered, with high evolutionary and economical interest, characterized by high genome size and different levels of ploidy (Fontana et al., 2001).

A. naccarii is a tetraploid species, endemic of the Adriatic Sea, with an estimated number of 240 chromosomes. The present database contains 55,282 transcribed sequences of A. naccarii, obtained from by sequencing 2 normalized libraries from 2 individuals: one male and one female with 454 FLX sequencing technology.

A total of 154,882 and 176,703 raw reads from the A. naccarii male and female respectively were cleaned and assembled with MIRA (Chevreux et al., 2004), giving 42,193 contigs (21.87 Mb) and 13,089 singletons (3.91 Mb). Final sequences were characterized by a mean length of 466 bp and mean coverage of 4.64 X.

GO annotation was achieved via Blast2GO (Conesa et al., 2005) starting from BLASTX results against NCBI non-redundant database. InterProScan annotation was also conducted via Blast2GO and obtained information for domains were merged in order to improve global annotations. The overall process finally results in 8,784 successful annotated contigs (16%).

The database is searchable by contig ID, keywords or BLAST against contig sequences; massive and customized data retrieval is allowed by the integrated query system.

For each contig, an entry reports the following data sections:

• - Contig information (ID, description and FASTA sequence)
• - Assembly (reads, contigs plus reads)
• - Gene Ontology (Molecular Function, Biological Process, Cellular Component)
• - Protein (NCBI nr database) BLAST results (Descriptions and Alignments)
• - Nucleotides (NCBI nt database) BLAST results (Descriptions and Alignments)

See example of contig.

Anaccariibase is an open project developed by the Molecular Ecology Group and the Computational Genomics Laboratory of the University of Padova. It is intended to be a public and expandable resource provided to the scientific community. New data contributions are welcome.

If you use data from this resource please cite:

Michele Vidotto, Alessandro Grapputo, Elisa Boscari, Federica Barbisan, Alessandro Coppe, Gilberto Grandi, Abhishek Kumar and Leonardo Congiu
Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon.
BMC Genomics volum, pag-pag   (year).

Contacts:

• Leonardo Congiu for A. naccarii genetics
  
• Michele Vidotto, Alessandro Coppe for bioinformatics
  

Downloads:

• anaccarii.fasta.zip: assembly (FASTA format)
• anaccarii_male_reads.fasta.zip: raw reads from the male library only (FASTA format)
• anaccarii_female_reads.fasta.zip: raw reads from the female library only (FASTA format)

References:

1. Fontana et al., Genetica 2001
2. Chevreux et al., Genome Res. 2004
3. Conesa et al., Bioinformatics 2005