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Title: Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes

Author
item GENET, CARINE - Institut National De La Recherche Agronomique (INRA)
item DEHAIS, PATRICE - Institut National De La Recherche Agronomique (INRA)
item Palti, Yniv
item GAVORY, FREDERICK - Genoscope
item WINCKER, PATRICK - Genoscope
item QUILLET, EDWIGE - Institut National De La Recherche Agronomique (INRA)
item BOUSSAHA, MEKKI - Institut National De La Recherche Agronomique (INRA)
item Gao, Guangtu

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/14/2011
Publication Date: 6/14/2011
Citation: Genet, C., Dehais, P., Palti, Y., Gavory, F., Wincker, P., Quillet, E., Boussaha, M., Gao, G. 2011. Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes. Biomed Central (BMC) Genomics. 12:314.

Interpretive Summary: Rainbow trout is one of the most important aquaculture species in the United States and around the world, but little is known about its genetic makeup. ARS scientists in Leetown, WV and cooperators in France teamed up to produce detailed genetic maps for trout that will be used to identify genes affecting key traits such as disease resistance, stress response, and growth. As part of this international collaboration we produced an integrated physical and genetic map for rainbow trout. A physical map shows the specific locations of a species' genes on chromosomes whereas genetic maps reveal relationships in how genes are inherited. These types of maps are important for finding genes that underlie important traits. We report the generation and characterization of 176,485 high quality DNA sequences that are used in the integration of the genome maps. Variation in genes that are tightly linked to aquaculture production traits can be exploited for improving rainbow trout breeding programs and ultimately improve the efficiency of producing this important source of nutritious protein and healthy unsaturated oil to the consumer.

Technical Abstract: Background: Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production and used as a model species to gain knowledge of many aspects of fish biology. As a salmonid, the species experienced recent whole genome duplication, making it a model for studying the evolution of tetraploidization and re-diploidization in vertebrates. However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. In order to enrich the genomic tools already available in the species and provide further insight on sequence and complexity content of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their content. Results: A total of 176,485 high quality BES, were generated, representing approximately 3.5 % of the trout genome. BES analyses identified 6,261 SSRs, of which 3,257 had high quality flanking sequences for PCR primers design. The first rainbow trout repeat elements database (INRA RT rep1.0) was developed. It contains 735 putative repeat elements. Approximately 9.3% of the trout BES had significant BLASTX hits against zebrafish, medaka, and stickleback protein databases. Comparative genomics using paired BAC-ends revealed several regions of synteny across all the fish species analyzed in this study. Conclusion: The characterization of BES provided insights on the rainbow trout genome. The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. The numerous microsatellites will serve for integrating the linkage and physical maps, for fine QTL mapping and for positional cloning of genes of interest for aquaculture production. Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and for elucidating sequence content and complexity in the rainbow trout genome.