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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION AND CHARACTERIZATION OF GENES AFFECTING COOL AND COLD WATER AQUACULTURE PRODUCTION

Location: Cool and Cold Water Aquaculture Research

Title: Generation of BAC-end sequences for rainbow trout genome analysis

Authors
item Genet, Carine - INRA, FRANCE
item Dehais, Patrice - INRA, FRANCE
item Palti, Yniv
item Gavory, Frederick - GENOSCOPE, FRANCE
item Wincker, Patrick - GENOSCOPE, FRANCE

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2008
Publication Date: January 12, 2009
Citation: Genet, C., Dehais, P., Palti, Y., Gavory, F., Wincker, P. 2009. Generation of BAC-end sequences for rainbow trout genome analysis. Plant and Animal Genome Conference. P580.

Technical Abstract: For non-sequenced genomes, BAC end sequences (BES) provide a valuable sample of repetitive elements and gene content. Here we report the results of BAC end sequencing of just over half of the rainbow trout (Oncorhynchus mykiss) Swanson HindIII library. We sequenced 177,860 BAC ends that generated 176,485 high-quality BES (99.22 %) with an average length of 546 bp. A total of 92,298,179 bases (Phred Q value >20) were obtained, representing approximately 3.2 % of the rainbow trout genome. The nucleotide composition was 57.96 % A+T and 42.01% G+C. We used the sequence data to generate a trout specific repeat library using RepeatModeler (http://www.repeatmasker.org/RepeatModeler.html). The trout repeat library contains 735 elements. Using RepeatMasker, a total of 43.78% and 58.75% of the base-pairs were masked by the cGRASP repbase 1.0 (DeBoer et al. 2007, BMC Genomics, 8:422) and our new trout repbase, respectively. A sum of 6,261 BES were found to contain microsatellite sequences of which 2,605 (41.6%) had a minimum of 100 bp flanking sequences on both sides, which is sufficient for PCR primers definition. We are currently using these BAC anchored microsatellite markers to integrate the physical and genetic linkage maps. The masked BAC end Sequences were subjected to a BLASTX searches against NR database to evaluate gene content. The BES data obtained will be useful for future anchoring of the BAC physical map with the Atlantic salmon genome sequence and with trout genome sequencing projects.

Last Modified: 7/25/2014
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