OakContigV1
BIOINFORMATIC ANALYSIS OF SANGER AND 454 ESTs IN OAK
[Data producers] BECKMAN COULTER GENOMICS and COGENICS GENOME EXPRESS, [CITATIONS]  Title: Bioinformatic analysis of Sanger and 454 ESTs in oak,  Authors: Ueno S., Le Provost G., Léger V., Klopp C., Noirot C., Frigerio J.M., Salin F., Salse J., Abrouk M., Murat F., Brendel O., Abadie P., Léger P., Cabane C., Barré A., de Daruvar A., Couloux A., Wincker P., Reviron M.P., Kremer A., Plomion C.,  Year: 2010,  Status: In preparation
The Fagaceae family comprises about 1000 woody species worldwide, spread throughout the northern hemisphere. About half belong to the Quercus family. These oaks are often a source of raw material for carpentry, furniture, cabinet making, veneer, cask industry and fuelwood. Pedonculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the combined bioinformatic analysis of 145827 Sanger ESTs and 1948579 454-reads. After unexploitable chromatograms and low quality sequences were eliminated, 1704117 EST sequences of Sanger and 454-read were assembled into 69154 tentative contigs and 153517 singletons, providing 222671 non-redundant sequences (including alternative transcripts). Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 16358 SSRs and 36411 putative SNPs. All of the results are available at the Oak Contig Browser (http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html) with user name (oak) and password (quercus33). This genomic resource provides a unique tool for discovering genes of interest, studying the oak transcriptome and developing new markers to investigate functional diversity in natural populations.