title: Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.
abstract: BACKGROUND
  The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate 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 development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity.
  
  
  RESULTS
  We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html.
  
  
  CONCLUSIONS
  This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.
authors.affiliation: INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France.
authors.forename: Saneyoshi
authors.initials: S
authors.lastname: Ueno
authors.forename: Grégoire
authors.initials: G
authors.lastname: Le Provost
authors.forename: Valérie
authors.initials: V
authors.lastname: Léger
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.forename: Céline
authors.initials: C
authors.lastname: Noirot
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Frigerio
authors.forename: Franck
authors.initials: F
authors.lastname: Salin
authors.forename: Jérôme
authors.initials: J
authors.lastname: Salse
authors.forename: Michael
authors.initials: M
authors.lastname: Abrouk
authors.forename: Florent
authors.initials: F
authors.lastname: Murat
authors.forename: Oliver
authors.initials: O
authors.lastname: Brendel
authors.forename: Jérémy
authors.initials: J
authors.lastname: Derory
authors.forename: Pierre
authors.initials: P
authors.lastname: Abadie
authors.forename: Patrick
authors.initials: P
authors.lastname: Léger
authors.forename: Cyril
authors.initials: C
authors.lastname: Cabane
authors.forename: Aurélien
authors.initials: A
authors.lastname: Barré
authors.forename: Antoine
authors.initials: A
authors.lastname: de Daruvar
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Marie-Pierre
authors.initials: MP
authors.lastname: Reviron
authors.forename: Antoine
authors.initials: A
authors.lastname: Kremer
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping; D020224:Expressed Sequence Tags; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D010455:Peptides / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D029963:Quercus / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013045:Species Specificity; D013696:Temperature; D014197:Trees / Q000235:genetics*
chemical_list: D010455:Peptides; D012333:RNA, Messenger