@article {136,
	title = {Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (<i>Quercus </i>spp.)},
	journal = {Molecular Ecology ResourcesMolecular Ecology Resources},
	volume = {11},
	number = {3},
	year = {2011},
	pages = {578-585},
	publisher = {Blackwell Publishing Ltd},
	abstract = {Abstract Multiplex PCR is a fast and cost-effective technique allowing increased genotyping throughput of microsatellites. We developed two multiplexes for Quercus petraea and Q.~robur, a 12-plex of EST-SSRs (eSSRs) and an 8-plex of genomic SSRs (gSSRs). We studied the origin of allele calling errors at the human reader and software levels. We showed that the robustness of allele identification can be improved by binning on raw peak sizes prior to genetic data analysis. We checked through simulation the power of these markers for species delimitation and hybrid detection. The resolution achieved with all 20 markers was greatly improved compared to that of previous studies based on a subset of the markers. Preliminary PCR tests suggest that these multiplexes might be useful to study other oak species as well. The strategy used for multiplex microsatellite development (from PCR conditions to the definition of allele calling rules) should be broadly applicable.},
	keywords = {manual binning, microsatellites, molecular identification, Quercus spp.},
	isbn = {1755-0998},
	author = {Guichoux, E. and Lagache, L. and Wagner, S. and Leger, P. and Petit, R. J.}
}
@article {130,
	title = {Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak},
	journal = {BMC GenomicsBMC Genomics},
	volume = {11},
	number = {650},
	year = {2010},
	note = {Using Smart Source ParsingNov 23},
	pages = {650},
	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.},
	keywords = {Base Sequence, Cluster Analysis, Computational Biology/ methods, Contig Mapping, Expressed Sequence Tags, Gene Library, Genes, Plant/genetics, Microsatellite Repeats/genetics, Peptides/genetics, Polymorphism, Single Nucleotide/genetics, Quercus/ genetics, RNA, Messenger/genetics/metabolism, Sequence Analysis, DNA/ methods, Sequence Homology, Nucleic Acid, Software, Species Specificity, Temperature, Trees/ genetics},
	isbn = {1471-2164 (Electronic)1471-2164 (Linking)},
	author = {Ueno, S. and Le Provost, G. and Leger, V. and Klopp, C. and Noirot, C. and Frigerio, J. M. and Salin, F. and Salse, J. and Abrouk, M. and Murat, F. and Brendel, O. and Derory, J. and Abadie, P. and Leger, P. and Cabane, C. and Barre, A. and de Daruvar, A. and Couloux, A. and Wincker, P. and Reviron, M. P. and Kremer, A. and Plomion, C.}
}
