Internet Archive Scholar

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne Da Silva, Jean-Charles Leplé, Florent Murat, Saneyoshi Ueno, Jerôme Bartholomé, Céline Lalanne, François Ehrenmann, Céline Noirot, Christian Burban (+15 others)
2015 BMC Genomics  

Preserved Fulltext

fulltext thumbnail
Web Archive Capture PDF (3.1 MB)
https://web.archive.org/web/20170817225255/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-015-1331-9?site=bmcgenomics.biomedcentral.com

A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL. The file type is application/pdf.

Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. Results: The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive
more » ... atalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. Conclusion: In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
doi:10.1186/s12864-015-1331-9 pmid:25765701 pmcid:PMC4350297 fatcat:xy4by7jpw5banjhierqsnslxjm
DOAJ
Citation

Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne Da Silva, Jean-Charles Leplé, Florent Murat, Saneyoshi Ueno, Jerôme Bartholomé, Céline Lalanne, François Ehrenmann, Céline Noirot, Christian Burban, Valérie Léger, Joelle Amselem, Caroline Belser, Hadi Quesneville, Michael Stierschneider, Silvia Fluch, Lasse Feldhahn, Mika Tarkka, Sylvie Herrmann, François Buscot, Christophe Klopp, Antoine Kremer, Jérôme Salse, Jean-Marc Aury, Christophe Plomion. "The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release." BMC Genomics 16.1 (2015) 112