Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

Patricia Faivre Rampant1*, Isabelle Lesur2, Clément Boussardon1, Frédérique Bitton1, Marie-Laure Martin-Magniette1, Catherine Bodénès2, Grégoire Le Provost2, Hélène Bergès3, Sylvia Fluch4, Antoine Kremer2 and Christophe Plomion2

Author Affiliations

1 INRA, URGV, Plant Genomics Research, F-91057 Evry, France

2 INRA, UMR1202 BIOGECO, F-33610 Cestas, France

3 INRA, CNRGV, F-31326 Castanet, France

4 Austrian Institute of Technology, A-2444 Seibersdorf, Austria

For all author emails, please log on.

BMC Genomics 2011, 12:292  doi:10.1186/1471-2164-12-292

Published: 6 June 2011

Abstract

Background

One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences.

Results

The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera.

Conclusions

This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.