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

Abstract

BackgroundOne 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.ResultsThe 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.ConclusionsThis 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.

Genomics of Fagaceae

“…This high-density linkage map will enable the reconstruction of chromosomes as long series of physical scaffolds. Finally, insights into the composition of the oak genome have also been achieved through the sequencing of BAC ends (Faivre-Rampant et al 2011) and clones from hypomethylated and genomic libraries ) and will be refined by the sequencing of a series of 20 BACs. Oak genomic resources have and will be made publicly accessible through the Quercus web portal: https:// w3.pierroton.inra.fr/QuercusPortal/index.php.…”

“…A second consortium was developed in France focusing on oak. BAC libraries were developed for Q. robur and BAC end sequences obtained (Faivre-Rampant et al 2011) to build long scaffolds in the framework of the oak genome sequencing project (funded by the French National Research Agency (ANR)). The large insert libraries produced by these two consortia are summarized in Table 3.…”

Interspecific gene flow and maintenance of species integrity in oaks

“…For this purpose, genome scans for outlier regions using for example Restriction Site Associated DNA (RAD) markers (Baird et al 2008) should be performed in different contact zones between species. In the near future, high resolution genetic linkage maps (Bodénès et al 2012) in Q. robur and Q. petraea anchored to scaffolds of the sequenced Q. robur genome (Faivre Rampant et al 2011, Neale & Kremer 2011 [https://w3.pierroton.inra.fr/Quercus Portal/] will allow to identify the location of outlier genes relative to species discriminating QTL. Reciprocal transplant experiments of seedlings between parental environments could be used to assess the impact of divergent selection on genes located in outlier and/or QTL regions.…”

Gall wasp community response to fragmentation of oak tree species: importance of fragment size and isolated trees

“…Oaks (Quercus species) are dominant late successional species in a wide range of habitats and offer key environmental services (i.e., carbon sequestration, energy production and water cycle regulation) (Faivre-Rampant et al 2011). Oaks support characteristic and species-rich assem-blages of associated organisms, particularly herbivorous insects (Tews et al 2004, TovarSánchez andOyama 2006a, b).…”