Sequencing the genome of Fraxinus excelsior (European ash)

Fraxinus excelsior (European ash) is a common tree in Europe with about 80 million individuals in the UK, and is of great ecological and economic value as a key forest species. Ash is diploid, with 2C = 46 chromosomes. Ash trees in Europe are currently threatened by the fungal pathogen Hymenoscyphus pseudoalbidus, which causes ash dieback. It is estimated that around 99% of the ash trees in the UK are at risk of infection. Natural genetic variation within ash populations includes a small percentage of low susceptibility individuals, as has been confirmed by a field study in Denmark. The British Ash Tree Genome Project is providing a reference F. excelsior genome sequence, to make the identification of genetic variants conferring low susceptibility possible on a genome-wide scale.

We extracted DNA from a young ash tree produced by the self-pollination of a low heterozygosity tree from the Cotswolds in England. Its 1C genome size was measured with flow cytometry as 880Mb. The genome was sequenced de novo using a combination of Illumina HiSeq2000 and Roche 454 FLX+ technologies at Eurofins. Comparing the results of several de novo assemblers, we have selected the best assembly, consisting of 90k scaffolds and an N50 of almost 100kb. It is available for download on the project’s website, www.ashgenome.org, along with the raw sequencing data. We are also annotating the assembly with RNA-seq data from five different tissues.

Our work lays foundations for the study of genome-wide polymorphisms in European ash, and selection of genes for resistance to Hymenoscyphus pseudoalbidus. This reference genome may also assist scientists working on the emerald ash borer infestation of F. pennsylvanica and F. americana in North America.