Developing Genomic Resources for Green Ash through Deep Transcriptome Sequencing and Low-Coverage Whole Genome Sequencing

Green ash (Fraxinus pennsylvanica) is a native North American hardwood tree of ecological and economic importance. Native ash species are under threat from both climate change and the emerald ash borer (Agrilus planipennis Fairmaire, EAB), an invasive beetle species that has killed millions of trees since its unintentional introduction in the late 1990s. To develop genetic and genomic tools for addressing these challenges, we undertook deep transcriptome sequencing and low-coverage whole genome sequencing of green ash. To explore transcript-level responses of green ash to both biotic and abiotic stresses, 55 RNASeq libraries were sequenced, including a variety of different mature tree tissue types and seedlings exposed to stressors such as increased ozone, heat, cold, drought and mechanical wounding. Additionally, libraries from leaves of both EAB-infested and control trees were sequenced. The resulting 84 Gigabases of data have been assembled into a reference transcriptome, and gene networks active in stress response and defense have been identified. The low-coverage whole genome sequencing effort yielded 4X coverage of the genome, and genomic SSR markers have been developed. The recently released British ash draft genome (http://www.ashgenome.org/) provides a reference for mapping both transcriptomic and genomic sequences, yielding information on species diversity and genetic variation. All resources are provided publicly through the project website, http://hardwoodgenomics.org.