Genome Sequencing, Comparative Genomics and Population Analyses of Aspen Species

Populus tremula and P. tremuloides are keystone species used as model systems for forest tree research and provide an ideal system for exploring the genetic architecture of complex phenotypes and studies of local adaptation. Genomics analyses in these species currently rely on the P. trichocarpa reference genome, which is limiting due to poor sequence alignment rates. We therefore sequenced two aspen genomes in addition to re-sequencing 24 P. tremula and 22 P. tremuloides individuals. Additional aspen species (P. grandidentata and P. davidiana) have also been sequenced. A P. tremula intra-specific genetic map using a new F₁ population is being generated.

We produced NGS based de novo genome assemblies that were ab initio annotated, then supplemented using RNA-Seq transcript profiling, enabling identification of novel, aspen specific genes. Genome assembly was challenging as a result of extensive heterozygosity, however, the gene space is comprehensively represented. Strategies to improve the assembly were investigated, demonstrating the potential for genome assembly using SMRT sequencing data.

This resource enabled comparative analysis to P. trichocarpa and among aspen species. Whole genome alignment and population level genotype data identified regions in aspen that have rapidly diverged from the reference P. trichocarpa genome. Chloroplast and nuclear genome analyses reconstructed the population history and phylogenetic trees for these species. We are now performing genome wide association studies and extensive RNA-Seq projects investigating controls of wood and leaf development, and exploring sexual dimorphism of gene expression and secondary metabolite biosynthesis.

The resources have been integrated in PlantGenIE.org.