Genome evolution is a powerful force which shapes genomes over time through processes like mutation, horizontal transfer, and sexual reproduction. Although questions which aim to explore genome evolution are broad, they are all understood through the discovery and comparison of genetic variation. For example, genetic diversity may explain differences in phenotypes, etiology of disease, and is essential for phylogenomic analysis. Recently, the democratization of next generation and third generation DNA sequencing technologies have allowed for genomics to produce large amounts of sequence data. This has facilitated the capture of genetic variation at species and population scales.
Populus and Salix are members of the Salicaceae family and are ecologically and economically important woody plants. Currently, there are multiple high-quality reference genomes available for these two genera. Two important sources of genome evolution that will be explored here are genetic novelty in the form of new genes and horizontal gene transfer from the organelle genomes. In the context of genome evolution, both processes have been shown to contribute to beneficial phenotypes as well as disease. The primary contributions of this dissertation research are to identify and assign putative functions to orphan and de novo genes in P. trichocarpa, identify and compare horizontal transfer from the organelle genomes to the nuclear genomes of P. trichocarpa and P. deltoides, and generate new organelle genome resources for 6 different Salix species
