Developments in Hardwood Genomics: The Generation and Application of Molecular Resources for Species Preservation

The field of plant genomics aims to better understand plants, and the threats they face, through analysis of their genomes. Plant species, particularly woody tree species, offer special challenges when compared to other genomes. Recent advances in sequencing technologies, and continually decreasing sequencing costs, have allowed for mre plant genomes to be produced. This project utilized bioinformatics technologies to characterize the genomes of economically important tree species by generating new genomes. My projects have a particular focus on green ash (Fraxinus pennsylvanica). Once a prominent forest species with economic and ecological importance, green ash is now threatened by the invasive emerald ash borer (EAB). In my first project, I report on a chromosome-level assembly for green ash and describe its annotation. This genome is used to characterize a whole genome duplication event within the genome, and is also used as a template for chromosome-scale scaffolds for 27 other ash species. In the following project, I explore the mechanisms of sex determination in green ash using this genome. I used a genotyping-by-sequencing (GBS) approach to identify a region of interest that was more likely to be present in female ash than in male ash. My final project focuses on the muscadine grape (Vitis rotundifolia), where I report a long-read assembly for the muscadine cultivar ‘Carlos.’ I used this assembly to generate a pan-genome using existing Vitis species genomes - including two other muscadine cultivars - and to identify unique genetic responses to inoculation with the bacterial pathogen Xylella fastidiosa subsp. fastidiosa compared to those of common grapevine (Vitis vinifera). This project demonstrates the utility of bioinformatics approaches in providing genomic resources to economically important or threatened species.