Lily D. Peck

Drought stress is a strong selective pressure for all plant species. Plants respond to water shortage through various strategies that confer drought tolerance. These strategies may be plastic responses that occur with the onset of stress or may comprise continuously expressed (constitutive) traits regardless of water availability. Here, we used RNA-seq to characterize transcriptional responses to dehydration in seedlings of a drought-tolerant oak, Quercus douglasii, from a local population in the Sierra Nevada Foothills in California. In the greenhouse, we subjected 24 seedlings from 6 maternal families to dry-down or well-watered treatments and prepared RNA libraries from tissue collected before and after each treatment (48 libraries). Upregulated genes were related to known drought response functions, while downregulated genes were enriched for gene ontology terms related to growth and carbohydrate metabolism. We discovered high constitutive expression of many putatively drought-responsive genes that had been found to exhibit gene expression plasticity in a different oak species, which is drought-sensitive. This novel finding demonstrates the potential for constitutive expression of genes involved in drought stress to provide an additional mechanism of drought tolerance for some tree species, such as Q. douglasii.

Outbreaks of fungal diseases have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogen Fusarium xylarioides severely impacted coffee production across sub-Saharan Africa. To improve the disease management of such pathogens, it is crucial to understand their genetic structure and evolutionary potential. We compared the genomes of 13 historic strains spanning 6 decades and multiple disease outbreaks to investigate population structure and host specialisation. We found that F. xylarioides comprised at least 4 distinct lineages: 1 host-specific to Coffea arabica, 1 to C. canephora var. robusta, and 2 historic lineages isolated from various Coffea species. The presence/absence of large genomic regions across populations, the higher genetic similarities of these regions between species than expected based on genome-wide divergence and their locations in different loci in genomes across populations showed that horizontal transfers of effector genes from members of the F. oxysporum species complex contributed to host specificity. Multiple transfers into F. xylarioides populations matched different parts of the F. oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of coffee wilt disease.