Date of Completion
Spring 5-30-2025
Thesis Advisor(s)
Jill Wegrzyn; Jelena Erceg
Honors Major
Molecular and Cell Biology
Disciplines
Bioinformatics | Biology | Ecology and Evolutionary Biology | Genetics and Genomics
Abstract
Juglans cinerea (butternut) is a critically threatened North American tree species experiencing severe declines due to the fungal pathogen Ophiognomonia clavigignentijuglandacearum. In contrast, its Asian relative, Juglans ailantifolia (Japanese walnut), shows natural resistance. To investigate the genomic and epigenetic factors underlying this difference, we constructed and analyzed high-quality, chromosome-level genome assemblies for both species from long-read sequencing data (J. ailantifolia: 527Mb; J. cinerea: 586Mb), focusing on transposable element (TE) content, DNA methylation patterns, and regulation of pathogen resistance genes (PRGs).
Repeat analysis revealed that J. cinerea has a slightly higher overall transposable element (TE) content, with LTR retrotransposons (particularly Gypsy and Copia elements) dominating both genomes. Notably, J. cinerea exhibits a recent expansion of Penelope-like elements (PLEs), which are highly methylated and enriched within pathogen resistance gene (PRG) regions. In contrast, J. ailantifolia maintains fewer TE insertions and lower methylation across PRGs, potentially supporting more flexible gene activation. While J. cinerea shows overall higher TE methylation, J. ailantifolia showed greater CHH methylation across the genome, a pattern that may reflect increased responsiveness to environmental cues. Together, these findings suggest species-specific differences in TE regulation and methylation landscapes that could be relevant to disease response.
Recommended Citation
Chagari, Keertana, "Comparative Methylation Analyses Across Juglans Species to Investigate Epigenetic Contributions to Fungal Resistance" (2025). Honors Scholar Theses. 1066.
https://digitalcommons.lib.uconn.edu/srhonors_theses/1066
