Projects

Epigenetics and the Evolution of Plant Genome Structure and Function

Transposable elements (TEs) represent the majority of angiosperm genomic DNA, and their presence is counteracted by a host response that includes DNA methylation and chromatin modifications.  Methylation affects not only the activity of transposable elements but also the function of nearby genes.  But some genes are also methylated.  We have been taking an evolutionary approach to study many aspects of methylation and other epigenetic features of plant genomes using evolutionary approaches. We seek to answer questions like – i.e., Why are genes methylated?  When did methylation evolve?  And to what extent do epigenetic modifications affects genome funtion?

Our current, NSF-funded work is in collaboration with Dr. JJ Emerson, who is also at UCI. This work is focused on characterizing secondary (2D) and tertiary (3D) structures in the maize Nested Association Mapping founders. Our ultimate goal is to infer the evolutionary processes that act on these structures, the epigenetic markers that affect them, and the functional implications of both structures and their markers. Here are three fairly recent papers that illustrate some of our ideas and approaches. Feel free to take a look!

Muyle, A. M., Seymour, D. K., Lv, Y., Huettel, B., & Gaut, B. S. (2022). Gene body methylation in plants: mechanisms, functions, and important implications for understanding evolutionary processes. Genome biology and evolution, 14(4), evac038.

Muyle, A., Ross-Ibarra, J., Seymour, D. K., & Gaut, B. S. (2021). Gene body methylation is under selection in Arabidopsis thaliana. Genetics, 218(2), iyab061.

Martin, G. T., Solares, E., Guadardo-Mendez, J., Muyle, A., Bousios, A., & Gaut, B. S. (2023). miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression. Genome Research, 33(11), 1932-1946.

Genetic Variation, landscapes and shifting climates

Genotypes and phenotypes vary across environments, often reflecting adaptation to local conditions. However, adaption is only one of many evolutionary processes that shape the distribution and maintenance of genetic variation across geographic space. Genetic diversity is also shaped by the forces of mutation, genetic drift, gene flow and dispersal. Each force is, in turn, affected directly or indirectly by environmental variability. Yet, our understanding of genetic diversity in the context of climates and landscapes is fragmentary, at best, despite ever-increasing emphases on landscape genomics and genotype-environment associations.

This work focuses on better understand genotype-environment relationships and to elucidate the combination of evolutionary processes that shape those relationships on landscape scales. The work has historically focused on plants, but moving forward it will be agnostic with respect to study system. Here are a few papers that illustrate some of the things we’re thinking about:

Aguirre-Liguori, J. A., Ramírez-Barahona, S., & Gaut, B. S. (2021). The evolutionary genomics of species’ responses to climate change. Nature Ecology & Evolution, 5(10), 1350-1360.

Aguirre‐Liguori, J. A., Morales‐Cruz, A., Gaut, B. S., & Ramírez‐Barahona, S. (2023). Sampling effect in predicting the evolutionary response of populations to climate change. Molecular Ecology Resources.

Morales-Cruz, A., Aguirre-Liguori, J., Massonnet, M., Minio, A., Zaccheo, M., Cochetel, N., … & Gaut, B. S. (2023). Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate. Communications biology, 6(1), 580.

The evolution of perennial crop species and their wild relatives

Perennial crops like grapes and olives are among the most important horticultural crops in the world.  But the domestication and evolution of perennial crops has generally been understudied, and this is particularly true of their wild relatives. Our ongoing work has characterized the genomes, population genomics and traits of perennial crops and their wild relatives. Much of this work has focused on the genus Vitis, which is fascinating in part because its wild relatives grow across a wide variety of ecological throughout North America and Asia. We also have ongoing interests in olives and avocados. Here are three fairly recent papers that illustrate the breadth of questions that interest us:

Xiao, H., Liu, Z., Wang, N., Long, Q., Cao, S., Huang, G., … & Zhou, Y. (2023). Adaptive and maladaptive introgression in grapevine domestication. Proceedings of the National Academy of Sciences, 120(24), e2222041120.

Cochetel, N., Minio, A., Guarracino, A., Garcia, J. F., Figueroa-Balderas, R., Massonnet, M., … & Cantu, D. (2023). A super-pangenome of the North American wild grape species. Genome Biology, 24(1), 290.

Solares, E., Morales-Cruz, A., Balderas, R. F., Focht, E., Ashworth, V. E., Wyant, S., … & Gaut, B. S. (2023). Insights into the domestication of avocado and potential genetic contributors to heterodichogamy. G3: Genes, Genomes, Genetics, 13(2), jkac323.