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EECG Embarkation: High country viruses: landscape genomics and plant virus diversity in the Rocky Mountains

**The AGA grants EECG Research Awards each year to graduate and post-doctoral researchers who are at a critical point in their research, where additional funds would allow them to conclude their research project and prepare it for publication. EECG awardees also get the opportunity to hone their science communication and write three posts over their grant tenure for the AGA Blog. In the first in the series, our EECG awardees write about their research and their interests as an ’embarkation’.



About the Author: Elizabeth (Lizzie) Lombardi (she/her) is a doctoral candidate in the Department of Ecology and Evolutionary Biology at Cornell University. While the breadth of her research spans biological scales, from 21 nucleotide contigs to hemispheric species distributions, the core question is always: what do viruses want, anyways? Her work on Boechera stricta examines the impact of environment on plant virus diversity and abundance, and considers possible outcomes of changing conditions for hosts and viruses alike. Follow Lizzie on Twitter @lombardi_EM or find more information about her research on her website.




Research Summary:

Viruses in natural plant communities are poorly understood despite mounting evidence that they are ubiquitous across taxa and impact plant biodiversity (Malstrom et al. 2011). Most studies of plant viruses have been conducted in host systems of agricultural importance or under highly-controlled laboratory settings. As a result, our scientific knowledge of plant-virus interactions lacks evolutionary and ecological context (Cooper & Jones, 2006), and we cannot predict or prepare for shifting biotic interactions under changing environments (Harvell et al. 2002, HilleRisLambers et al. 2013). In order to address this gap, I have undertaken a field-based survey to quantify virus diversity and host immunity across a well-studied elevational cline. Historically, technological and resource limitations have disallowed comprehensive studies of wild viruses, but next generation genomic tools have revolutionized available methods for discovery of novel viruses in wild host species. As a result of these advancements and thanks to the support of the American Genetics Association, I will employ deep sequencing to conduct the first comprehensive survey of plant-virus interactions under changing alpine environments. Overall, the objective of my project is to build a virus diversity baseline in hosts experiencing environmental change, and to develop a conservation genomics approach to alpine plant epidemiology.

Figure 1: Map of Boechera stricta populations that I have located and sampled over the course of my doctoral research. While my field work has been spatially expansive, the focus on the present study will be on a well-studied and tractable elevational cline in central Colorado (red dots).

To collect the samples needed for this project, I have journeyed far and high across the full host species range looking for my diminutive but objectively-cute plants (Figure 1). The host populations included in the present study are from five sites in the Elk Mountains of west-central Colorado, including the area around Rocky Mountain Biological Laboratory. Total RNA from leaf tissue has been isolated from individuals at each of the focal populations, pooled by population and will be sequenced for viral RNA genomes. In addition, I will use host transcripts to assess gene expression amongst infected and uninfected hosts.

With luck and good fortune, this project will 1) provide the first rigorous and systematic study of virus diversity across an experimental biogeographical cline, 2) characterize patterns of viral diversity in a host population genomics context and 3) develop a non-model system for simultaneously studying host, pathogen and environment. This latter objective is especially critical in light of rapid and significant environmental change, which has already thrown a number of figurative wrenches in our understanding of host-virus interactions.

Host Study System:

Boechera stricta is a perennial forb with a native range across the North American mountain west (Figure 2). As is characteristic for most members of Brassicaceae, vegetative growth occurs first in rosette form until 1) sufficient energy is stored, 2) death seems imminent or 3) the mood is just right and the plant decides that it is ready to be a parent. At this point, an inflorescence bursts forth like teenage acne, announcing the plant’s fertility with a crown of four-petaled flowers and volatile phenolics to boot. Then, after at least a year of preparation for this momentous occasion, the plant mostly self-pollinates without the help of insects or wind (Song et al. 2005) making the whole flowering routine seem completely contrived.

Figure 2: Image of Boechera stricta in the North Pole Basin host population (3,300 meter elevation), Elk Mountains of Colorado. Photo taken by E. Lombardi.

Why study this species? There are a few reasons, none of which are necessarily ‘right’ or ‘wrong’ but most of which match my temperament and goals. First, B. stricta grows across an elevational gradient that facilitates research into abioticially-mediated immune response across relatively short distances. The idea here is that variables such as precipitation, temperature and seasonality vary dramatically across the same slope. Thus, an enterprising young researcher could traverse vast environmental clines in the course of day hiking, and sample many host populations efficiently. Furthermore, B. stricta is already the subject of much scientific attention from a community of exceptional researchers who have, for some reason, accepted me into their fold. Ecologists and evolutionary biologists, including Dr. Thomas Mitchell-Olds (Duke University), Dr. Maggie Wagner (University of Kansas), Dr. Susana Wadgymar (Davidson College) and Dr. Jill Anderson (University of Georgia), have studied B. stricta around the Rocky Mountain Biological Laboratory; I count myself lucky to be engaged with such a stellar research crew. Dr. Anderson in particular has been a mentor and champion for this work, and I hope that this project will continue to serve our shared goal of understanding how best to protect alpine plants facing dramatic climate change.



Cooper, I., & Jones, R. A. C. (2006). Wild Plants and Viruses: Under‐Investigated Ecosystems. In Advances in Virus Research (Vol. 67, pp. 1–47). Elsevier.

Harvell, C. D., Mitchell, C. E., Ward, J. R., Altizer, S., Dobson, A. P., Ostfeld, R. S., & Samuel, M. D. (2002). Climate warming and disease risks for terrestrial and marine biota. Science (New York, N.Y.), 296(5576), 2158–2162.

HilleRisLambers, J., Harsch, M. A., Ettinger, A. K., Ford, K. R., & Theobald, E. J. (2013). How will biotic interactions influence climate change–induced range shifts? Annals of the New York Academy of Sciences, 1297(1), 112–125.

Malmstrom, C. M., Melcher, U., & Bosque-Pérez, N. A. (2011). The expanding field of plant virus ecology: Historical foundations, knowledge gaps, and research directions. Virus Research, 159(2), 84–94.

Song, B.-H., Clauss, M. J., Pepper, A., & Mitchell‐Olds, T. (2006). Geographic patterns of microsatellite variation in Boechera stricta, a close relative of Arabidopsis. Molecular Ecology, 15(2), 357–369.

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