Eric H Lyons

Eric H Lyons

Associate Professor, Plant Science
Associate Professor, Agricultural-Biosystems Engineering
Advisor, CALS' Office of the Assoc Dean - Research for Cyber Initiatives in Agricultural / Life - Vet Science
Associate Professor, Genetics - GIDP
Associate Professor, BIO5 Institute
Primary Department
Department Affiliations
Contact
(520) 626-5070

Research Interest

Eric Lyons, PhD is an assistant professor at the University of Arizona School of Plant Sciences. Dr. Lyons is internationally known for his work in understanding the evolution, structure, and dynamics of genomes. Core to his research activities is the development of software systems for managing and analyzing genomic data and cyberinfrastructure for the life sciences.Dr. Lyons has published over 30 original research papers and 5 book chapters, many in collaboration with investigators from around the world. He is a frequent presenter at national and international meetings, and has been invited to teach workshops on the analysis of genomic data to plant, vertebrate, invertebrate, microbe, and health researchers.Prior to joining the faculty in the School of Plant Sciences, Dr. Lyons worked with the iPlant Collaborative developing cyberinfrastructure, and managing its scientific activities. In addition, he spent five years working in industry at biotech, pharmaceutical, and software companies. Dr. Lyons’ core software system for managing and analyzing genomic data is called CoGe, and is available for use at http://genomevolution.org

Publications

Ming, R., Hou, S., Feng, Y., Qingyi, Y. u., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., L., K., Salzberg, S. L., Feng, L., Jones, M. R., Skelton, R. L., Murray, J. E., Chen, C., Qian, W., Shen, J., Peng, D. u., , Eustice, M., et al. (2008). The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 452(7190), 991-996.

PMID: 18432245;PMCID: PMC2836516;Abstract:

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties. ©2008 Nature Publishing Group.

VanBuren, R., Bryant, D., Edger, P. P., Tang, H., Burgess, D., Challabathula, D., Spittle, K., Hall, R., Gu, J., Lyons, E., & others, . (2015). Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.. Nature.
Schnable, J. C., Freeling, M., & Lyons, E. (2012). Genome-wide analysis of syntenic gene deletion in the grasses. Genome biology and evolution, 4(3), 265-77.

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community.

Albert, V. A., Barbazuk, W. B., Der, J. P., Leebens-Mack, J., Ma, H., Palmer, J. D., Rounsley, S., Sankoff, D., Schuster, S. C., Soltis, D. E., & others, . (2013). The Amborella Genome and the Evolution of Flowering Plants. Science, 342(6165), 1241089.
Wu, Y., Sheehan, P. D., Males, J. R., Close, L. M., Morzinski, K. M., Teske, J. K., Haug-Baltzell, A., Merchant, N., & Lyons, E. (2017). An ALMA and MagAO study of the substellar companion GQ Lup B. The Astrophysical Journal, 836(2), 223.