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

Tang, H., Bomhoff, M. D., Briones, E., Zhang, L., Schnable, J. C., & Lyons, E. (2015). SynFind: compiling syntenic regions across any set of genomes on demand. Genome biology and evolution, 7, 3286--3298.
Reneker, J., Lyons, E., Conant, G. C., Pires, J. C., Freeling, M., Shyu, C., & Korkin, D. (2012). Long identical multispecies elements in plant and animal genomes. Proceedings of the National Academy of Sciences of the United States of America, 109(19), E1183-E1191.

PMID: 22496592;PMCID: PMC3358895;Abstract:

Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and located in syntenic positions in at least two genomes. Although hundreds of UCEs have been found in animal genomes, little is known about the incidence of ultraconservation in plant genomes. Using an alignment-free information-retrieval approach, we have comprehensively identified all long identical multispecies elements (LIMEs), which include both syntenic and nonsyntenic regions, of at least 100 identical base pairs shared by at least two genomes. Among six animal genomes, we found the previously known syntenic UCEs as well as previously undescribed nonsyntenic elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. LIMEs can also be classified as either simple (repetitive) or complex (non-repetitive), they may occur in multiple copies in a genome, and they are often spread across multiple chromosomes. Although complex LIMEs were found in both animal and plant genomes, they differed significantly in their composition and copy number. Further analyses of plant LIMEs revealed their functional diversity, encompassing elements found near rRNA and enzyme-coding genes, as well as those found in transposons and noncoding DNA. We conclude that despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.

Xu, S., Brockm\"oller, T., Navarro-Quezada, A., Kuhl, H., Gase, K., Ling, Z., Zhou, W., Kreitzer, C., Stanke, M., Tang, H., & others, . (2017). Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proceedings of the National Academy of Sciences, 114(23), 6133--6138.
Tang, H., & Lyons, E. (2012). Unleashing the genome of Brassica rapa. Frontiers in Plant Science, 3.
Tang, H., Lyons, E., & Town, C. D. (2015). Optical mapping in plant comparative genomics. genome, 1, 8.