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

Ibarra-Laclette, E., Lyons, E., Hernández-Guzmán, G., Pérez-Torres, C. A., Carretero-Paulet, L., Chang, T., Lan, T., Welch, A. J., Jazmín, M., Simpson, J., Fernández-Cortés, A., Arteaga-Vázquez, M., Góngora-Castillo, E., Acevedo-Hernández, G., Schuster, S. C., Himmelbauer, H., Minoche, A. E., Sen, X. u., Lynch, M., , Oropeza-Aburto, A., et al. (2013). Architecture and evolution of a minute plant genome. Nature, 498(7452), 94-98.

PMID: 23665961;Abstract:

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism. © 2013 Macmillan Publishers Limited. All rights reserved.

Joyce, B., Baltzell, A., Bomhoff, M., & Lyons, E. (2017). Comparative Genomics Using CoGe, Hook, Line, and Sinker. Bioinformatics in Aquaculture: Principles and Methods, 461--487.
Bombarely, A., Moser, M., Amrad, A., Bao, M., Bapaume, L., Barry, C. S., Bliek, M., Boersma, M. R., Borghi, L., Bruggmann, R., & others, . (2016). Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature plants, 2, 16074.
Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, J., Falentin, C., Koh, C. S., Le Clainche, I., Bernard, M., Bento, P., Noel, B., , Labadie, K., et al. (2014). Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science (New York, N.Y.), 345(6199), 950-3.

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Nelson, A. D., Devisetty, U. K., Palos, K., Haug-Baltzell, A. K., Lyons, E., & Beilstein, M. A. (2017). Evolinc: A tool for the identification and evolutionary comparison of long intergenic non-coding RNAs. Frontiers in genetics, 8, 52.