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

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., St John, J. A., Capella-Gutiérrez, S., Castoe, T. A., Kern, C., Fujita, M. K., Opazo, J. C., Jurka, J., Kojima, K. K., Caballero, J., Hubley, R. M., Smit, A. F., Platt, R. N., , Lavoie, C. A., et al. (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.), 346(6215), 1254449.

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

Tang, H., Lyons, E., & Schnable, J. C. (2014). Early History of the Angiosperms. Advances in Botanical Research, 69, 195-222.

Abstract:

The flowering plants, also known as the angiosperms, are the most diverse group of plants. The basal flowering plant lineages diverged at very early stage in flowering plant evolution, followed by rapid diversification of the magnoliids, the eudicots and the monocots. Genomic comparisons within and across plant lineages help identify the critical events that occurred during the evolution of major groups of flowering plants. In this chapter, we first review the basic concepts and analytic methods for studying ancient polyploidy-a prominent feature during plant evolution. We then highlight recent progress on the dating of deep polyploidies in the eudicot and monocot lineage, respectively. With a clear knowledge of genomic history, we can effectively compare the eudicot genomes to monocot genomes, which promise to bridge functional equivalence between genes of the two well-studied groups. Finally, we deduce the composition and structure of the 'ancestral genome' on the basis of the arrangements of genes in the extant species. The in silico reconstruction of the ancestral genome provides an integrated framework under which conservation of modern plant genomes can be systematically studied. © 2014 Elsevier Ltd.

Lyons, E., & Freeling, M. (2008). How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant Journal, 53(4), 661-673.

PMID: 18269575;Abstract:

There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text. © 2008 The Authors.

Zheng, C., Kononenko, A., Leebens-Mack, J., Lyons, E., & Sankoff, D. (2014). Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants. BMC genomics, 15(Suppl 6), S8.

Chaining is a major problem in constructing gene families.

Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R., & Lisch, D. (2008). Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research, 18(12), 1924-1937.

PMID: 18836034;PMCID: PMC2593585;Abstract:

Previous to this work, typical genes were thought to move from one position to another infrequently. On the contrary, we now estimate that between one-fourth and three-fourths of the genes in Arabidopsis transposed in the Brassicales. We used the CoGe comparative genomics system to perform and visualize multiple orthologous chromosomal alignments. Using this tool, we found large differences between different categories of genes. Ten of the gene families examined, including genes in most transcription factor families, exhibited a median frequency of 5% transposed genes. In contrast, other gene families were composed largely of transposed genes: NB-LRR disease-resistance genes, genes encoding MADS-box and B3 transcription factors, and genes encoding F-box proteins. A unique method involving transposition-rich regions of genome allowed us to obtain an indirect estimate of the positional stability of the average gene. The observed differences between gene families raise important questions concerning the causes and consequences of gene transposition. ©2008 by Cold Spring Harbor Laboratory Press.