Eric H Lyons

Eric H Lyons

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

Research Interest

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


Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., DePamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Gustavo, L., , Dacre, M., et al. (2011). The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 332(6032), 960-963.
BIO5 Collaborators
Michael S Barker, Eric H Lyons

PMID: 21551031;PMCID: PMC3166216;Abstract:

Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

Chen, E. C., Najar, C. F., Zheng, C., Brandts, A., Lyons, E., Tang, H., Carretero-Paulet, L., Albert, V. A., & Sankoff, D. (2013). The dynamics of functional classes of plant genes in rediploidized ancient polyploids. BMC Bioinformatics, 14(Suppl 15), S19.
Woodhouse, M. R., Schnable, J. C., Pedersen, B. S., Lyons, E., Lisch, D., Subramaniam, S., & Freeling, M. (2010). Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS biology, 8(6), e1000409.

Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity to be easily identifiable. Using sorghum exons as the query sequence, we studied the fate of both orthologous genes in maize following the maize tetraploidy. We show that genes are predominantly lost, not relocated, and that single-gene loss by deletion is the rule. Based on comparisons with orthologous sorghum and rice genes, we also infer that the sequences present before the deletion events were flanked by short direct repeats, a signature of intra-chromosomal recombination. Evidence of this deletion mechanism is found 2.3 times more frequently on one of the maize homologs, consistent with earlier observations of biased fractionation. The over-fractionated homolog is also a greater than 3-fold better target for transposon removal, but does not have an observably higher synonymous base substitution rate, nor could we find differentially placed methylation domains. We conclude that fractionation is indeed biased in maize and that intra-chromosomal or possibly a similar illegitimate recombination is the primary mechanism by which fractionation occurs. The mechanism of intra-chromosomal recombination explains the observed bias in both gene and transposon loss in the maize lineage. The existence of fractionation bias demonstrates that the frequency of deletion is modulated. Among the evolutionary benefits of this deletion/fractionation mechanism is bulk DNA removal and the generation of novel combinations of regulatory sequences and coding regions.

Zheng, C., Albert, V. A., Lyons, E., & Sankoff, D. (2012). Ancient angiosperm hexaploidy meets ancestral eudicot gene order. 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012.


We propose a protocol for reconstructing and analyzing the post-polyploidization ancestor of a set of genomes. Our method, applied to the post-hexaploid ancestor of six core eudicot flowering plants, reconstructs ancestral gene order, based on orthologs obtained for each pair of data genomes, harmonized into disjoint ortholog sets for multiple genomes. © 2012 IEEE.

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.