Fay-Wei Li

Assistant Professor
Fay-Wei Li
Office/Lab: 121
Phone: Office Phone:
Office/Lab: 121
Email: fl329@cornell.edu
Office Phone: 607-254-1244
Research Overview

We are broadly interested in the evolutionary processes at the gene, genome, and microbiome levels that shaped the plant diversity. We mostly focus on “seed-free” plants (ferns, lycophytes, and bryophytes), and anything that has a weird biology. Check out my lab website for details.


Current Projects

Fern genomics

Ferns are one of the final frontiers in plant genomics. The dearth of fern genomic resources is due primarily to their notoriously high chromosome numbers and large genome sizes—ferns can have chromosome numbers as high as 2n=1440, and genome sizes as high as 1C=71 Gb (>470 times larger than Arabidopsis). However, we have recently discovered that Azolla and Salvinia (two closely related aquatic fern genera) have the smallest fern genomes known to date (0.75 Gband 0.25 Gb respectively), while the average fern genome size is over 12 Gb. The assemblies and analyses of Azolla filiculoides and Salvinia cucullata genomes were recently published (Li et al 2018 Nature Plants).

Currently we are collaborating with 10KP to broadly sequence genomes across the fern tree of life. We have around a dozen species in the pipeline. These new fern genomes will make possible many exciting research opportunities. We are interested in examining the patterns of paleopolyploidization, genome expansion/contraction, as well as transposable element activities in ferns, and contrast them across other plant genomes. We are also curious about how gene family evolution—particularly those that play critical roles in reproduction and development—influences the origin and evolution of plant life forms. Finally, we are keen to find out what drove the remarkable variation in both genome size and chromosome number across land plants.


Hornworts as a new model system

Hornworts are one of the three bryophyte lineages (together with mosses and liverworts), and have a suite of fascinating biological features. For example, some hornwort species have a unique carbon-concentration mechanism to boost photosynthesis, like C4 or CAM but at the single-cell level. In addition, every single hornwort species are capable to form symbiosis with cyanobacteria, and thus hold the key to understand plant interactions with nitrogen-fixing microbes.

Working with Peter Szoevenyi (University of Zurich), Juan Carlos Villarreal (Laval University), Keiko Sakakibara (Rikkyo University) and Eftychios Frangedakis (University of Cambridge), we have assembled complete genomes from three hornwort species. We have also been developing tools for genetic transformation as well as CRISPR-Cas9 genome editing to enable reverse genetic interrogation in hornworts. We hope to apply these tools and genomic resources to tackle various research questions, from the origin of cyanobacteria symbiosis to the evolution of plant body plans.


Plant-cyanobacteria symbiosis

Plant-bacterial symbiosis is a major driver in evolution, and its role in nitrogen fixation is particularly important in agriculture. Past studies of plant-bacteria interactions have focused primarily on the legume-Rhizobium system. Although significant, this particular symbiosis has had only a single evolutionary origin, thus limiting its utility as a model for understanding the genetic mechanisms underlying other symbiotic plant-bacteria partnerships. In contrast, symbioses with the other group of nitrogen-fixing bacteria––the cyanobacteria—have independently evolved multiple times, in liverworts, hornworts, ferns (i.e. Azolla), cycads, and flowering plants. We aim to leverage the power of such convergent evolution––independently evolved in each of these disparate plant groups––to identify the genetic commonalities that were repeatedly recruited to assemble this mutually-beneficial association. Specifically, we will be looking for signatures of convergent evolution at the genome, gene and amino acid levels. At the genome level, we will focus on concerted gene family expansion or contraction, loss or retention of metabolic pathways, proliferation or purging of transposable elements, and horizontal gene transfer between cyanobacteria and plants. At the gene level, we will identify genes that exhibit similar expression profiles when a cyanobacterial symbiosis is present versus absent. And at the amino acid levels, we will reconstruct gene phylogenies for all orthologous genes and examine if similar, positively- selected amino acid substitutions occurred each time a symbiotic event evolved. The genetic elements identified through this comparative genomic analysis will be instrumental for engineering artificial nitrogen-fixing symbiosis onto crop plants.

  • BTI Researchers Publish High-Impact Nature Papers

    We would like to congratulate a pair of BTI faculty members who recently published high-impact research papers in the prestigious research journal Nature. Frank Schroeder and colleagues discovered the first clues on how gut health influences brain health. Published on October 23, the researchers describe new cellular and molecular processes underlying communication between gut microbes […] Read more »
  • BTI Researchers Unlocking Hornworts’ Secrets

    Hornworts are a little-studied, ancient group of plants with some very unique biology, including their methods of securing carbon and nitrogen. Unlocking these secrets may help researchers boost agricultural output and use less synthetic fertilizer, as well as provide broader insights into plant evolution. Unfortunately, there are no genetic tools for determining the functions of […] Read more »
  • BTI Welcomes Summer Student Interns

  • NSF awards BTI $1M to study plant-bacteria symbiosis

    Professor Dr. Fay-Wei Li has been awarded a $1.1 million NSF grant to study hornwort/bacteria symbiosis. The hornwort plant relies on nitrogen-fixing soil bacteria to give it life and unlocking the secrets to how that works may help reduce agricultural dependence on synthetic fertilizer. “Hornwort is a remarkable plant, and only a few remarkable plants […] Read more »
  • Fern-tastic! Crowdfunded fern genomes published in Nature Plants

    With crowdfunded support, researchers have sequenced the first two fern genomes ever. Their results, including the discovery of an ancient gene transfer and novel symbiosis mechanisms, appear this month in Nature Plants. Read more »

Intern Projects

Seed-free plant genomics and symbioses

The Li lab uses genomic tools to investigate the evolution and biology of seed-free plants: ferns, fern allies, and bryophytes (mosses, liverworts, and hornworts). We are particularly interested in their symbioses with N2-fixing cyanobacteria, which provide plants with their own source of nitrogen fertilizer. We aim to understand the evolution and mechanisms of plant-cyanobacteria symbioses, and the results of which will lay the foundation for future engineering of “self-fertilizing” crops with less reliance on synthetic nitrogen fertilizers. To this end, we are surveying the diversity of cyanobacterial symbionts in hornworts, and using RNA-sequencing to uncover putative symbiosis-related genes.

Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution
Bell, D., Lin, Q., Gerelle, W.K., Joya, S., Chang, Y., Taylor, Z.N., Rothfels, C.J., Larsson, A., Vi…
American Journal of Botany.
One thousand plant transcriptomes and the phylogenomics of green plants
Leebens-Mack, J.H., Barker, M.S., Carpenter, E.J., Deyholos, M.K., Gitzendanner, M.A., Graham, S.W.,…
Ferns: the final frond-tier in plant model systems
Petlewski, A.R., Li, Fay-Wei
American Fern Journal.
A Roadmap for Fern Genome Sequencing
Kuo, L.Y., Li, Fay-Wei
American Fern Journal.
Updating Taiwanese pteridophyte checklist: a new phylogenetic classification
Chang, H.M., Chen, C.W., Huang, Y.M., Li, Fay-Wei, Huang, Y.F., Shao, W., Lu, P.F., Chen, C.W., Chan…
Phylogenetic Methods to Study Light Signaling
Li, Fay-Wei, Mathews, S.
Methods Mol Biol.
Reconstructing trait evolution in plant evo-devo studies.
Delaux, P.M., Hetherington, A.J., Coudert, Y., Delwiche, C., Dunand, C., Gould, S., Kenrick, P., Li,…
Curr Biol.
Large-scale phylogenomic analysis suggests three ancient superclades of the WUSCHEL-RELATED HOMEOBOX transcription factor family in plants.
Wu, C.C., Li, Fay-Wei, Kramer, E.M.
PLoS One.
On the evolutionary significance of horizontal gene transfers in plants.
Wickell, D.A., Li, Fay-Wei
New Phytol.
Complete genomes of symbiotic cyanobacteria clarify the evolution of Vanadium-nitrogenase.
Nelson, J., Hauser, D., Gudiño, J.A., Guadalupe, Y.A., Meeks, J.C., Salazar, N., Villarreal, J.C., …
Genome Biology and Evolution.
NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches
Yang, E.J., Yoo, C.Y., Liu, J., Wang, H., Cao, J., Li, Fay-Wei, Pryer, K.M., Sun, T.P., Weigel, D., …
Nature Communications.
A first glimpse at genes important to the Azolla–Nostoc symbiosis
Eily, A.N., Pryer, K.M., Li, Fay-Wei
Fern genomes elucidate land plant evolution and cyanobacterial symbioses
Li, Fay-Wei, P. Brouwer, L. Carretero-Paulet, S. Cheng, J. de Vries, P.-M. Delaux, A.N. Eily, N. Kop…
Nature Plants.
Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing and its increase during hornwort diversification
Villarreal, J.C., Turmel, M., Bourgouin-Couture, M., Laroche, J., Salazar, N., Li, Fay-Wei, Chen, S.…
A worldwide phylogeny of Adiantum (Pteridaceae) reveals remarkable convergent evolution in leaf blade architecture
Huiet, L., Li, Fay-Wei, Kao, T.-T., Prado, J., Smith, A.R., Schuettpelz, E., Pryer, K.M.
Order-level fern plastome phylogenomics: new insights from Hymenophyllales
Kuo, L.-Y., Qi, X., Ma, H., Li, Fay-Wei
American Journal of Botany.
Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales)
Kuo, L.-Y., Tang, T.-Y., Li, Fay-Wei, Su, H.-J., Chiou, W.-L., Huang, Y.-M., Wang, C.-N.
Frontiers in Plant Science.
Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade
Schilling, M. P., Gompert, Z., Li, Fay-Wei, Windham, M. D., Wolf, P. G.
BMC Evolutionary Biology.
10KP: A phylodiverse genome sequencing plan
Cheng, S., Melkonian, M., Smith, S. A., Brockington, S., Archibald, J. M., Delaux, P. M., Li, Fay-We…
A guide to sequence your favorite plant genomes
Li, Fay-Wei, Harkess, A.
Applications in Plant Sciences.


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