Fay-Wei Li

Assistant Professor
Fay-Wei Li
fl329@cornell.edu
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.

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.
Fern genomes elucidate land plant evolution and cyanobacterial symbioses
2018.
Li, Fay-Wei, P. Brouwer, L. Carretero-Paulet, S. Cheng, J. de Vries, P.-M. Delaux, A.N. Eily, N. Kop…
Nature Plants.
4
:
460–472
Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing and its increase during hornwort diversification
2018.
Villarreal, J.C., Turmel, M., Bourgouin-Couture, M., Laroche, J., Salazar, N., Li, Fay-Wei, Chen, S.…
PLoS ONE.
13
:
e0200491
A worldwide phylogeny of Adiantum (Pteridaceae) reveals remarkable convergent evolution in leaf blade architecture
2018.
Huiet, L., Li, Fay-Wei, Kao, T.-T., Prado, J., Smith, A.R., Schuettpelz, E., Pryer, K.M.
Taxon.
67
:
488–502
Order-level fern plastome phylogenomics: new insights from Hymenophyllales
2018.
Kuo, L.-Y., Qi, X., Ma, H., Li, Fay-Wei
American Journal of Botany.
105
:
1545–1555
Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales)
2018.
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.
9
:
Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade
2018.
Schilling, M. P., Gompert, Z., Li, Fay-Wei, Windham, M. D., Wolf, P. G.
BMC Evolutionary Biology.
18
:
10KP: A phylodiverse genome sequencing plan
2018.
Cheng, S., Melkonian, M., Smith, S. A., Brockington, S., Archibald, J. M., Delaux, P. M., Li, Fay-We…
GigaScience.
7
:
1–9
A guide to sequence your favorite plant genomes
2018.
Li, Fay-Wei, Harkess, A.
American Journal of Botany.
6
:
e1030–e1030
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
2018.
Lang, D., Ullrich, K. K., Murat, F., Fuchs, J., Jenkins, J., Haas, F. B., Piednoel, M., Gundlach, H.…
The Plant Journal.
93
:
515–533
A novel chloroplast gene reported for flagellate plants
2018.
Song, M., Kuo, L. Y., Huiet, L., Pryer, K. M., Rothfels, C. J., Li, Fay-Wei
American Journal of Botany.
105
:
117–121
Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify
2018.
Dijkhuizen, L. W., Brouwer, P., Bolhuis, H., Reichart, G. J., Koppers, N., Huettel, B., Bolger, A. M…
New Phytologist.
217
:
453–466
The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2
2017.
Rockwell, N. C., Martin, S. S., Li, Fay-Wei, Mathews, S., Lagarias, J. C.
New Phytologist.
214
:
1145–1157
Hornworts: An Overlooked Window into Carbon-Concentrating Mechanisms
2017.
Li, Fay-Wei, Villarreal, J. C., Szövényi, P.
Trends in Plant Science.
22
:
275–277
Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
2017.
Rothfels, C. J., Pryer, K. M., Li, Fay-Wei
New Phytologist.
213
:
413–429
Boechera microsatellite website: An online portal for species identification and determination of hybrid parentage
2017.
Li, Fay-Wei, Rushworth, C. A., Beck, J. B., Windham, M. D.
Database : the journal of biological databases and curation.
2017
:
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
2016.
Hsu, P. Y., Calviello, L., Wu, H. YL, Li, Fay-Wei, Rothfels, C. J., Ohler, U., Benfey, P. N.
Proceedings of the National Academy of Sciences.
113
:
E7126–E7135
Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants
2016.
Jia, Q., Li, G., Kollner, T. G., Fu, J., Chen, X., Xiong, W., Crandall-Stotler, B. J., Bowman, J. L.…
Proceedings of the National Academy of Sciences.
113
:
12328–12333
Maidenhair Ferns, Adiantum , are Indeed Monophyletic and Sister to Shoestring Ferns, Vittarioids (Pteridaceae)
2016.
Pryer, K. M., Huiet, L., Li, Fay-Wei, Rothfels, C. J., Schuettpelz, E.
Systematic Botany.
41
:
17–23
Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content
2016.
Li, Fay-Wei, Kuo, L. Y., Pryer, K. M., Rothfels, C. J.
Genome biology and evolution.
8
:
2452–2458
Asplenium pifongiae (Aspleniaceae: Polypodiales), a New Species from Taiwan
2016.
Li, Fay-Wei, Kuo, L. Y., Chang, Y. H., Hsu, T. C., Hung, H. C., Chiou, W. L., Rothfels, C. J., Huang…
Systematic Botany.
41
:
24–31

Contact:

Boyce Thompson Institute
533 Tower Rd.
Ithaca, NY 14853
607.254.1234
contact@btiscience.org