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  • Hornworts, an overlooked window into carbon-concentrating mechanism 2017

    Li, F.-W., J.C. Villarreal, P. Szovenyi
    Trends in Plant Science 22,  275-277
  • Boechera Microsatellite Database: an online portal for species identification and hybrid relationship resolution 2017

    Li, F.-W., C.A. Rushworth, J.B. Beck, M.D. Windham
    Database 1,  baw169
    Full text...
  • The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2 2017

    Rockwell, N.C., S.S. Martin, F.-W. Li, S. Mathews, J.C. Lagarias
    New Phytologist 214,  1145-1157
  • Genes translocated into the plastid inverted repeat show decelerated substitution rates and elevated GC content 2016

    Li, F.-W., L.-Y. Kuo, K.M. Pryer, C.J. Rothfels
    Genome Biology and Evolution 8,  2452-2458
    Full text...
  • Asplenium pifongiae (Aspleniaceae: Polypodiales), a new species from Taiwan 2016

    Li, F.-W., L.Y. Kuo, Y.H. Chang, T.C. Hsu, H.C. Hung, W.L. Chiou, C.J. Rothfels, Y.M. Huang
    Systematic Botany 41,  24-31
    Full text...
  • Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis 2016

    Hsu, P.Y., L. Calviello, H.-.Y. L. Wu*, F.-W. Li*, C.J. Rothfels, U. Ohler, P.N. Benfey.
    Proceedings of the National Academy of Sciences USA 113,  E7126-E7135
  • Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants 2016

    Jia, Q., G. Li, T.G. Köllner, J. Fu, X. Chen, W. Xiong, B.J. Crandall-Stotler, J.L. Bowman, D.J. Weston, Y. Zhang, L. Chen, Y. Xie, F.-W. Li, C.J. Rothfels, A. Larsson, S.W. Graham, D.W. Stevenson, G.K.-S. Wong, J. Gershenzon, F. Chen.
    Proceedings of the National Academy of Sciences USA 113,  12328-12333
  • Next-generation polyploid phylogenetics: Rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing 2016

    Rothfels, C.J., K.M. Pryer, F.-W. Li
    New Phytologist 213,  413-429
  • Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR): a regulator of ABA responses unique to basal land plants, required for desiccation tolerance 2016

    Stevenson, S.R., Y. Kamisugi, J. Schmutz, J.W. Jenkins, J. Grimwood, W. Muchero, G.A. Tuskan, S.A. Rensing, D. Lang, R. Reski, C. Trinh, M. Melkonian, C.J. Rothfels, F.-W. Li, A. Larsson, G.K.S. Wong, T. Edwards, A.C. Cuming.
    Plant Cell 28,  1310–1327
  • Maidenhair ferns, Adiantum, are indeed monophyletic, and sister to to the shoestring ferns, vittaroids (Pteridaceae) 2016

    Pryer, K.M., L. Huiet, F.-W. Li, C.J. Rothfels, E. Schuettpelz
    Systematic Botany 41,  14-23
  • A community-derived classification for extant lycophytes and ferns 2016

    The Pteridophyte Phylogeny Group.
    Journal of Systematics and Evolution 54,  563-603
  • Phytochrome diversity in green plants and the origin of canonical plant phytochromes 2015

    Li, F.-W., M. Melkonian, C.J. Rothfels, J.C. Villareal, D. Stevenson, S.W. Graham, G.K.-S. Wong, K.M. Pryer, S. Mathews
    Nature Communications 6,  7852
  • The origin and evolution of phototropins in plants 2015

    Li, F.-W., C.J. Rothfels, M. Melkonian, J.C. Villarreal, D.W. Stevenson, S.W. Graham, G.K.-S. Wong, S. Mathews, and K.M. Pryer
    Frontiers in Plant Science 6,  637
  • Evolutionary aspects of plant photoreceptors 2015

    Li, F.-W., S. Mathews
    Journal of Plant Research 129,  115-122
  • Searching for diamonds in the apomictic rough: A case study involving Boechera lignifera (Brassicaceae). 2015

    Windham, M.D., J.B. Beck, F.-W. Li, A. Allphin, J.G. Carman, C.A. Rushworth, E.M. Sigel, P.J. Alexander, C.D. Bailey, I.A. Al-Shehbaz
    Systematic Botany 40,  1031-1044
  • An exploration into fern genome space 2015

    Wolf, P.G., E.B. Sessa, D.B. Marchant, F.-W. Li, C.J. Rothfels, E.M. Sigel, M.A. Gitzendanner, C.J. Visger, J.A. Banks, D.E. Soltis, P.S. Soltis, K.M. Pryer, and J.P. Der
    Genome Biology and Evolution 7,  2533-2544
  • The evolutionary history of ferns inferred from 25 single-copy nuclear genes 2015

    Rothfels C.J., F.-W. Li, E.M Sigel., L. Huiet, A. Larsson, D.O. Burge, M. Ruhsam, M. Deyholos, D. Soltis, N. Stewart, S. Shaw, L.M. Pokorny, T. Chen, C. dePamphilis, L. DeGironimo, D.W. Stevenson, S.W. Graham, G.K.-S. Wong, and K.M. Pryer
    American Journal of Botany 102,  1089-1107
  • Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns 2014

    Li, F.-W., J.C. Villarreal, S. Kelly, C.J. Rothfels, M. Melkonian, E. Frangedakis, M. Ruhsam, E. M. Sigel, J.P. Der, J. Pittermann, D.O. Burge, L. Pokorny, A. Larsson, T. Chen, S. Weststrand, P. Thomas, E. Carpenter, Y. Zhang, Z. Tian, L. Chen, Z. Yan, Y. Zhu, X. Sun, J. Wang, D.W. Stevenson, B.J. Crandall-Stotler, A.J. Shaw, M.K. Deyholos, D.E. Soltis, S.W. Graham, M.D. Windham, J.A. Langdale, G.K.S. Wong, S. Mathews & K.M. Pryer
    Proceedings of the National Academy of Sciences USA, 111,  6672-6677
  • Crowdfunding the Azolla fern genome project: a grassroots approach 2014

    Li, F.-W., K.M. Pryer
    GigaScience 3,  16
  • Between two fern genomes 2014

    Sessa, E.B., J.A. Banks, M.S. Barker, J.P. Der, A.M. Duffy, S.W. Graham, M. Hasebe, J. Langdale, F.-W. Li, D.B. Marchant, K.M. Pryer, C.J. Rothfels, S.J. Roux, M.L. Salmi, E.M. Sigel, D.E. Soltis, P.S. Soltis, D.W. Stevenson, P.G. Wolf
    GigaScience 3,  15
  • The hybrid origin of Adiantum meishanianum (Pteridaceae): a rare and endemic species in Taiwan 2014

    Zhang, W.Y., L.Y. Kuo, F.-W. Li, C.N. Wang, W.L. Chiou
    Systematic Botany 39,  1034-1041
  • Transcriptome-mining for fern single-copy nuclear regions 2013

    Rothfels, C.J., A. Larsson, F.-W. Li, E.M. Sigel, L. Huiet, D.O. Burge, M. Ruhsam, S. Graham, D. Stevenson, G.K.S. Wong, P. Korall, K.M. Pryer
    PLoS One 8,  e76957
  • Gaga, a new genus segregated from Cheilanthes (Pteridaceae) 2012

    Li, F.-W., K.M. Pryer, M.D. Windham
    Systematic Botany 37,  845-860
  • rbcL and matK earn two thumbs up as the core DNA barcode for ferns 2011

    Li, F.-W., L.Y. Kuo, C.J. Rothfels, A. Ebihara, W.L. Chiou, M.D. Windham, K.M. Pryer
    PLoS One 6,  e26597
  • Book review: Knapp, Ralf. 2011. Ferns and Fern Allies of Taiwan 2011

    Li, F.-W.
    Taxon 60,  1233-1234
  • The first insight into fern matK phylogeny 2011

    Kuo*, L.Y., F.-W. Li*, W.L. Chiou, C.N. Wang.
    Molecular Phylogenetics and Evolution 59: 556-566 59,  556-566
  • Tissue-Direct PCR, a rapid and extraction-free method for barcoding of ferns 2010

    Li*, F.-W., L.Y. Kuo*, Y.M. Huang, W.L. Chiou, C.N. Wang
    Molecular Ecology Resources 10,  92-95
  • Identifying a mysterious aquatic fern gametophyte 2009

    Li, F.-W., B.C. Tan, V. Buchbender, R.C. Moran, G. Rouhan, C.N. Wang, D. Quandt
    Plant Systematics and Evolution 281,  77-86

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
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    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 Azollaand Salvinia (two closely related aquatic fern genera) have the smallest fern genomes known to date (0.75 Gb and 0.25 Gb respectively), while the average fern genome size is over 12 Gb. We have already assembled and annotated the whole genomes of Azolla filiculoides and Salvinia cucullata.

    These first 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
    Read more

    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 Juan Carlos Villarreal at Laval University, Peter Szoevenyi at University of Zurich, and Shifeng Cheng at BGI, 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
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    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.

  • Plant photoreceptor evolution

    “Light exerts a powerful influence on most vegetable tissues, and there can be no doubt that it generally tends to check
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    “Light exerts a powerful influence on most vegetable tissues, and there can be no doubt that it generally tends to check their growth” – Charles Darwin, 1880

    Light is the ultimate source of energy for much of life on earth, and inevitably governs the growth and physiology of photosynthetic organisms. Plants “see” light through photoreceptors. To understand how plants adapted to, and thrived in, the diverse environments they inhabit, the roles of photoreceptors cannot be ignored. Our research has been focusing on neochrome, a bizarre chimeric photoreceptor that fuses red-sensing phytochrome and blue-sensing phototropin together in a single protein. Neochromes were once thought to be unique to ferns, and were hypothesized to a play important role in facilitating ferns’ recent radiation in low-light environments.

    By sieving through transcriptomic and genomic data, we recently discovered novel neochrome homologs in hornworts (a bryophyte lineage), and demonstrated that ferns acquired neochrome from hornworts via horizontal gene transfer (Li et al. 2014 PNAS). This work has important implications for the significance of horizontal gene transfer among eukaryotes, and was widely publicized in the media. In addition, we reconstructed the evolutionary histories of phytochromes and phototropins across land plants (Li et al. 2015 Frontiers in Plant Science; Li et al. 2015 Nature Communications), and we are building upon such framework to interpret what we know about Arabidopsis photobiology within a broader evolutionary context.

Research Overview

We are broadly interested in the evolutionary processes at the gene, genome, and microbiome levels that shaped the plant diversity. At the gene level, we study the molecular evolution of photoreceptors and examine how that influences plant diversification. At the genome level, we generate and analyze fern genomes to investigate genome evolution across the major transitions in land plant evolution. At the microbiome level, we focus on the multiple origins of plant-cyanobacteria symbiosis and aim to elucidate the genetic mechanisms governing these interactions. Check out my lab website for details.