Now showing items 1-18 of 18

    • A novel chloroplast gene reported for flagellate plants. 

      Song, Michael; Kuo, Li-Yaung; Huiet, Layne; Pryer, Kathleen M; Rothfels, Carl J; Li, Fay-Wei (American journal of botany, 2018-01)
      PREMISE OF THE STUDY:Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS:We ...
    • A step-by-step protocol for meiotic chromosome counts in flowering plants: A powerful and economical technique revisited. 

      Windham, Michael D; Pryer, Kathleen M; Poindexter, Derick B; Li, Fay-Wei; Rothfels, Carl J; Beck, James B (Applications in plant sciences, 2020-04-23)
      Premise:Counting chromosomes is a fundamental botanical technique, yet it is often intimidating and increasingly sidestepped. Once mastered, the basic protocol can be applied to a broad range of taxa and research questions. ...
    • An Exploration into Fern Genome Space. 

      Wolf, Paul G; Sessa, Emily B; Marchant, Daniel Blaine; Li, Fay-Wei; Rothfels, Carl J; Sigel, Erin M; Gitzendanner, Matthew A; ... (13 authors) (Genome Biol Evol, 2015-08-26)
      Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, ...
    • Between two fern genomes. 

      Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; ... (19 authors) (Gigascience, 2014)
      Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution ...
    • Crowdfunding the Azolla fern genome project: a grassroots approach. 

      Li, Fay-Wei; Pryer, Kathleen M (Gigascience, 2014)
      Much of science progresses within the tight boundaries of what is often seen as a "black box". Though familiar to funding agencies, researchers and the academic journals they publish in, it is an entity that outsiders rarely ...
    • Fern genomes elucidate land plant evolution and cyanobacterial symbioses. 

      Li, Fay-Wei; Brouwer, Paul; Carretero-Paulet, Lorenzo; Cheng, Shifeng; de Vries, Jan; Delaux, Pierre-Marc; Eily, Ariana; ... (42 authors) (Nature plants, 2018-07-02)
      Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata ...
    • Gaga, a new fern genus segregated from cheilanthes (pteridaceae) 

      Li, Fay-Wei; Pryer, Kathleen M; Windham, Michael D (Systematic Botany, 2012-10-01)
      Ongoing molecular phylogenetic studies of cheilanthoid ferns confirm that the genus Cheilanthes (Pteridaceae) is polyphyletic. A monophyletic group of species within the hemionitid clade informally called the "C. marginata ...
    • Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content. 

      Li, Fay-Wei; Kuo, Li-Yaung; Pryer, Kathleen M; Rothfels, Carl J (Genome biology and evolution, 2016-08-25)
      Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced ...
    • Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. 

      Li, Fay-Wei; Villarreal, Juan Carlos; Kelly, Steven; Rothfels, Carl J; Melkonian, Michael; Frangedakis, Eftychios; Ruhsam, Markus; ... (36 authors) (Proceedings of the National Academy of Sciences of the United States of America, 2014-05)
      Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and ...
    • Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify. 

      Dijkhuizen, Laura W; Brouwer, Paul; Bolhuis, Henk; Reichart, Gert-Jan; Koppers, Nils; Huettel, Bruno; Bolger, Anthony M; ... (15 authors) (The New phytologist, 2018-01)
      Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome ...
    • NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches. 

      Yang, Emily J; Yoo, Chan Yul; Liu, Jiangxin; Wang, He; Cao, Jun; Li, Fay-Wei; Pryer, Kathleen M; ... (11 authors) (Nature communications, 2019-06-14)
      Phytochromes initiate chloroplast biogenesis by activating genes encoding the photosynthetic apparatus, including photosynthesis-associated plastid-encoded genes (PhAPGs). PhAPGs are transcribed by a bacterial-type RNA polymerase ...
    • Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. 

      Rothfels, Carl J; Pryer, Kathleen M; Li, Fay-Wei (The New phytologist, 2017-01)
      Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate ...
    • Phytochrome diversity in green plants and the origin of canonical plant phytochromes. 

      Li, Fay-Wei; Melkonian, Michael; Rothfels, Carl J; Villarreal, Juan Carlos; Stevenson, Dennis W; Graham, Sean W; Wong, Gane Ka-Shu; ... (9 authors) (Nat Commun, 2015-07-28)
      Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across ...
    • rbcL and matK earn two thumbs up as the core DNA barcode for ferns. 

      Li, Fay-Wei; Kuo, Li-Yaung; Rothfels, Carl J; Ebihara, Atsushi; Chiou, Wen-Liang; Windham, Michael D; Pryer, Kathleen M (PloS one, 2011-01)
      BACKGROUND: DNA barcoding will revolutionize our understanding of fern ecology, most especially because the accurate identification of the independent but cryptic gametophyte phase of the fern's life history--an endeavor ...
    • Seeing the Light: the Origin and Evolution of Plant Photoreceptors 

      Li, Fay-Wei (2015)
      Plants use an array of photoreceptors to measure the quality, quantity, and direction of light in order to respond to ever-changing light environments. Photoreceptors not only determine how and when individual plants complete ...
    • The evolutionary history of ferns inferred from 25 low-copy nuclear genes. 

      Rothfels, Carl J; Li, Fay-Wei; Sigel, Erin M; Huiet, Layne; Larsson, Anders; Burge, Dylan O; Ruhsam, Markus; ... (23 authors) (Am J Bot, 2015-07)
      UNLABELLED: • PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison ...
    • The origin and evolution of phototropins. 

      Li, Fay-Wei; Rothfels, Carl J; Melkonian, Michael; Villarreal, Juan C; Stevenson, Dennis W; Graham, Sean W; Wong, Gane K-S; ... (9 authors) (Front Plant Sci, 2015)
      Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their ...
    • Transcriptome-mining for single-copy nuclear markers in ferns. 

      Rothfels, Carl J; Larsson, Anders; Li, Fay-Wei; Sigel, Erin M; Huiet, Layne; Burge, Dylan O; Ruhsam, Markus; ... (12 authors) (PloS one, 2013-01)
      BACKGROUND:Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. ...