Publications

– lab members in bold –

In review/In press

Robison, T.A., Z.G. Oh, D. Lafferty, X. Xu, J.C.A. Villarreal, L.H. Gunn#, F.-W. Li#. Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants. Nature Plants in press. #Corresponding authors

Schafran, P.#, D.A. Hauser, J.M. Nelson, X. Xu, L.A. Mueller, S. Kulshrestha, I. Smalley, S. de Vries, I. Irisarri, J. de Vries, K. Davies, J.C.A. Villarreal, F.-W. Li#. Pan-phylum genomes of hornworts revealed conserved autosomes but dynamic accessory and sex chromosomes. Nature Plants in press. #Corresponding authors

Oh, Z.G., T.A. Robison, D.H. Loh, W.S.L. Ang, J. Ng, F.-W. Li#, L.H. Gunn#. Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems. Molecular Plant in press. #Corresponding authors

Peñaloza-Bojacá, G., A. Maciel-Silva, D.C. Cargill, D. Bell, E.B. Sessa, F.-W. Li, J.G. Burleigh, S.F. McDaniel, E.C. Davis, L. Endara, N. Salazar, P. Schafran, S. Chantanaorrapint, J. Duckett, S. Pressel, C. Solís-Lemus, K. Renzaglia, J.C. Villarreal A. Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification. Annals of Botany, in revision.

Uveges, B., K.L. Sparks, W.S. Ang, H. Monti, F.-W. Li, J.P. Sparks. Contamination of commercial 15N2: potential impacts on nitrogen fixation assays and a simple method for quantification. in review.

Song, M.J., F. Freund, C.M. Tribble, E. Toffelmier, C. Miller, H.B. Shaffer, F.-W. Li, C.J. Rothfels. The nitrogen-fixing fern Azolla has a complex microbiome characterized by multiple modes of transmission. American Journal of Botany, in revision.

Song, M.J., F.-W. Li, F. Freund, M. Escalona, E. Toffelmier, C. Miller, H.B. Shaffer, O. Nguyen, M.P.A. Marimuthu, N. Chumchim, C.M. Tribble, C.W. Fairbairn, W. Seligmann, C.J. Rothfels. The genome assembly of the duckweed fern, Azolla caroliniana. Journal of Heredity, in review. 

Ang, W.S.L., M.M. Blaszynski, J.B. Cai, L.M. Markowitz, E.A. Maunders, A. Norlin, H.R. Womack, F.-W. Li. Genome sequences of two Nostoc strains isolated from hornworts. Microbiology Resource Announcements, in review.  

2024

Suissa, J.S., F.-W. Li, C.S. Moreau. Convergent evolution of nectaries in ferns and the co-option of ant bodyguards from flowering plants. Nature Communications 15: 4392. 

Li C.*, D. Wickell*, L.-Y. Kuo, X. Chen, B. Nie, X. Liao, D. Peng, J. Ji, J. Jenkins, M. Williams, S. Shu, C. Plott, K. Barry, S. Rajasekar, J. Grimwood, X. Han, S. Sun, Z. Hou, W. He, G. Dai, C. Sun, J. Schmutz, J.H. Leebens-Mack, F-W. Li#, L. Wang#. 2024. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proceedings of the National Academy of Sciences USA 121: e2312607121. *Equally contributed; #Corresponding authors

Wickell, D., J. Landis, E. Zimmer. F.-W. Li. 2024. Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a ‘diploids-first’ approach to conservation. Annals of Botany 133: 261–272.

Lafferty, D.C., T.A. Robison, A. Gunadi, P.W. Schafran, L.H. Gunn, J. Van Eck, F.-W. Li. 2024. Biolistic-mediated transformation of hornworts and its application to study pyrenoid protein localization. Journal of Experimental Botany erae243.

Feng, X., J. Zheng, I. Irisarri, H. Yu, B. Zheng, Z. Ali, S. de Vries, J. Keller, J.M.R. Fürst-Jansen, A. Dadras, J.M.S. Zegers, T.P. Rieseberg, A.D. Ashok, T. Darienko, M.J. Bierenbroodspot, L. Gramzow, R. Petroll, F.B. Haas, N. Fernandez-Pozo, O. Nousias, T. Li, E. Fitzek, W.S. Grayburn, N. Rittmeier, C. Permann, F. Rümpler, J. M. Archibald, G. Theißen, J. P. Mower, M. Lorenz, H. Buschmann, K. von Schwartzenberg, L. Boston, R.D. Hayes, C. Daum, K. Barry, I.V. Grigoriev, X. Wang, F.-W. Li, S.A. Rensing, J.B. Ari, N. Keren, A. Mosquna, A. Holzinger, P.-M. Delaux, C. Zhang, J. Huang, M. Mutwil, J. de Vries, Y. Yin. 2024. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nature Genetics 56: 1018–1031.

2023

Li, F.-W. 2023. The chromosome hoarding syndrome of (some) ferns and lycophytes. Nature Reviews Genetics 24: 735–737.

Rahmatpour, N., L.-Y. Kuo, J. Kang, E. Herman, L. Lei, M. Li, S. Srinivasan, R. Z, S.M. Wolniak, C. Delwiche, S. Mount, F.-W. Li. 2023. Analyses of Marsilea vestita genome and transcriptomes do not support widespread intron retention during spermatogenesis. New Phytologist 237: 1490–1494.

Hisanaga, T., S. Wu, P. Schafran, E. Axelsson S. Akimcheva, L. Dolan, F.-W. Li, F. Berger. The ancestral chromatin landscape of land plants. New Phytologist 240: 2085–2101. 

Jiang, H.-W., H.-Y. Wu, C.-H. Wang, C.-H. Yang, J.-T. Ko, H.-C. Ho, M.-D. Tsai, D. Bryant, F.-W. Li, M.-C. Ho. M.-Y. Ho. A relict phycobilisome structure discovered from a thylakoid-free cyanobacterium. Nature Communications 14: 8009.

Schafran, P., F.-W. Li, C.J. Rothfels. 2023. PURC: a program for improved sequence inference for polyploid phylogenetics and other manifestations of the multiple-copy problem. Methods in Molecular Biology 2545:189–206. 

Kumar, S., Y. Wang, Y. Zhou, L. Dillard, F.-W. Li, C.A. Sciandra, N. Sui, R. Zentella, E. Zahn, J. Shabanowitz, D.F. Hunt, M.J. Borgnia, A. Bartesaghi, T.-p. Sun, P. Zhou. 2023. Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY. Nature Communications 14: 1538.

de Vries, S., C. Herrfurth, F.-W. Li, I. Feussner, J. de Vries. 2023. An ancient route towards salicylic acid and its implications for the perpetual Trichormus–Azolla symbiosis. Plant, Cell & Environment 46: 2884–2908. 

De La Cerda, G.Y., J.B. Landis, E. Eifler, A. Hernandez, F.-W. Li, J. Zhang, C.M Tribble, N. Karimi, P. Chan, T. Givnish, S. Strickler, C. Specht. 2023. Balancing read length and sequencing depth: optimizing Nanopore sequencing for monocots with an emphasis on Liliales. Applications in Plant Sciences 11: e11524. 

Song, M.J., C.J. Rothfels, E. Schuettpelz, J. Nitta, L. Huiet, F.-W. Li, K.M. Wefferling. 2023. Resolving deep relationships and revealing ancient whole-genome duplications in Pteridaceae using transcriptomic data. American Fern Journal 113: 191–210. 

Ang, W.S.L.*, O. Burleigh*, S. Frail*, Y.V.S. Santos*, B. Tyagi*, F.-W. Li. 2023. Genome sequence of a symbiotic cyanobacterium from the flowering plant Gunnera tinctoria. Microbiology Resource Announcements e00563-23. *Equally contributed (team project from the Molecular and Cell Biology of Symbiosis course at Marine Biological Laboratory)

Rizzieri, Y.C., A. Lipari, L.H. Gunn, F.-W. Li. 2023. Twelve new bacterial genomes from a non-axenic culture of Griffithsia monilis (Rhodophyta). Microbiology Resource Announcements e00728-23.

2022

Huang, X.*, W. Wang*, T. Gong*, D. Wickell*, L.-Y. Kuo, X. Zhang, J. Wen, H. Kim, F. Lu, H. Zhao, S. Chen, H. Li, W. Wu, C. Yu, S. Chen, W. Fan, S. Chen, X. Bao, L. Li, D. Zhang, L. Jiang, X. Yan, Z. Liao, G. Zhou, Y. Guo, J. Ralph, R.R. Sederoff, H. Wei#, P. Zhu#, F.-W. Li#, R. Ming#, Q. Li#. 2022. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. Nature Plants 8: 500–512. Cover *Equally contributed; #Corresponding authors
     Featured in: Science, New York Times, Scientific American

Robison, T.A., J.M. Nelson, D.A. Hauser, L.A. Lewis, F.-W. Li. 2022. Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon. American Journal of Botany 6: 939–951.
     Featured in: The Hill, Slate, Blavity, Cornell Chronicle

Petlewski, A.R., D.A. Hauser, M. Kim, J. Schmutz, J. Grimwood, F.-W. Li. 2022. Re-evaluating the systematics of Dendrolycopodium using restriction-site associated DNA-sequencing. Frontiers in Plant Science 13: 912080.

Ke, B-.F., G.-J. Wang, P.H. Labiak, G. Rouhan, Goflag Consortium, C.-W. Chen, L. Shepherd, D.J. Ohlsen, M.A.M. Renner, K.G. Karol, F.-W. Li, L.-Y. Kuo. 2022. Systematics and plastome evolution in Schizaeaceae. Frontiers in Plant Science 13: 885501.

Chatterjee, P., P. Schafran, F.-W. Li, J.C. Meeks. 2022. Nostoc talks back: Differential gene expression during nitrogen starvation of Anthoceros and establishment of its symbiosis with Nostoc. Molecular Plant-Microbe Interactions 35: 917–932.

Gunadi, A., F.-W. Li, J. Van Eck. 2022. Accelerating the gametophyte growth of the model hornwort Anthoceros agrestis (Anthocerotaceae). Applications in Plant Sciences 10: e11460.

Neubauer, A., S. Ruaud, M. Waller, E. Frangedakis, F.-W. Li, S.I. Nötzold, S. Wicke, A. Bailly, P. Szövényi. 2022. Step-by-step protocol for isolation and transient transformation of hornwort protoplasts. Applications in Plant Sciences 10: e11456.

Petlewski, A.R., A. Patterson, F.-W. Li. 2022. Characterizing culturable bacterial endophytes of five Lycopodiaceae species. American Fern Journal 112: 79–92.

Trigoboff, N., F.-W. Li. 2022. Crepidomanes intricatum (Hymenophyllaceae), a sporophyte-less filmy fern new to Central New York. American Fern Journal 112: 139–141.

Powell, A.F. J. Zhang, D.A. Hauser, J. Vilela, A. Hu, D.J. Gates, L.A. Mueller, F.-W. Li, S. Strickler, S.D. Smith. 2022. Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae. The Plant Genome e20223. 

2021

Li, F.-W. 2021. Decolonizing botanical genomics. Nature Plants 7: 1542–1543. 

Wickell, D., L.-Y. Kuo, H.-P. Yang, A.D. Ashok, I. Irisarri, A. Dadras, S. de Vries, J. de Vries, Y.-M. Huang, Z. Li, M.S. Barker, N.T. Hartwick, T.P. Michael, F.-W. Li. 2021. Underwater CAM photosynthesis elucidated by Isoetes genome. Nature Communications 12: 6348. 
     Featured in: Cornell Chronicle

Rahmatpour, N., D.A. Hauser, J.M. Nelson, P.Y. Chen, J.C. Villarreal, M.-Y. Ho, F.-W. Li. 2021. A novel thylakoid-less isolate fills a billion-year gap in the evolution of Cyanobacteria. Current Biology 31: 2857–2867. Cover
     Featured in: Cornell Chronicle, Current Biology Dispatch

Szövényi, P., A. Gunadi, F.-W. Li. 2021. Charting the genomic landscape of seed-free plants. Nature Plants 7: 554–565.

Yang, H.-P., M. Wenzel, D.A. Hauser, J.M. Nelson, X. Xu, M. Eliáš, F.-W. Li. 2021. Monodopsis and Vischeria genomes shed new light on the biology of eustigmatophyte algae. Genome Biology and Evolution 13: evab233.

Nelson, J.M., D.A. Hauser, F.-W. Li. 2021. The diversity and community structure of symbiotic cyanobacteria in hornworts inferred from long-read amplicon sequencing. American Journal of Botany 108: 1731–1744. 
     Featured in: AJB News and Views 

Frangedakis, E., M. Waller, T. Nishiyama, H. Tsukaya, X. Xu, Y. Yue, M. Tjahjadi, A. Gunadi, J. Van Eck, F.-W. Li, P. Szövényi, K. Sakakibara. 2021. An Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis. New Phytologist 232: 1488–1505.

Frangedakis, E., M. Shimamura, J.C. Villarreal, F.-W. Li, M. Tomaselli, M. Waller, K. Sakakibara, K.S. Renzaglia, and P. Szövényi. 2021. The hornworts: morphology, evolution and development. New Phytologist 229: 735–754. Cover

2020

Li, F.-W., T. Nishiyama, M. Waller, E. Frangedakis, J. Keller, Z. Li, N. Fernandez-Pozo, M.S. Barker, T. Bennett, M.A. Blázquez, S. Cheng, A.C. Cuming, J. de Vries, S. de Vries, P.-M. Delaux, I.S. Diop, J. Harrison, D. Hauser, J. Hernández-García, A. Kirbis, J.C. Meeks, I. Monte, S.K. Mutte, A. Neubauer, D. Quandt, T. Robison, M. Shimamura, S.A. Rensing, J.C. Villarreal, D. Weijers, S. Wicke, G.K.-S. Wong, K. Sakakibara, P. Szövényi. 2020. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nature Plants 6: 259–272.
     Featured in: Cornell Chronicle

Radhakrishnan, G.V, J. Keller, M.K. Rich, T. Vernié, D.L. Mbaginda, N. Vigneron, L. Cottret, H.S. Clemente, C. Libourel, J. Cheema, A.-M. Linde, D.M. Eklund, S. Cheng, G.K.-S. Wong, U. Lagercrantz, F.-W. Li, G.E.D. Oldroyd, P.-M. Delaux. 2020. An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses. Nature Plants 6: 280–289.

Kuo, L.-Y., Y.-H. Chang, Y.-H. Huang, W. Testo, A. Ebihara, G. Rouhan, L.G. Quintanilla, J.E. Watkins Jr, Y.-M. Huang, F.-W. Li. 2020. A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision, historical biogeography and evolution of leaf architecture. Cladistics 36: 164–183. 

Wickell, D.A. and F.-W. Li. 2020. On the evolutionary significance of horizontal gene transfers in plants. New Phytologist 225: 113–117.

Windham, M.D., K.M. Pryer, D.B. Poindexter,  F.-W. Li, C.J. Rothfels, and J.B. Beck. 2020. A step‐by‐step protocol for meiotic chromosome counts in flowering plants: A powerful and economical technique revisited. Applications in Plant Sciences 8: e11342.

Bell, D., Q. Lin, W.K. Gerelle, S. Joya, Y. Chang, Z.N. Taylor, C.J. Rothfels, A. Larsson, J.C. Villarreal, F.-W. Li, L. Pokorny, P. Szövényi, B. Crandall-Stotler, L. DeGironimo, S.K. Floyd, D.J. Beerling, M.K. Deyholos, M. von Konrat, S. Ellis, A.J. Shaw, T. Chen, G.K.-S. Wong, D.W. Stevenson, J.D. Palmer, S.W. Graham. 2020. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships, and provide new insights into bryophyte molecular evolution. American Journal of Botany 107: 91–115.

Bouchard, R., Peñaloza-Bojacá, G., S. Toupin, Y. Guadalupe, J. Gudiño, N. Salazar Allen, F.-W. Li, J.C. Villarreal. 2020. Contrasting bacteriome of the hornwort Leiosporoceros dussii in two nearby sites with emphasis on the hornwort-cyanobacterial symbiosis. Symbiosis 81:39–52.

Dawes, T., J.C. Villarreal, P. Szövényi, I. Bisang, F.-W. Li, D.A. Hauser, D. Quandt, D.C. Cargill, L.L. Forrest. 2020. Extremely low genetic diversity in the European clade of the model bryophyte Anthoceros agrestis. Plant Systematics and Evolution 306: 49.

2019

Delaux, P.-M., A.J. Hetherington, Y. Coudert, C. Delwiche, C. Dunand, S. Gould, P. Kenrick, F.-W. Li, H. Philippe, S.A. Rensing, M. Rich, C. Strullu-Derrien, J. de Vries. 2019. Reconstructing trait evolution: A guideline for plant evo-devo studies (and beyond). Current Biology 29: R1105–R1121.

One Thousand Plants Initiative. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574: 679–685. Reprint PDF, Cover (image shot by Alaina!!)

Nelson, J.M., D.A. Hauser, J.A. Gudiño, Y.A. Guadalupe, J.C. Meeks, N. Salazar, J.C. Villarreal, F.-W. Li. 2019. Complete genomes of symbiotic cyanobacteria clarify the evolution of Vanadium-nitrogenase. Genome Biology and Evolution 11: 1959–1964. Reprint PDF

Petlewski, A.R. and F.-W. Li. 2019. Ferns: the final frond-tier in plant model systems. American Fern Journal 109:192–211 (2019). Reprint PDF

Kuo, L.-Y. and F.-W. Li. 2019. A roadmap for fern genome sequencing. American Fern Journal 109:212–223. Reprint PDF

Eily, A.N., K.M. Pryer, F.-W. Li. 2019. A first glimpse at genes important to the Azolla–Nostoc symbiosis. Symbiosis 78: 149–162. Reprint PDF

Kuo, L.-Y., T.-C. Hsu, Y.-S. Chao, W.-T. Liou, H.-M. Chang, C.-W. Chen, Y.-M. Huang, F.-W. Li, Y.-F. Huang, W. Shao, P.-F. Lu, C.-W. Chen, Y.-H. Chang, W.-L, Chiou. 2019. Updating Taiwanese pteridophyte checklist: a new phylogenetic classification. Taiwania 64: 367–395. Reprint PDF

Li, F.-W. and S. Mathews. 2019. Phylogenetic method to study light signaling. In A. Hiltbrunner (Ed.), Phytochromes: Methods and Protocols. Springer Nature (New York). 

Wu, C.-C., F.-W. Li, E.M. Kramer. 2019 Large-scale phylogenomic analysis suggests three ancient superclades of the WUSCHEL-RELATED HOMEOBOX transcription factor family in plants. PLoS ONE 14: e0223521. Reprint PDF

Yang, E. J., C. Y. Yoo, J. Liu, H. Wang, J. Cao, F.-W. Li, K.M. Pryer, T.-P. Sun, D. Weigel, P. Zhu, M. Chen. 2019. NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches. Nature Communications 10: 2630. Reprint PDF

2018

Li, F.-W., P. Brouwer, L. Carretero-Paulet, S. Cheng, J. de Vries, P.-M. Delaux, A.N. Eily, N. Koppers, L.-Y. Kuo, Z. Li, M. Simenc, I. Small, E. Wafula, S. Angarita, M.S. Barker, A. Braeutigam, C. dePamphilis, S. Gould, P.S. Hosmani, Y.-M. Huang, B. Huettel, Y. Kato, X. Liu, S. Maere, R. McDowell, L.A. Mueller, K.G.J. Nierop, S.A. Rensing, T. Robison, C.J. Rothfels, E.M. Sigel, Y. Song, P.R. Timilsina, Y. Van de Peer, H. Wang, P. K.I. Wilhelmsson, P.G. Wolf, X. Xu, J.P. Der, H. Schluepmann, G.K.-S. Wong, and K.M. Pryer. 2018. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants 4: 460–472. Reprint PDF, Cover
     Featured in: Discover Magazine, Mongabay, Cosmos, Mother Nature Network, Earth.com, Quartz, Yale Environmental 360, NSF Science360 News, Cornell Chronicle, BTI press release, Faculty of 1000, Nature Plants News&Views

Li, F.-W., and A. Harkess. 2018. A guide to sequence your favorite plant genomes. Applications in Plant Sciences [special issue “Methods for Exploring the Plant Tree of Life”] 6: e1030. Reprint PDF

Kuo, L.-Y., X Qi, H. Ma, F.-W. Li. 2018. Order-level fern plastome phylogenomics: new insights from Hymenophyllales. American Journal of Botany 105: 1545-1555.

Song, M*., L.-Y. Kuo*, L. Huiet, K.M. Pryer, C.J. Rothfels, F.-W. Li. 2018. A novel chloroplast gene reported for flagellate plants. American Journal of Botany 105: 117–121. Reprint PDF
*Equally contributed
     Featured in: AJB News and Views 

Huiet, L., F.-W. Li, T.-T. Kao, J. Prado, A.R. Smith, E. Schuettpelz, K.M. Pryer. 2018. A worldwide phylogeny of Adiantum (Pteridaceae) reveals remarkable convergent evolution in leaf blade architecture. Taxon 67: 488-502. Reprint PDF

Cheng, S., M. Melkonian, S. Smith, S. Brockington, J.M. Archibald, P.-M. Delaux, F.-W. Li, B. Melkonian, E.V. Mavrodiev, W. Sun, Y. Fu, H. Yang, D.E. Soltis, S.W. Graham, P.S. Soltis, X. Liu, X. Xu, G.K.-S. Wong. 2018. 10KP: A Phylodiverse Genome Sequencing Plan. GigaScience 7: giy013. Reprint PDF 

Kuo  L.-Y., T.-Y. Tang, F.-W. Li, H.-J. Su, W.-L. Chiou, Y.-M. Huang, C.-N. Wang. 2018. Organelle genome inheritances in Deparia ferns (Athyriaceae, Aspleniineae, Polypodiales). Frontiers in Plant Science 9: 486. Reprint PDF

Dijkhuizen, L., P. Brouwer, H. Bolhuis, G.-J. Reichart, N. Koppers, B. Huettel, A. Bolger, F.-W. Li, S. Cheng, X. Liu, G.K.-S. Wong, K.M. Pryer, A. Weber, A. Bräutigam, H. Schluepmann. 2018. Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N₂ but may denitrify. New Phytologist 217: 453-466. Reprint PDF

Villarreal, J.C., M. Turmel, M. Bourgouin-Couture, J. Laroche, N. Salazar, F.-W. Li, S. Chen, K. Renzaglia, C. Lemieux. Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing and its increase during hornwort diversification. PLoS ONE. 13: e0200491. Reprint PDF

Schilling, M.P., Z. Gompert, F.-W. Li, M.D. Windham, P.G. Wolf. 2018. Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade. BMC Evolutionary Biology 18: 61. Reprint PDF

Lang, D., K. Ullrich, F. Murat, J. Fuchs, J. Jenkins, F. Haas, M. Piednoel, H. Gundlach, M. Van Bel, R. Meyberg, C. Vives, J. Morata, A. Symeonidi, M. Hiss, W. Muchero, Y. Kamisugi, O, Saleh, G. Blanc, E. Decker, N. van Gessel, J. Grimwood, R. Hayes, S. Graham, L. Gunter, S. McDaniel, S. Hoernstein, A. Larsson, F.-W. Li, P.-F. Perroud, J. Philipps, P. Ranjan, D. Rokhsar, C.J. Rothfels, L. Schneider, S. Shu, D. Stevenson, F. Thümmler, M. Tillich, J.C. Villarreal, T. Widiez, G.K.-S. Wong, A. Wymore, Y. Zhang, A. Zimmer, R. Quatrano, K. Mayer, D. Goodstein, J. Casacuberta, K. Vandepoele, R. Reski, A. Cuming, G. Tuskan, F. Maumus, J. Salse, J. Schmutz, S. Rensing. 2018. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant Journal 93: 515-533. Reprint PDF

2017

Li, F.-W., J.C. Villarreal, P. Szovenyi. 2017. Hornworts, an overlooked window into carbon-concentrating mechanism. Trends in Plant Science 22: 275-277. Reprint PDF

2016

Li, F.-W., L.-Y. Kuo, K.M. Pryer, C.J. Rothfels. 2016. Genes translocated into the plastid inverted repeat show a marked deceleration in substitution rates and an elevated GC content. Genome Biology and Evolution 8: 2452-2458. Reprint PDF; Cover 

Li, F.-W., L.Y. Kuo, Y.H. Chang, T.C. Hsu, H.C. Hung, W.L. Chiou, C.J. Rothfels, Y.M. Huang. 2016. Asplenium pifongiae (Aspleniaceae: Polypodiales), a new species from Taiwan. Systematic Botany 41: 24-31. Reprint PDF

Hsu, P.Y., L. Calviello, H.-.Y. L. Wu*, F.-W. Li*, C.J. Rothfels, U. Ohler, P.N. Benfey. 2016. Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proceedings of the National Academy of Sciences USA 113: E7126-E7135. Reprint PDF
     *Equally contributed 

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. 2016. Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants. Proceedings of the National Academy of Sciences USA 113: 12328-12333. Reprint PDF

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. 2016. 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. Plant Cell 28 1310–1327. Reprint PDF

Pryer, K.M., L. Huiet, F.-W. Li, C.J. Rothfels, E. Schuettpelz. 2016. Maidenhair ferns, Adiantum, are indeed monophyletic, and sister to to the shoestring ferns, vittaroids (Pteridaceae). Systematic Botany 41: 14-23. Reprint PDF

The Pteridophyte Phylogeny Group. 2016. A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution 54: 563-603. Reprint PDF

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. 2015. Phytochrome diversity in green plants and the origin of canonical plant phytochromes. Nature Communications 6: 7852. Reprint PDF
     Featured in: Duke Today, Science Daily, Phys.org, Faculty of 1000

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. 2015. The origin and evolution of phototropins in plants. Frontiers in Plant Science: 6: 637. Reprint PDF

Li, F.-W., S. Mathews. 2015. Evolutionary aspects of plant photoreceptors [invited review]. Journal of Plant Research 129: 115-122. Reprint PDF

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. 2015. The evolutionary history of ferns inferred from 25 single-copy nuclear genes. American Journal of Botany 102: 1089-1107. Reprint PDF

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. 2015. Searching for diamonds in the apomictic rough: A case study involving Boechera lignifera (Brassicaceae). Systematic Botany 40: 1031-1044. Reprint PDF

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. 2015. An exploration into fern genome space. Genome Biology and Evolution 7: 2533-2544. Reprint PDF

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. 2014. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences USA, 111: 6672-6677. Reprint PDF
     Featured in: New York Times, The Economist, National Geographic, Scientific American, Aeon, Faculty of 1000, Current Biology, Nature Reviews Genetics

Li, F.-W., K.M. Pryer. 2014. Crowdfunding the Azolla fern genome project: a grassroots approach. GigaScience, 3: 16. Reprint PDF
     Featured in: GigaScience Editor’s pick

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. 2014. Between two fern genomes. GigaScience, 3:15. Reprint PDF

Zhang, W.Y., L.Y. Kuo, F.-W. Li, C.N. Wang, W.L. Chiou. 2014. The hybrid origin of Adiantum meishanianum (Pteridaceae): a rare and endemic species in Taiwan. Systematic Botany, 39: 1034-1041. Reprint PDF

2009-2013

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. 2013. Transcriptome-mining for fern single-copy nuclear regions. PLoS One 8: e76957. Reprint PDF

Li, F.-W., K.M. Pryer, M.D. Windham. 2012. Gaga, a new genus segregated from Cheilanthes (Pteridaceae). Systematic Botany 37: 845-860. Reprint PDF
     Featured in: New York Times, Rolling Stone, National Geographic, Huffington Post, Wired, The Guardian

Li, F.-W., L.Y. Kuo, C.J. Rothfels, A. Ebihara, W.L. Chiou, M.D. Windham, K.M. Pryer. 2011. rbcL and matK earn two thumbs up as the core DNA barcode for ferns. PLoS One 6: e26597. Reprint PDF

Li, F.-W. 2011. Book review: Knapp, Ralf. 2011. Ferns and Fern Allies of Taiwan. Taxon 60: 1233-1234. Reprint PDF

Kuo*, L.Y., F.-W. Li*, W.L. Chiou, C.N. Wang. 2011. The first insight into fern matK phylogeny. Molecular Phylogenetics and Evolution 59: 556-566. Reprint PDF
     *Equally contributed 

Li*, F.-W., L.Y. Kuo*, Y.M. Huang, W.L. Chiou, C.N. Wang. 2010. Tissue-Direct PCR, a rapid and extraction-free method for barcoding of ferns. Molecular Ecology Resources 10: 92-95. Reprint PDF
     *Equally contributed 

Li, F.-W., B.C. Tan, V. Buchbender, R.C. Moran, G. Rouhan, C.N. Wang, D. Quandt. 2009. Identifying a mysterious aquatic fern gametophyte. Plant Systematics and Evolution 281: 77-86. Reprint PDF