Publications

in review

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. in review. 

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

Kuo, L.-Y., X Qi, H. Ma, F.-W. Li. Order-level fern plastome phylogenomics: new insights from Hymenophyllales. in review.

2018

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

Song, M*., L.-Y. Kuo*, L. Huiet, K.M. Pryer, C.J. Rothfels, F.-W. Li. A novel chloroplast gene reported for flagellate plants. American Journal of Botany. in press.
*Equally contributed

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. 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. in press.

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. The P. patens chromosome-scale assembly reveals moss genome structure and evolution. Plant Journal. in press.

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

Li, F.-W., C.A. Rushworth, J.B. Beck, M.D. Windham. 2017. Boechera Microsatellite Website: an online portal for species identification and hybrid relationship resolution. Database 1: baw169. Reprint PDF
Source code, Website

Rockwell, N.C., S.S. Martin, F.-W. Li, S. Mathews, J.C. Lagarias. 2017. The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2. New Phytologist 214: 1145-1157. Reprint PDF

Rothfels, C.J., K.M. Pryer, F.-W. Li. 2017. Next-generation polyploid phylogenetics: Rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. New Phytologist 213: 413-429. Reprint PDF
*I am the major developer of the PURC pipeline. Source code 

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

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 ArabidopsisProceedings 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 inDuke 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

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

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

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, AeonFaculty 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 TimesRolling Stone, National GeographicHuffington 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