Publications – Fay-Wei Li

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts
2020.
Li, Fay-Wei, Nishiyama, T., Waller, M., Frangedakis, E., Keller, J., Li, Z., Fernandez-Poze, N., Bar…
Nature Plants.
6
:
259–272
View
An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages.
2020.
Radhakrishnan, G.V., Keller. J., Rich, M.K., Vernié, T., Mbadinga Mbadinga, D.L., Vigneron, N., Cot…
Nat Plants..
:
View
Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution
2019.
Bell, D., Lin, Q., Gerelle, W.K., Joya, S., Chang, Y., Taylor, Z.N., Rothfels, C.J., Larsson, A., Vi…
American Journal of Botany.
107
:
1–25
View
One thousand plant transcriptomes and the phylogenomics of green plants
2019.
Leebens-Mack, J.H., Barker, M.S., Carpenter, E.J., Deyholos, M.K., Gitzendanner, M.A., Graham, S.W.,…
Nature.
574
:
679–685
View
Ferns: the final frond-tier in plant model systems
2019.
Petlewski, A.R., Li, Fay-Wei
American Fern Journal.
109
:
192–211
View
A Roadmap for Fern Genome Sequencing
2019.
Kuo, L.Y., Li, Fay-Wei
American Fern Journal.
109
:
212–223
View
Updating Taiwanese pteridophyte checklist: a new phylogenetic classification
2019.
Chang, H.M., Chen, C.W., Huang, Y.M., Li, Fay-Wei, Huang, Y.F., Shao, W., Lu, P.F., Chen, C.W., Chan…
Taiwania.
64
:
367–395
View
Phylogenetic Methods to Study Light Signaling
2019.
Li, Fay-Wei, Mathews, S.
Methods Mol Biol.
2026
:
265–276
View
Reconstructing trait evolution in plant evo-devo studies.
2019.
Delaux, P.M., Hetherington, A.J., Coudert, Y., Delwiche, C., Dunand, C., Gould, S., Kenrick, P., Li,…
Curr Biol.
29
:
R1110–R1118
View
Large-scale phylogenomic analysis suggests three ancient superclades of the WUSCHEL-RELATED HOMEOBOX transcription factor family in plants.
2019.
Wu, C.C., Li, Fay-Wei, Kramer, E.M.
PLoS One.
14
:
e0223521
View
On the evolutionary significance of horizontal gene transfers in plants.
2019.
Wickell, D.A., Li, Fay-Wei
New Phytol.
225
:
113–117
View
Complete genomes of symbiotic cyanobacteria clarify the evolution of Vanadium-nitrogenase.
2019.
Nelson, J., Hauser, D., Gudiño, J.A., Guadalupe, Y.A., Meeks, J.C., Salazar, N., Villarreal, J.C., …
Genome Biology and Evolution.
11
:
1959–1964
View
NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches
2019.
Yang, E.J., Yoo, C.Y., Liu, J., Wang, H., Cao, J., Li, Fay-Wei, Pryer, K.M., Sun, T.P., Weigel, D., …
Nature Communications.
10
:
2630
View
A first glimpse at genes important to the Azolla–Nostoc symbiosis
2019.
Eily, A.N., Pryer, K.M., Li, Fay-Wei
Symbiosis.
78
:
149–162
View
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
View
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
View
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
View
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
View
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
:
View
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
:
View
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
View
A guide to sequence your favorite plant genomes
2018.
Li, Fay-Wei, Harkess, A.
Applications in Plant Sciences.
6
:
e1030–e1030
View
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
View
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
View
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
View
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
View
Hornworts: An Overlooked Window into Carbon-Concentrating Mechanisms
2017.
Li, Fay-Wei, Villarreal, J. C., Szövényi, P.
Trends in Plant Science.
22
:
275–277
View
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
View
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
:
View
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
View
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
View
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
View
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
View
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
View
A community-derived classification for extant lycophytes and ferns
2016.
Schuettpelz, E., Schneider, H., Smith, A. R., Hovenkamp, P., Prado, J., Rouhan, G., Salino, A., Sund…
Journal of Systematics and Evolution.
54
:
563–603
View
Evolutionary aspects of plant photoreceptors
2016.
Li, Fay-Wei, Mathews, S.
Journal of Plant Research.
129
:
115–122
View
Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance
2016.
Stevenson, S. R., Kamisugi, Y., Trinh, C. H., Schmutz, J., Jenkins, J. W., Grimwood, J., Muchero, W.…
The Plant Cell.
28
:
1310–1327
View
Searching for Diamonds in the Apomictic Rough: A Case Study Involving Boechera lignifera (Brassicaceae)
2015.
Windham, M. D., Beck, J. B., Li, Fay-Wei, Allphin, L., Carman, J. G., Sherwood, D. A., Rushworth, C.…
Systematic Botany.
40
:
1031–1044
View
The origin and evolution of phototropins
2015.
Li, Fay-Wei, Rothfels, C. J., Melkonian, M., Villarreal, J. C., Stevenson, D. W., Graham, S. W., Won…
Frontiers in Plant Science.
6
:
View
An Exploration into Fern Genome Space
2015.
Wolf, P. G., Sessa, E. B., Marchant, D. B., Li, Fay-Wei, Rothfels, C. J., Sigel, E. M., Gitzendanner…
Genome biology and evolution.
7
:
2533–2544
View
The evolutionary history of ferns inferred from 25 low-copy nuclear genes
2015.
Rothfels, C. J., Li, Fay-Wei, Sigel, E. M., Huiet, L., Larsson, A., Burge, D. O., Ruhsam, M., Deyhol…
American Journal of Botany.
102
:
1089–1107
View
Phytochrome diversity in green plants and the origin of canonical plant phytochromes
2015.
Li, Fay-Wei, Melkonian, M., Rothfels, C. J., Villarreal, J. C., Stevenson, D. W., Graham, S. W., Won…
Nature Communications.
6
:
7852–7852
View
Between Two Fern Genomes
2014.
Sessa, E. B., Banks, J. A., Barker, M. S., Der, J. P., Duffy, A. M., Graham, S. W., Hasebe, M., Lang…
GigaScience.
3
:
View
Crowdfunding the Azolla fern genome project: a grassroots approach
2014.
Li, Fay-Wei, Pryer, K. M.
GigaScience.
3
:
View
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
2014.
Li, Fay-Wei, Villarreal, J. C., Kelly, S., Rothfels, C. J., Melkonian, M., Frangedakis, E., Ruhsam, …
Proceedings of the National Academy of Sciences.
111
:
6672–6677
View
The Hybrid Origin of Adiantum meishanianum (Pteridaceae): A Rare and Endemic Species in Taiwan
2014.
Zhang, W. Y., Kuo, L. Y., Li, Fay-Wei, Wang, C. N., Chiou, W. L.
Systematic Botany.
39
:
1034–1041
View
Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns
2013.
Rothfels, C. J., Larsson, A., Li, Fay-Wei, Sigel, E. M., Huiet, L., Burge, D. O., Ruhsam, M., Graham…
PLOS One.
8
:
e76957–e76957
View
Gaga, a New Fern Genus Segregated from Cheilanthes (Pteridaceae)
2012.
Li, Fay-Wei, Pryer, K. M., Windham, M. D.
Systematic Botany.
37
:
845–860
View
First insights into fern matK phylogeny
2011.
Kuo, L. Y., Li, Fay-Wei, Chiou, W. L., Wang, C. N.
Molecular Phylogenetics and Evolution.
59
:
556–566
View
rbcL and matK Earn Two Thumbs Up as the Core DNA Barcode for Ferns
2011.
Li, Fay-Wei, Kuo, L. Y., Rothfels, C. J., Ebihara, A., Chiou, W. L., Windham, M. D., Pryer, K. M.
PLOS One.
6
:
e26597–e26597
View
Tissue-direct PCR, a rapid and extraction-free method for barcoding of ferns
2010.
Li, Fay-Wei, KUO, L. Y., HUANG, Y. M., CHIOU, W. L., WANG, C. N.
Molecular Ecology Resources.
10
:
92–95
View
Identifying a mysterious aquatic fern gametophyte
2009.
Li, Fay-Wei, Tan, B. C., Buchbender, V., Moran, R. C., Rouhan, G., Wang, C. N., Quandt, D.
Plant Systematics and Evolution.
281
:
77–86
View
Support BTI Science!
 

Contact:

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