Publications – Fay-Wei Li

Decolonizing botanical genomics
2021.
Li, Fay-Wei
Nat. Plants.
:
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The diversity and community structure of symbiotic cyanobacteria in hornworts inferred from long-read amplicon sequencing
2021.
Nelson, J.M., Hauser, D.A., Li, Fay-Wei
American Journal of Botany.
108
:
1731–1744
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Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae
2021.
Yang, H.-P., Wenzel, M., Hauser, D.A., Nelson, J.M., Xu, X., Eliáš, M., Li, Fay-Wei
Genome Biology and Evolution.
13
:
evab233
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Underwater CAM photosynthesis elucidated by Isoetes genome.
2021.
Wickell, D., Kuo, L.Y., Yang, H.P., Dhabalia, A.A., Irisarri, I., Dadras, A., de Vries, S., de Vries…
Nat Commun..
12
:
6348
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An Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis
2021.
Frangedakis, E., Waller, M., Nishiyama, T., Tsukaya, H., Xu, X., Yue, Y., Tjahjadi, M., Gunadi, A., …
New Phytologist.
232
:
1488–1505
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A novel thylakoid-less isolate fills a billion-year gap in the evolution of Cyanobacteria
2021.
Rahmatpour, N., Hauser, D.A., Nelson, J.M., Chen, P.Y., Villarreal, J.C., Ho, M.Y., Li, Fay-Wei
Current Biology.
31
:
2857–2867
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Charting the genomic landscape of seed-free plants
2021.
Szövényi, P., Gunadi, A., Li, Fay-Wei
Nat Plants..
7
:
554–565
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The Hornworts: Morphology, evolution and development
2021.
Frangedakis, E., Shimamura, M., Villarreal, J.C., Li, Fay-Wei, Tomaselli, M., Waller, M., Sakakibara…
New Phytol..
229
:
735–754
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A step-by-step protocol for meiotic chromosome counts in flowering plants: A powerful and economical technique revisited.
2020.
Windham, M.D., Pryer, K.M., Poindexter, D.B., Li, Fay-Wei, Rothfels, C.J., Beck, J.B.
Appl Plant Sci..
8
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Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future
2020.
Henkhaus, N., Barlett, M., Gang, D., Grumet, R., Jordon-Thaden, I., Lorence, A., Lyons, E., Miller, …
Plant Direct..
4
:
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Contrasting bacteriome of the hornwort Leiosporoceros dussii in two nearby sites with emphasis on the hornwort-cyanobacterial symbiosis
2020.
Bouchard, R. Peñaloza-Bojacá, G., Toupin, S., Guadalupe, Y., Gudiño, J., Salazar Allen, N., Li, F…
Symbiosis.
:
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Extremely low genetic diversity in the European clade of the model bryophyte Anthoceros agrestis
2020.
Dawes, T.N., Villarreal, J.C., Szövényi, P., Bisang, I., Li, Fay-Wei, Hauser, D.A., Quandt, D., Ca…
Plant Systematics and Evolution.
306
:
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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
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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..
6
:
280–289
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On the evolutionary significance of horizontal gene transfers in plants.
2020.
Wickell, D.A., Li, Fay-Wei
New Phytol.
225
:
113–117
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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
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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
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Ferns: the final frond-tier in plant model systems
2019.
Petlewski, A.R., Li, Fay-Wei
American Fern Journal.
109
:
192–211
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A Roadmap for Fern Genome Sequencing
2019.
Kuo, L.Y., Li, Fay-Wei
American Fern Journal.
109
:
212–223
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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
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Phylogenetic Methods to Study Light Signaling
2019.
Li, Fay-Wei, Mathews, S.
Methods Mol Biol.
2026
:
265–276
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
:
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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
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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
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A guide to sequence your favorite plant genomes
2018.
Li, Fay-Wei, Harkess, A.
Applications in Plant Sciences.
6
:
e1030–e1030
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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
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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
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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
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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
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Hornworts: An Overlooked Window into Carbon-Concentrating Mechanisms
2017.
Li, Fay-Wei, Villarreal, J. C., Szövényi, P.
Trends in Plant Science.
22
:
275–277
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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
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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
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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
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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
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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
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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
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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
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Evolutionary aspects of plant photoreceptors
2016.
Li, Fay-Wei, Mathews, S.
Journal of Plant Research.
129
:
115–122
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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
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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
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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
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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
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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
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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
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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
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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
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Gaga, a New Fern Genus Segregated from Cheilanthes (Pteridaceae)
2012.
Li, Fay-Wei, Pryer, K. M., Windham, M. D.
Systematic Botany.
37
:
845–860
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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
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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
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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
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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
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