(*equally contributed)
in press or review
Pelosi JA, Davenport R, Barbazuk WB, Sessa EB, Kuo L-Y. An efficient and effective RNA extraction protocol for ferns. In review.
Lin L, Li C, Chang C-C, Du R, Ji J, Kuo L-Y, Wang L, Chen K-H. Contrasting endophytic fungal communities in two Lycopodiaceae plant species: unraveling potential HupA-producing fungi and fungal interactions. In review.
Tseng Y-H*, Kuo L-Y*, Borokini I *, Fawcett S *. The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae. In review.
2024
Kuo L-Y, Su H-J, Koubínová D, Xie P-J, Whitehouse C, Ebihara A, Grant J. 2024. Organellar phylogenomics of Ophioglossaceae fern genera. Frontiers in Plant Science 14: 1294716.
Li C, Wickell D, Kuo L-Y, Chen X, Nie B, Liao X, Peng D, Ji J, Jenkins J, Williams M, et al. 2024. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. Proceedings of the National Academy of Sciences 121: e2312607121.
Shen Z-Y, Terada T, LandryJ-F, Hoare RJB, Kuo L-Y, Chou M-H, Hsu Y-F, Huang J-P. 2024. Systematics and evolutionary dynamics of insect-fern interactions in the specialized fern-spore feeding Cuprininae (Lepidoptera, Stathmopodidae). Molecular Phylogenetics and Evolution 194: 108040.
Xie Q-Y, Kuo L-Y, Chang C, Lin C-J, Chen K-H. Subtropical fern Ophioderma pendulum discloses prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves within epiphytic environments. American Journal of Botany, in press.
2023
Tang SK, Lee P-H, Liou W-T, Lin C-H, Huang Y-M, and Kuo L-Y. 2023. Fern spores－“ready-to-use” standards for plant genome size estimation using a flow cytometric approach. Plants 12: 140.
Xie P-J, Ke Y-T, Kuo L-Y. 2023. Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns. Applications in Plant Sciences 11: e11526.
Salino A, Rouhan G, Kuo L-Y, Almeida TE. 2023. Editorial: Biology, systematics, and evolution of ferns and lycophytes in the omics era. Frontiers in Plant Science 14: 1146829.
Helsen K*, Viana J*, Lin T-Y, Kuo L-Y, Zelený D. Comparing trait syndromes between Taiwanese subtropical terrestrial and epiphytic ferns at the species and community level. Journal of Vegetation Science 34: e13220.
Ebihara A, Tagane S, Hirota SK, Suyama Y, Kuo L-Y. 2023. Resurrection of Spicantopsis hancockii (Blechnaceae) as an endemic species to Taiwan － Reidentification of Spicantopsis in the Tokara Islands, Japan. Taiwania 68: 148–154.
Rahmatpour N, Kuo L-Y, Kang J, Herman E, Lei L, Li M, Srinivasan S, Zipper R, Wolniak SM, Delwiche C, et al. 2023. Analyses of Marsilea vestita genome and transcriptomes do no support widespread intron retention during spermatogenesis. New Phytologist 237: 1490–1494.
Sundue M, Triana-Moreno LA, Yañez A, Kuo L-Y, Rothfels CJ, Pena NTL, Schwartsburd PB. 2023. Phylogenetic revision of Dennstaedtioideae (Dennstaedtiaceae: Polypodiales) with description of Mucura, gen. nov. Taxon 72: 20–46.
2022
Ke B-F, Wang G-J, Labiak PH, Rouhan G, GoFlag Consortium, Chen C-W, Shepherd L, Ohlsen DJ, Renner MAM, Karol KG, Li F-W, Kuo L-Y. 2022. Systematics and plastome evolution in Schizaeaceae. Frontiers in Plant Science 13: Article 885501.
Quinlan A*, Lee P-H*, Tang T-Y, Huang Y-M, Chiou W-L, Kuo L-Y. 2022. Providing the missing links in fern life history: insights from a phenological survey of the gametophyte stage. Applications in Plant Sciences 10: e11473.
Wu Y-H, Ke Y-T, Chan Y-Y, Wang G-J, Kuo L-Y. 2022. Integrating tissue‐direct PCR into genetic identification: an upgraded molecular ecology way to survey fern field gametophytes. Applications in Plant Sciences: e11462.
Chen K-H, Xi Q-Y, Chang C-C, Kuo L-Y. 2022. Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques. Applications in Plant Sciences 10: e11461.
Huang X, Wang W, Gong T, Wickell D, Kuo L-Y, Zhang X, Wen J, Kim H, Lu F, Li H, et al. 2022. The flying spider-monkey tree fern genome: insights into fern evolution and arborescence. Nature Plants 8: 500–512.
Du X-Y, Kuo L-Y, Zuo Z-Y, Li D-Z, Lu J-M. 2022. Structural variation of plastomes provides key insight into the deep phylogeny of ferns. Frontiers in Plant Science 13: Article 862772.
Lu JM*, Du XY*, Kuo L-Y, Ebihara A, Perrie LR, Zuo ZY, Shang H, ChangY-H, LiD-Z. 2022. Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae. BMC Plant Biology 22: 511.
Triana‐Moreno LA, Schwartsburd PB, Yañez A, Pena NTL, Kuo L-Y, Rothfels C, Sundue M. 2022. (2892) Proposal to conserve the name Dennstaedtia (Dennstaedtiaceae) with a conserved type. Taxon 71: 688–690.
2021
Kuo L-Y, Tang SK, Kao T-T, Ebihara A, Fawcett S, Hsiao M-C, Shinohara W, Dauphin B. 2021. A dormant resource for genome size estimation in ferns: C‐value inference of the Ophioglossaceae using herbarium specimen spores. Applications in Plant Sciences 9: e11452.
Wu Y-H, Sun C-Y, Ebihara A, Lu NT, Rouhan G, Kuo L-Y. 2021. Two new species in the fern genus Lomariopsis (Lomariopsidaceae) from East Asia. PhytoKeys 187: 161–176.
Wickell D, Kuo L-Y, Yang H-P, Ashok AD, Irisarri I, Dadras A, de Vries S, DeVries J, Huang Y-M, Li Z, et al. 2021. Underwater CAM photosynthesis elucidated by Isoetes genome. Nature Communications 12: 6348.
Du X-Y*, Lu J-M*, Zhang L-B, Wen J, Kuo L-Y, Mynssen C, Schneider H, Li D-Z. Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic. Cladistics, doi: 10.1111/cla.12457.
Ebihara A, Nakato N, Chang Y-H, Kuo L-Y. 2021. Coryphopteris castanea (Thelypteridaceae), a Polymorphic Diploid Species Distributed in Taiwan and Japan. Bulletin of the National Museum of Nature and Science, Series B 47: 71–77.
Fawcett S, Smith AR, Sundue M, Burleigh JG, Sessa EB, Kuo L-Y, Chen C-W, Testo WL, Kessler M, Consortium G, et al. 2021. A global phylogenomic study of the Thelypteridaceae. Systematic Botany 46: 891–915.
Chang Z-X, Hsu T-C, Kuo L-Y. 2021. Four new records for the fern flora of Taiwan. Taiwan Journal of Biodiversity 23: 13–25.
2020
Kuo L-Y, Chang Y-H, Huang Y-H, Testo W, Ebihara A, Rouhan G, Quintanillag LG, Watkins JEJ, Huang Y-M, Li F-W. 2020. A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision, historical biogeography and leaf architecture. Cladistics 26: 164–183.
Chang Z-X*, Kuo L-Y*, P-F Lu, Y-M Huang. New addition to the Asplenium normale complex (Aspleniaceae): an endemic forma in Taiwan. Taiwania, 65: 253–260.
2019
Kuo L-Y, Li F-W. 2019. A roadmap for fern genome sequencing. American Fern Journal 109: 212–223.
TPG. 2019. Updating Taiwanese pteridophyte checklist: a new phylogenetic classification. Taiwania 64: 367–395.
Ebihara A, Nakato N, Kuo L-Y, Miyazaki H, Serizawa S. 2019. Allopolyploid origin and distribution range of Acystopteris taiwaniana (Cystopteridaceae: Polypodiales). Acta Phytotaxonomica et Geobotanica 70: 19–28.
2018
Kuo L-Y, Ebihara A, Kato M, Rouhan G, Ranker TA, Wang C-N, Chiou W-L. 2018. Morphological characterization of infra-generic lineages in Deparia (Athyriaceae; Polypodiales). Cladistics 34: 78–92.
Kuo L-Y, Tang T-Y, Li F-W, Su H-J, Chiou W-L, Huang Y-M, Wang C-N. 2018. Organelle genome inheritance in Deparia ferns (Athyriaceae, Aspleniineae, Polypodiales). Frontiers in Plant Science 9: Article 486.
Kuo L-Y, Qi X, Huang Y-M, H. Ma, Li F-W. 2018. Order-level fern plastome phylogenomics: new insights from Hymenophyllales. American Journal of Botany 105: 1545–1555.
Kuo L-Y, Ebihara A, Hsu T-C, Rouhan G, Huang Y-M, Wang C-N, Chiou W-L, Kato M. 2018. Infrageneric revision of the fern genus Deparia (Athyriaceae, Aspleniineae, Polypodiales). Systematic Botany 43: 645–655.
Song M*, Kuo L-Y*, Huiet L, Pryer KM, Rothfels CJ, Li F-W. 2018. A novel chloroplast gene reported for flagellate plants. American Journal of Botany 105: 117–121.
Li F-W, Carretero-Paulet L, Cheng S, Vries J de, Delaux P-M, Eily A, Koppers N, Kuo L-Y, Li Z, Simenc M, et al. 2018. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants 4: 460–472.
Qi X, Kuo L-Y, Guo C, Li H, Li Z, Qi J, Wang L, Hu Y, Zhang C, Guo J, et al. 2018. A well-resolved fern nuclear phylogeny and expansion of numerous transcription factor families. Molecular Phylogenetics and Evolution 127: 961–977.
Chen C-W, Lindsay S, Mynssen CM, Kuo L-Y, Amoroso VB, Huang Y-M. 2018. A new Haplopteris species from the Philippines and clarification of the status of H. amboinensis in China and Indochina. Gardens’ Bulletin Singapore 70: 177–190.
2017
Kuo L-Y, Huang Y-J, Chang J, Chiou W-L, Huang, Y-M. 2017. Evaluating the spore genome sizes of ferns and lycophytes: a flow cytometry approach. New Phytologist 213: 407–416.
Kuo L-Y*, Chen C-W*, Shinohara W, Ebihara A, Kudoh H, Sato H, Huang Y-M, Chiou W-L. 2017. Not only in the temperate zone: independent gametophytes of two vittarioid ferns (Pteridaceae, Polypodiales) in East Asian subtropics. Journal of Plant Research 130: 255–262.
Kuo L-Y, Huang Y-M. 2017. Determining genome size from spores of seedless vascular plants. Bioprotocol 7: e2322.
Chen C-W, Lindsay S, Kuo L-Y, Fraser-Jenkins CR, Ebihara A, Luu HT, Park CW, Chao YS, Huang Y-M, Chiou W-L. 2017. A systematic study of East Asian vittarioid ferns (Pteridaceae, Vittarioideae). Botanical Journal of the Linnean Society 187: 545–560.
Chen C-W*, Sundue M*, Kuo L-Y, Huang Y-M. 2017. Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae. PhytoKeys 78: 83–107.
Hori K, Kuo L-Y, Chiou W-L, Ebihara A, Murakami, N. 2017. Geographical distribution of sexual and apogamous types of Dryopteris formosana and Dryopteris varia (Dryopteridaceae) in Taiwan. Acta Phytotaxonomica et Geobotanica 68: 23–32.
Pinson JB, Chambers SM, Nitta JH, Kuo L-Y, Sessa EB. 2017. The separation of generations: biology and biogeography of long-lived sporophyteless fern gametophytes. International Journal of Plant Sciences 178: 1–18.
You C*, Cui J*, Wang H, Qi X, Kuo L-Y, Ma H, Gao L, Mo B, Chen X. 2017.Conservation and divergence of small RNA pathways and microRNAs in land plants. Genome Biology 18: 158.
Tseng M-H, Lin K-H, Huang Y-J, Chang Y-L, Huang S-C, Kuo L-Y, Huang Y-M. 2017. Detection of chlorophylls in spores of seven ferns. Journal of Plant Research 130: 407–416.
2016
Kuo L-Y, Ebihara A, Shinohara W, Rouhan G, Wood KR, Wang C-N, Chiou W-L. 2016. Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy. Molecular Phylogenetics and Evolution 104: 123–134.
Kuo L-Y, Chang Y-H, Glowienka JMO, Amoroso VB, Dong S-Y, Kao T-T, Wang C-N, Chiou W-L. 2016. A revised framework of Dryopteris subg. Nothoperanema (Dryopteridaceae) inferred from phylogenetic evidence, with descriptions of two new sections. Systematic Botany 41: 596–605.
Kuo L-Y, Hsu T-C, Chang Y-H, Huang Y-M, Chiou W-L. 2016. Systematics of the Adiantum philippense complex (Pteridaceae, Polypodiales) in Taiwan. Phytotaxa 263: 113–121.
Li F-W*, Kuo L-Y*, Chang Y-H, Hsu T-C, Hung H-C, Chiou W-L, Rothfels CJ, Huang Y-M. 2016. Asplenium pifongiae (Aspleniaceae: Polypodiales), a new species from Taiwan. Systematic Botany 41: 24–31.
Ebihara A, Nakato N, Amoroso VB, Hidayat A, Kuo L-Y. 2016. The Japanese endemic Monachosorum arakii Tagawa (Dennstaedtiaceae) is a relict ‘inter-national’ hybrid: a reassessment of the Monachosorum species. Systematic Botany 41: 586–595.
Li F-W, Kuo L-Y, Pryer KM, Rothfels CJ. 2016. Genes translocated into the plastid inverted repeat show decelerated substitution rates and elevated GC content. Genome Biology and Evolution 8: 2452–2458. (2017 5-year-IF: 4.171, 24.6% ranked in Genetics & Heredity)
Pteridophyte Phylogeny Group I. 2016. A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution 54: 563–603.
2014
Zhang W-Y*, Kuo L-Y*, Li F-W, Wang C-N, Chiou W-L. 2014. The hybrid origin of Adiantum meishanianum (Pteridaceae): a rare and endemic species in Taiwan. Systematic Botany 39: 1034–1041. (2017 5-year-IF: 1.515, 45% ranked in Plant Sciences)
Ebihara A, Nakato N, Matsumoto S, Chao Y-S, Kuo L-Y. 2014. Cytotaxonomic studies on thirteen ferns of Taiwan. Bulletin of the National Museum of Nature and Science. Series B, Botany 40: 19–28.
2013
Chang Y-H, Kuo L-Y, Chiou W-L, Chen C-W, Chang H-M, Amoroso VB. 2013. Stenolepia Alderw. (Dryopteridaceae), a fern genus new to the Philippines. Philippine Journal of Science 142: 83–88.
Chen C-W, Huang Y-M, Kuo L-Y, Chang Y-H, Liu Y-C, Chiou W-L. 2013. A new vittarioid fern species, Haplopteris heterophylla (Pteridaceae). Systematic Botany 38: 901–909.
Chen C-W, Huang Y-M, Kuo L-Y, Nguyen QD, Luu HT, Callado JR, Farrar DR, Chiou W-L. 2013. TrnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae). Annals of Botany 111: 663–673.
2012
Rothfels CJ*, Larsson A*, Kuo L-Y*, Korall P, Chiou W-L, Pryer KM. 2012. Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns. Systematic Biology 61: 490–509.
Chen C-W, Kuo L-Y, Wang C-N, Chiou W-L. 2012. Development of PCR primer sets for intron 1 of the low-copy gene LEAFY in Davalliaceae. American Journal of Botany 99: e223–225.
Rothfels CJ*, Sundue MA*, Kuo L-Y, Larsson A, Kato M, Schuettpelz E, Pryer KM. 2012. A revised family-level classification for eupolypod II ferns (Polypodiidae: Polypodiales). Taxon 61: 515–533. (2017 5-year-IF: 2.680, 23.9% ranked in Plant Sciences)
2011
Kuo L-Y*, Li F-W*, Chiou W-L, Wang C-N. 2011. First insights into fern matK phylogeny. Molecular Phylogenetics and Evolution 59: 556–566. (2017 5-year-IF: 4.294, 19.9% ranked in Genetics & Heredity)
Li F-W, Kuo L-Y, Rothfels CJ, Ebihara A, Chiou W-L, Windham MD, Pryer KM. 2011. RbcL and matK earn two thumbs up as the core DNA barcode for ferns. PLoS ONE 6: e26597.
2010
Li F-W*, Kuo L-Y*, Huang Y-M, Chiou W-L, Wang C-N. 2010. Tissue-direct PCR, a rapid and extraction-free method for barcoding of ferns. Molecular Ecology Resources 10: 92–95.