Li-Yaung Kuo

National Tsing Hua University | NTHU · Institute of Molecular & Cellular Biology

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 million years ago (MYA). Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no genomic data has...

Premise: Efficient protocols for extracting high-molecular-weight (HMW) DNA from ferns facilitate the long-read sequencing of their large and complex genomes. Here, we perform two cetyltrimethylammonium bromide (CTAB)-based protocols to extract HMW DNA and evaluate their applicability in diverse fern taxa for the first time. Methods and results:...

Spicantopsis hancockii (Blechnaceae) was once thought to be endemic to Taiwan, and later known to occur in the Tokara Islands in southern Japan. Because of its high morphological similarity to S. niponica endemic to Japan, the identification of the Tokara Archipelago populations has been controversial. MIG-seq analysis using 2324 SNPs revealed that...

Spores and pollen of plants were used as flow cytometric materials to efficiently infer genome sizes. Given this advantage, they hold great potential for various flow cytometric applications , particularly as plant genome size standards. To develop such novel standards, we investigated conditions of pretreatment (bead vortex), buffer, and reliable...

We undertook a molecular phylogenetic revision of hayscented ferns (Dennstaedtiaceae: Dennstaedtioideae) using four plastid markers. Our sampling represents ca. 40% of the extant diversity and includes the type species for each of the relevant segregate genera. We coded 18 discrete morphological characters which we used to find diagnosable clades....

Background: Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly und...

Hymenophyllum chamaecyparicola T.C.Hsu & Z.X.Chang, a new filmy fern species (Hymenophyllaceae) has been described from Taiwan and illustrated based on morphological and phylogenetic evidence. Although the new species resembles members in the subgenus Mecodium, namely H. wrightii, our plastid phylogeny has revealed that it is genetically distant fr...

While the family Schizaeaceae (Schizaeales) represents only about 0.4% of the extant fern species diversity, it differs from other ferns greatly in gross morphologies, niche preferences, and life histories. One of the most notable features in this family is its mycoheterotrophic life style in the gametophytic stage, which appears to be associated w...

Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns we...

To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome du...

Premise: The entire life cycle of ferns has been documented, yet their life histories are still poorly understood. In particular, the phenology of fern gametophytes remains largely unknown. To address this issue, we demonstrated a new ecological approach to explore the phenological link between spore release and gametophyte maturation within the l...

Premise: The gametophytes of different fern species collected in the field can be difficult to distinguish because of their morphological similarities. Nonetheless, emerging molecular ecology techniques are starting to be used to tackle such limitations. Here, using case studies and a detailed protocol, we demonstrate a convenient methodology, tis...

Premise: Several ferns and lycophytes produce subterranean gametophytes, including the Ophioglossaceae, Psilotaceae, and some members of the Schizaeaceae, Gleicheniaceae, and Lycopodiaceae. Despite the surge in plant-microbiome research, which has been particularly boosted by high-throughput sequencing techniques, the microbiomes of these inconspi...

The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing the approximately 1200 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships, especially for neotropical taxa, hav...

Two East Asian Lomariopsis (Lomariopsidaceae, Polypodiales) species, Lomariopsis moorei and Lomariopsis longini, which were previously misidentified as L. spectabilis, are here described as new species based on evidence from morphological characters and a molecular phylogeny. The two species differ from the three other described species in East Asi...

Premise: The great variation of genome size (C-value) across land plants is linked to various adaptative features. Flow cytometry (FCM), the standard approach to estimating C-values, relies mostly on fresh materials, performing poorly when used with herbarium materials. No fern C-value reports have been derived from herbarium specimens; however, t...

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO 2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has...

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has...

Diploid chromosome number 2n = 62 observed in the Taiwanese populations of Coryphopteris castanea supported the distinctness of this species from tetraploid Thelypteris (Coryphopteris) japonica. Although much variation in frond size was observed across its populations of Taiwan and Iriomote Island in southern Ryukyu of Japan, their alleles of nucle...

Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints refle...

Evolutionary histories of species complexes in ferns are usually complicated with hybridization and polyploidization. In the Asplenium normale D.Don complex, we here identify a new taxon-Asplenium normale f. scythiforme Z.X. Chang, f. nov., by clarifying its position in the reticulated tree of the species complex. Our phylogenetic and flow cytometr...

The thelypteroid fern genus Stegnogramma s.l. contains around 18–35 species and has a global, cross‐continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a gl...

We describe a new species of Stegnogramma (Thelypteridaceae; Polypodiales) as Stegnogramma australis. Morphologically, it is most similar to S. griffithii, sharing the character of pinnate fronds with ternate terminal pinnae. However, S. australis can be distinguished from S. griffithii by having more free pinna pairs, shorter distal stipe hairs, a...

The large genomes of ferns have long deterred genome sequencing efforts. To date, only two heterosporous ferns with remarkably small genomes, Azolla filiculoides and Salvinia cucullata, have been sequenced. However, as sequencing technologies continue to improve and become more affordable, generating high-quality, “normal-sized” fern genomes is wit...

Ferns and lycophytes of Taiwan display an extraordinarily high diversity. Despite the detailed species documentation, the pteridophyte flora of Taiwan as a whole has never been organized into a phylogenetic framework. Here we provide an updated, phylogeny-based checklist that includes a total of 824 (infra)species taxa, of which eleven are first re...

Acystopteris taiwaniana, formerly known only from Taiwan, is newly recorded in Japan (northern and central Honshu and Shikoku). Chromosome counts and DNA sequences (plastid rbcL and nuclear PgiC) suggested that it is an allotetraploid species originating from hybridization between diploid A. japonica and an unknown diploid species. Acystopteris tai...

PREMISE OF THE STUDY: Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To bett...

Current molecular phylogenetic analyses support the monophyly and circumscription of the athyrioid fern genus Deparia (Athyr-iaceae), which includes previously recognized genera including Athyriopsis, 3Depazium, Dictyodroma, Dryoathyrium (5 Parathyrium), Lunathyrium, and Neotriblemma (5 Triblemma Ching), and 3Neotribleparia. This broad generic conc...

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one...

Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 f...

A new fern species from the Philippines, Haplopteris mindanaoensis S.Linds. & C.W.Chen, is described and illustrated based on the results of detailed morphological comparison and molecular phylogenetic analysis. Morphologically, Haplopteris mindanaoensis is characterised by having obovoid (rather than funnel-shaped) soral paraphyses and deep soral...

Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome...

Premise of the study: Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. Methods: We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and mat...

Litchi (Litchi chinensis) is popular fruit in Asia and has been domesticated more than thousand years. Nowadays, it is widely grown in more than 20 countries around subtropical area. However, since growers asexually propagate various cultivars to maintain certain favored traits, the name of these litchi cultivars are usually confusing. Morphologica...

Background As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and fe...

Seedless vascular plants, including ferns and lycophytes, produce spores to initiate the gametophyte stage and to complete sexual reproduction. Approximately 10% of them are apomictic through the production of genomic unreduced spores. Being able to measure the spore nuclear DNA content is therefore important to infer their reproduction mode. Here...

The monotypic fern genus Dryopolystichum Copel. combines a unique assortment of characters that obscures its relationship to other ferns. Its thin-walled sporangium with a vertical and interrupted annulus, round sorus with peltate indusium, and petiole with several vascular bundles place it in suborder Poly-podiineae, but more precise placement has...

Figure S1. Maximum likelihood phylogram of Polypodiineae obtained from the combined (rbcL + rps4-trnS + trnL-F) dataset.

Figure S4. Maximum likelihood phylogram of Polypodiineae obtained from the trnL-F dataset.

Figure S2. Maximum likelihood phylogram of Polypodiineae obtained from the rbcL dataset.

Figure S3. Maximum likelihood phylogram of Polypodiineae obtained from the rps4-trnS dataset.

Deparia, including the previously recognized genera Lunathyrium, Dryoathyrium (=Parathyrium), Athyriopsis, Triblemma, and Dictyodroma, is a fern genus comprising about 70 species in Athyriaceae. In this study, we inferred a robust Deparia phylogeny based on a comprehensive taxon sampling (~81% of species) that captures the morphological diversity d...

A systematic study of the vittarioid ferns of East Asia including China, Japan, Korea and Taiwan is presented based on an integrated analysis of morphology and molecular phylogeny. Several new taxonomic insights are derived from well-resolved phylogenetic trees and detailed morphological comparison. The morphological variation and molecular phyloge...

Fern spores were traditionally classified into chlorophyllous (green) and nonchlorophyllous (nongreen) types based on the color visible to the naked eye. Recently, a third type, “cryptochlorophyllous spores”, is recognized, and these spores are nongreen under white light but contain chlorophylls. Epifluorescence microscopy was previously used to de...

Independent gametophyte ferns are unique among vascular plants because they are sporophyteless and reproduce asexually to maintain their populations in the gametophyte generation. Such ferns had been primar- ily discovered in temperate zone, and usually hypothesized with (sub)tropical origins and subsequent extinction of sporophyte due to climate c...

Premise of research. Ferns (monilophytes) and lycophytes are unique among land plants in having two independent life stages: the gametophyte generation, which is generally small, cordiform, and short-lived, senescing after fertilization, and the sporophyte generation, which is considered the dominant, long-lived portion of the life cycle produced f...

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based a...

Ferns and lycophytes produce spores to initiate the gametophyte stage for sexual reproduction. Approximately 10% of these seedless vascular plants are apomictic, and produce genomic unreduced spores. Genome size comparisons between spores and leaves are a reliable, and potentially easier way to determine their reproductive mode compared to traditio...

Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is...

Adiantum philippense s.l. is a member of once-pinnate Adiantum but comprise several cytotaxa with different ploidies and reproductive modes. According to the differences of cytotypes, the up-to-date revision had identified three subspecies under the A. philippense complex. In Taiwan, different ploidies and reproductive modes had also been found in...