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Fay-Wei Li

Fay-Wei Li

Scholar In Residence in the Department of Biology
Biology

Selected Publications

An unconventional Rubisco small subunit underpins the CO<sub>2</sub>-concentrating organelle in land plants.

Journal Article Science (New York, N.Y.) · March 2026 In many algae, photosynthesis is boosted by biophysical CO2-concentrating mechanisms, which pack the CO2-fixing enzyme Rubisco into liquid-like organelles called pyrenoids. Engineering C3 crops with algal pyrenoids could in ... Full text Cite

The genome of the vining fern <i>Lygodium microphyllum</i> highlights genomic and functional differences between life phases of an invasive plant.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · September 2025 Functional and genomic studies on the differences between the gametophyte and sporophyte life phases of plants remain scarce, yet unraveling these dynamics is crucial to understanding the biology of plants and the success of each phase under different cond ... Full text Cite

The genome assembly of the duckweed fern, Azolla caroliniana.

Journal Article The Journal of heredity · August 2025 Azolla is a genus of freshwater ferns that is economically important as a nitrogen-fixing biofertilizer, biofuel, bioremediator, and for potential carbon sequestration, but also contains weedy invasive species. In California, only 2 species are currently r ... Full text Cite

Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification.

Journal Article Annals of botany · July 2025 Background and aimsResolving the phylogeny of hornworts is critical in understanding the evolution of key morphological characters that are unique to the group, including the pyrenoid. Extensive phylogenomic analyses have revealed unexpected compl ... Full text Cite

Genome sequences of two cyanobacteria strains isolated from hornworts.

Journal Article Microbiology resource announcements · May 2025 We report two complete genome assemblies of symbiotic cyanobacteria isolated from the hornwort species Notothylas orbicularis and Phaeoceros carolinianus. These new datasets will facilitate future comparative genomic studies across symbiotic ... Full text Cite

The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.

Journal Article American journal of botany · March 2025 PremiseAzolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of ... Full text Cite

Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes.

Journal Article Nature plants · January 2025 Hornworts, one of the three bryophyte phyla, show some of the deepest divergences in extant land plants, with some families separated by more than 300 million years. Previous hornwort genomes represented only one genus, limiting the ability to infer evolut ... Full text Cite

Hornworts reveal a spatial model for pyrenoid-based CO<sub>2</sub>-concentrating mechanisms in land plants.

Journal Article Nature plants · January 2025 Pyrenoid-based CO2-concentrating mechanisms (pCCMs) turbocharge photosynthesis by saturating CO2 around Rubisco. Hornworts are the only land plants with a pCCM. Owing to their closer relationship to crops, hornworts could offer greate ... Full text Cite

Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems.

Journal Article Molecular plant · December 2024 Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco's CO2 fixation, yet hornwort Rubisco remains poorly characterized. Here we assembled the hornwort Anthoceros agrestis Rubisco (AaRubisco) using the Arabidopsis thalian ... Full text Cite

Biolistics-mediated transformation of hornworts and its application to study pyrenoid protein localization.

Journal Article Journal of experimental botany · August 2024 Hornworts are a deeply diverged lineage of bryophytes and a sister lineage to mosses and liverworts. Hornworts have an array of unique features that can be leveraged to illuminate not only the early evolution of land plants, but also alternative paths for ... Full text Cite

Convergent evolution of fern nectaries facilitated independent recruitment of ant-bodyguards from flowering plants.

Journal Article Nature communications · May 2024 Plant-herbivore interactions reciprocally influence species' evolutionary trajectories. These interactions have led to many physical and chemical defenses across the plant kingdom. Some plants have even evolved indirect defense strategies to outsource thei ... Full text Cite

Genomes of multicellular algal sisters to land plants illuminate signaling network evolution.

Journal Article Nature genetics · May 2024 Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophycea ... Full text Cite

Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a 'diploids-first' approach to conservation.

Journal Article Annals of botany · April 2024 Background and aimsAllopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However, many studies have questioned the importance of extant polyploid lineages, suggesting that the va ... Full text Cite

Phaeocerosperpusillus var. scabrellus (Notothyladaceae, Anthocerotophyta), a new taxon from northern Thailand.

Journal Article PhytoKeys · January 2024 A new variety of hornwort from northern Thailand, Phaeocerosperpusillusvar.scabrellus is described based on morphological characters and molecular phylogenetic analyses. In this study, phylogenetic analyses supported that the new variety is closely related ... Full text Cite

Twelve new metagenome-assembled genomes from non-axenic culture of Griffithsia monilis (Rhodophyta).

Journal Article Microbiology resource announcements · January 2024 We report 12 metagenome-assembled genomes from a non-axenic culture of the red alga Griffithsia monilis Harvey, some of which are distantly related to publicly available genomes. ... Full text Cite

The ancestral chromatin landscape of land plants.

Journal Article The New phytologist · December 2023 Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the moss Physcomitrium patens and the liverwort Marchantia polymorpha. Mos ... Full text Cite

A structure of the relict phycobilisome from a thylakoid-free cyanobacterium.

Journal Article Nature communications · December 2023 Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been chal ... Full text Cite

Genome sequence of a symbiotic cyanobacterium from the flowering plant Gunnera tinctoria.

Journal Article Microbiology resource announcements · November 2023 Metagenomic analysis of the symbiotic cyanobacteria colonies within Gunnera tinctoria stems revealed a new strain of Nostoc. Here, we report its genome sequence. ... Full text Cite

The chromosome hoarding syndrome of (some) ferns and lycophytes.

Journal Article Nature reviews. Genetics · November 2023 Full text Cite

Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales.

Journal Article Applications in plant sciences · May 2023 PremiseWe present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output. The goal is to help those interested in genera ... Full text Cite

Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY.

Journal Article Nat Commun · March 20, 2023 SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is distinct from ER-localized POFUTs and contains N-terminal tetr ... Full text Open Access Link to item Cite

Nostoc Talks Back: Temporal Patterns of Differential Gene Expression During Establishment of Anthoceros-Nostoc Symbiosis.

Journal Article Molecular plant-microbe interactions : MPMI · October 2022 Endosymbiotic associations between hornworts and nitrogen-fixing cyanobacteria form when the plant is limited for combined nitrogen (N). We generated RNA-seq data to examine temporal gene expression patterns during the culturing of N-starved Anthoceros ... Full text Cite

Dynamic genome evolution in a model fern.

Journal Article Nature plants · September 2022 The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, tran ... Full text Cite

Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon.

Journal Article American journal of botany · June 2022 PremiseChaetopeltidales is a poorly characterized order in the Chlorophyceae, with only two plastid and no mitochondrial genomes published. Here we describe a new taxon in Chaetopeltidales, Gormaniella terricola gen. et sp. nov. and characterize b ... Full text Cite

The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence.

Journal Article Nature plants · May 2022 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 pseudochromoso ... Full text Cite

Extremely low genetic diversity in the European clade of the model bryophyte Anthoceros agrestis

Journal Article Plant Syst Evol · April 2022 The hornwort Anthoceros agrestis is emerging as a model system for the study of symbiotic interactions and carbon fixation processes. It is an annual species with a remarkably small and compact genome. Single accessions of the plant have been shown to be r ... Full text Cite

Step-by-step protocol for the isolation and transient transformation of hornwort protoplasts.

Journal Article Applications in plant sciences · March 2022 PremiseA detailed protocol for the protoplast transformation of hornwort tissue is not yet available, limiting molecular biological investigations of these plants and comparative analyses with other bryophytes, which display a gametophyte-dominant ... Full text Cite

Re-evaluating the Systematics of Dendrolycopodium Using Restriction-Site Associated DNA-Sequencing.

Journal Article Frontiers in plant science · January 2022 The genus Dendrolycopodium (Lycopodiaceae) includes four to five species across North America and East Asia. Species identification in Dendrolycopodium is difficult due to limited or inconsistent characters. In addition, plants with intermedi ... Full text Cite

Decolonizing botanical genomics.

Journal Article Nature plants · December 2021 Full text Cite

Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae.

Journal Article Genome biology and evolution · November 2021 Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been ... Full text Cite

An Agrobacterium-mediated stable transformation technique for the hornwort model Anthoceros agrestis.

Journal Article The New phytologist · November 2021 Despite their key phylogenetic position and their unique biology, hornworts have been widely overlooked. Until recently there was no hornwort model species amenable to systematic experimental investigation. Anthoceros agrestis has been proposed as the mode ... Full text Cite

Underwater CAM photosynthesis elucidated by Isoetes genome.

Journal Article Nature communications · November 2021 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 ... Full text Cite

The diversity and community structure of symbiotic cyanobacteria in hornworts inferred from long-read amplicon sequencing.

Journal Article American journal of botany · September 2021 PremiseNitrogen-fixing endosymbioses with cyanobacteria have evolved independently in five very different plant lineages. Expanding knowledge of these symbioses promises to improve the understanding of symbiosis evolution and broaden the toolkit f ... Full text Cite

A novel thylakoid-less isolate fills a billion-year gap in the evolution of Cyanobacteria.

Journal Article Current biology : CB · July 2021 Cyanobacteria have played pivotal roles in Earth's geological history, especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution has been limited by their extremely lopsided tree of lif ... Full text Cite

Charting the genomic landscape of seed-free plants.

Journal Article Nature plants · May 2021 During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insigh ... Full text Cite

The hornworts: morphology, evolution and development.

Journal Article The New phytologist · January 2021 Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and live ... Full text Cite

Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future.

Journal Article Plant direct · August 2020 Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020-2030 frames our ability to perform vital and far-reaching research in plant systems sciences, essential to ... Full text Cite

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts.

Journal Article Nature plants · March 2020 Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating ... Full text Cite

An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages.

Journal Article Nature plants · March 2020 Plants are the foundation of terrestrial ecosystems, and their colonization of land was probably facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following this founding event, plant diversification has led to the emergence of a t ... Full text Cite

Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution.

Journal Article American journal of botany · January 2020 PremisePhylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives us ... Full text Cite

On the evolutionary significance of horizontal gene transfers in plants.

Journal Article The New phytologist · January 2020 Horizontal gene transfer (HGT) has long been seen as a crucial process in the evolution of prokaryotic species, but until recently it was thought to have little, if any, effect on the evolution of eukaryotic life forms. Detecting and describing HGT events ... Full text Cite

One thousand plant transcriptomes and the phylogenomics of green plants.

Journal Article Nature · October 2019 Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetat ... Full text Open Access Cite

Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase.

Journal Article Genome biology and evolution · July 2019 Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant-microbe interaction. However, very few complete genomes exist for plant cyanob ... Full text Cite

Ferns: The final frond-tier in plant model systems

Journal Article American Fern Journal · July 1, 2019 Ferns are one of the most speciose lineages of land plants, and occupy an important phylogenetic position sister to seed plants. Despite this, ferns remain one of the last groups of land plants that do not have a fully developed model system. Here we revie ... Full text Cite

NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches.

Journal Article Nat Commun · June 14, 2019 Phytochromes initiate chloroplast biogenesis by activating genes encoding the photosynthetic apparatus, including photosynthesis-associated plastid-encoded genes (PhAPGs). PhAPGs are transcribed by a bacterial-type RNA polymerase (PEP), but how phytochrome ... Full text Open Access Link to item Cite

Order-level fern plastome phylogenomics: new insights from Hymenophyllales.

Journal Article American journal of botany · September 2018 Premise of the studyFilmy 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 inconclusiv ... Full text Cite

A guide to sequence your favorite plant genomes.

Journal Article Applications in plant sciences · March 2018 With the rapid development of sequencing technology and the plummeting cost, assembling whole genomes from non-model plants will soon become routine for plant systematists and evolutionary biologists. Here we summarize and compare several of the latest gen ... Full text Cite

10KP: A phylodiverse genome sequencing plan.

Journal Article GigaScience · March 2018 Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and char ... Full text Cite

A novel chloroplast gene reported for flagellate plants

Journal Article American journal of botany · 2018 Open Access Cite

The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2.

Journal Article The New phytologist · May 2017 Land plant phytochromes perceive red and far-red light to control growth and development, using the linear tetrapyrrole (bilin) chromophore phytochromobilin (PΦB). Phytochromes from streptophyte algae, sister species to land plants, instead use phycocyanob ... Full text Cite

Hornworts: An Overlooked Window into Carbon-Concentrating Mechanisms.

Other Trends in plant science · April 2017 Hornworts are the only land plant lineage harboring a biophysical carbon-concentrating mechanism (CCM). Here, we argue that hornworts are a promising, yet currently overlooked, model system to study the evolution and genetic basis of CCMs. The results of s ... Full text Cite

Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage.

Journal Article Database : the journal of biological databases and curation · January 2017 Boechera (Brassicaceae) has many features to recommend it as a model genus for ecological and evolutionary research, including species richness, ecological diversity, experimental tractability and close phylogenetic proximity to Arabidopsis . However, effo ... Full text Cite

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · November 2016 Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the li ... Full text Cite

A community-derived classification for extant lycophytes and ferns

Journal Article Journal of Systematics and Evolution · November 1, 2016 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 c ... Full text Cite

Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2016 The vast abundance of terpene natural products in nature is due to enzymes known as terpene synthases (TPSs) that convert acyclic prenyl diphosphate precursors into a multitude of cyclic and acyclic carbon skeletons. Yet the evolution of TPSs is not well u ... Full text Cite

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.

Journal Article The Plant cell · June 2016 The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonrespons ... Full text Cite

Evolutionary aspects of plant photoreceptors.

Journal Article Journal of plant research · March 2016 Plant photoreceptors link environmental light cues with physiological responses, determining how individual plants complete their life cycles. Structural and functional evolution of photoreceptors has co-occurred as plants diversified and faced the challen ... Full text Cite

Asplenium pifongiae (Aspleniaceae: Polypodiales), a New Species from Taiwan

Journal Article Systematic botany · February 2016 We describe and illustrate a new species, Asplenium pifongia., currently known only from Taiwan. Although superficially similar to A. monanthe., this species is a sexual diploid and has little perforation on its spore surfaces. Phylogenetic analyses demons ... Full text Cite

Searching for Diamonds in the Apomictic Rough: A Case Study Involving Boechera lignifera (Brassicaceae)

Journal Article Systematic Botany · December 1, 2015 The genus Boechera is one of the most difficult species complexes in North America, with about 70 sexual diploids and hundreds of apomictic taxa representing diverse combinations of nearly every known sexual genome. In this study, we set out to clarify the ... Full text Cite

The origin and evolution of phototropins

Journal Article Frontiers in plant science · 2015 Open Access Cite

The Hybrid Origin of Adiantum meishanianum (Pteridaceae): A Rare and Endemic Species in Taiwan

Journal Article Systematic botany · October 2014 Adiantum meishanianum is an endemic species distributed only in Meishan village, Kaohsiung, Taiwan. Because its sporangia contain only abortive spores, A. meishanianum has been regarded as having a hybrid origin, presumably with A. caudatum, A. malesianum, ... Full text Cite

Between two fern genomes

Journal Article Gigascience · September 2014 Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all l ... Open Access Cite

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Journal Article Proceedings of the National Academy of Sciences · 2014 Open Access Cite

Crowdfunding the Azolla fern genome project: a grassroots approach.

Journal Article GigaScience · January 2014 Much of science progresses within the tight boundaries of what is often seen as a "black box". Though familiar to funding agencies, researchers and the academic journals they publish in, it is an entity that outsiders rarely get to peek into. Crowdfunding ... Full text Open Access Cite

First insights into fern matK phylogeny.

Journal Article Molecular phylogenetics and evolution · June 2011 MatK, the only maturase gene in the land plant plastid genome, is a very popular phylogenetic marker that has been extensively applied in reconstructing angiosperm phylogeny. However, the use of matK in fern phylogeny is largely unknown, due to difficultie ... Full text Cite

Tissue-direct PCR, a rapid and extraction-free method for barcoding of ferns.

Journal Article Molecular ecology resources · January 2010 Fern gametophytes and young sporophytes often provide too little material for DNA extraction and are particularly difficult to identify to genus. Here we developed an efficient procedure called 'Tissue-direct PCR', in which a slice of fern tissue is mixed ... Full text Cite

Identifying a mysterious aquatic fern gametophyte

Journal Article Plant Systematics and Evolution · June 17, 2009 Süßwassertang, a popular aquatic plant that is sold worldwide in aquarium markets, has been long considered a liverwort because of its ribbon-like thallus. However, its antheridia are remarkably fern-like in morphology. To corroborate the hypothesis that S ... Full text Cite