Fay-Wei Li

Publications87
h-index27
Citations3,565
Highly Influential Citations138
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A community‐derived classification for extant lycophytes and ferns
TLDR
A modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach, that uses monophyly as the primary criterion for the recognition of taxa, but also aims to preserve existing taxa and circumscriptions that are both widely accepted and consistent with the understanding of pteridophyte phylogeny.
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
TLDR
More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes, it is found that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle.
The evolutionary history of ferns inferred from 25 low-copy nuclear genes.
TLDR
A curated phylogenomics approach is taken to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling with focused character sampling, along with rigorous alignment, orthology inference and model selection.
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
TLDR
This study confirmed computationally predicted noncanonical translation events and uncovered unannotated small proteins that likely have important functions in plants and provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
First insights into fern matK phylogeny.
One thousand plant transcriptomes and the phylogenomics of green plants
  • James H. Michael S. Eric J. Michael K. Matthew A. Sean W Leebens-Mack Barker Carpenter Deyholos Gitzendanne, J. Leebens-Mack, G. Wong
  • Biology, Environmental Science
    Nature
  • 7 October 2019
TLDR
It is found that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns.
Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.
TLDR
A high-throughput protocol and an associated bioinformatics pipeline that is able to generate nuclear data quickly and conveniently that makes it easy and economical to study the phylogenetics of polyploids, and facilitates investigation of broad patterns ofpolyploid evolution.
Fern genomes elucidate land plant evolution and cyanobacterial symbioses
TLDR
The genomes of two fern species, Azolla filiculoides and Salvinia cucullata, are reported and insights into fern-specific whole-genome duplications, f Fern-specific insect-resistant gene evolution and fern–cyanobacterial symbiosis are provided.
Phytochrome diversity in green plants and the origin of canonical plant phytochromes
TLDR
It is shown that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants) and Surprisingly, the phy tochrome portions of algal and land plant neochromes, a chimera ofphytochrome and phototropin, appear to share a common origin.
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
TLDR
Surprisingly, it is discovered that fern neochrome was derived from a bryophyte lineage via horizontal gene transfer (HGT), providing the first evidence that a plant-to-plant HGT can have a profound evolutionary impact but also has implications for the evolution of photosensory systems in plants.
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