We are broadly interested in the evolutionary processes at the gene, genome, and microbiome levels that shaped the plant diversity. At the gene level, we study the molecular evolution of photoreceptors and examine how that influences plant diversification. At the genome level, we generate and analyze fern genomes to investigate genome evolution across the major transitions in land plant evolution. At the microbiome level, we focus on the multiple origins of plant-cyanobacteria symbiosis and aim to elucidate the genetic mechanisms governing these interactions. Check out my lab website for details.
Ferns are one of the final frontiers in plant genomics. The dearth of fern genomic resources is due primarily to their notoriously high chromosome numbers and large genome sizes—ferns can have chromosome numbers as high as 2n=1440, and genome sizes as high as 1C=71 Gb (>470 times larger than Arabidopsis). However, we have recently discovered that Azollaand Salvinia (two closely related aquatic fern genera) have the smallest fern genomes known to date (0.75 Gb and 0.25 Gb respectively), while the average fern genome size is over 12 Gb. We have already assembled and annotated the whole genomes of Azolla filiculoides and Salvinia cucullata. These first fern genomes will make possible many exciting research opportunities. We are interested in examining the patterns of paleopolyploidization, genome expansion/contraction, as well as transposable element activities in ferns, and contrast them across other plant genomes. We are also curious about how gene family evolution—particularly those that play critical roles in reproduction and development—influences the origin and evolution of plant life forms. Finally, we are keen to find out what drove the remarkable variation in both genome size and chromosome number across land plants.
Hornworts as a new model system
Hornworts are one of the three bryophyte lineages (together with mosses and liverworts), and have a suite of fascinating biological features. For example, some hornwort species have a unique carbon-concentration mechanism to boost photosynthesis, like C4 or CAM but at the single-cell level. In addition, every single hornwort species are capable to form symbiosis with cyanobacteria, and thus hold the key to understand plant interactions with nitrogen-fixing microbes. Working with Juan Carlos Villarreal at Laval University, Peter Szoevenyi at University of Zurich, and Shifeng Cheng at BGI, we have assembled complete genomes from three hornwort species. We have also been developing tools for genetic transformation as well as CRISPR-Cas9 genome editing to enable reverse genetic interrogation in hornworts. We hope to apply these tools and genomic resources to tackle various research questions, from the origin of cyanobacteria symbiosis to the evolution of plant body plans.
Plant-bacterial symbiosis is a major driver in evolution, and its role in nitrogen fixation is particularly important in agriculture. Past studies of plant-bacteria interactions have focused primarily on the legume-Rhizobium system. Although significant, this particular symbiosis has had only a single evolutionary origin, thus limiting its utility as a model for understanding the genetic mechanisms underlying other symbiotic plant-bacteria partnerships. In contrast, symbioses with the other group of nitrogen-fixing bacteria––the cyanobacteria—have independently evolved multiple times, in liverworts, hornworts, ferns (i.e. Azolla), cycads, and flowering plants. We aim to leverage the power of such convergent evolution––independently evolved in each of these disparate plant groups––to identify the genetic commonalities that were repeatedly recruited to assemble this mutually-beneficial association. Specifically, we will be looking for signatures of convergent evolution at the genome, gene and amino acid levels. At the genome level, we will focus on concerted gene family expansion or contraction, loss or retention of metabolic pathways, proliferation or purging of transposable elements, and horizontal gene transfer between cyanobacteria and plants. At the gene level, we will identify genes that exhibit similar expression profiles when a cyanobacterial symbiosis is present versus absent. And at the amino acid levels, we will reconstruct gene phylogenies for all orthologous genes and examine if similar, positively- selected amino acid substitutions occurred each time a symbiotic event evolved. The genetic elements identified through this comparative genomic analysis will be instrumental for engineering artificial nitrogen-fixing symbiosis onto crop plants.
Plant photoreceptor evolution
“Light exerts a powerful influence on most vegetable tissues, and there can be no doubt that it generally tends to check their growth” – Charles Darwin, 1880 Light is the ultimate source of energy for much of life on earth, and inevitably governs the growth and physiology of photosynthetic organisms. Plants “see” light through photoreceptors. To understand how plants adapted to, and thrived in, the diverse environments they inhabit, the roles of photoreceptors cannot be ignored. Our research has been focusing on neochrome, a bizarre chimeric photoreceptor that fuses red-sensing phytochrome and blue-sensing phototropin together in a single protein. Neochromes were once thought to be unique to ferns, and were hypothesized to a play important role in facilitating ferns’ recent radiation in low-light environments. By sieving through transcriptomic and genomic data, we recently discovered novel neochrome homologs in hornworts (a bryophyte lineage), and demonstrated that ferns acquired neochrome from hornworts via horizontal gene transfer (Li et al. 2014 PNAS). This work has important implications for the significance of horizontal gene transfer among eukaryotes, and was widely publicized in the media. In addition, we reconstructed the evolutionary histories of phytochromes and phototropins across land plants (Li et al. 2015 Frontiers in Plant Science; Li et al. 2015 Nature Communications), and we are building upon such framework to interpret what we know about Arabidopsis photobiology within a broader evolutionary context.
- With crowdfunded support, researchers have sequenced the first two fern genomes ever. Their results, including the discovery of an ancient gene transfer and novel symbiosis mechanisms, appear this month in Nature Plants. Read more »
- The offices of data scientists at BTI emptied out earlier this month as a contingent of researchers flew to San Diego for the 25th annual Plant and Animal Genome Conference. Read more »
Seed-free plant genomics and symbioses
The Li lab uses genomic tools to investigate the evolution and biology of seed-free plants: ferns, fern allies, and bryophytes (mosses, liverworts, and hornworts). We are particularly interested in their symbioses with N2-fixing cyanobacteria, which provide plants with their own source of nitrogen fertilizer. We aim to understand the evolution and mechanisms of plant-cyanobacteria symbioses, and the results of which will lay the foundation for future engineering of “self-fertilizing” crops with less reliance on synthetic nitrogen fertilizers. To this end, we are surveying the diversity of cyanobacterial symbionts in hornworts, and using RNA-sequencing to uncover putative symbiosis-related genes.