In the cover story of the latest issue of Nature Genetics, researchers from Shenzhen Fairy Lake Botanical Garden and BGI-Research, together with international partners, report the most extensive genomic resource yet assembled for bryophytes (mosses, liverworts and hornworts), descendants of ancestors that colonized land roughly half a billion years ago. By analyzing 123 newly sequenced genomes alongside existing data, the team provides systematic evidence that bryophytes maintain a broader diversity of gene families than vascular plants such as trees and flowering crops.
These small plants appear to rely less on structural complexity and more on a large and dynamic "parts catalog" of gene families, many of which are either rare or unique. This diversity stems from two key processes: the de novo birth of new genes from previously non-coding DNA and the acquisition of genes from microbes over evolutionary time. The comprehensive analysis reveals bryophytes possess significantly more non-redundant gene families than vascular plants, alongside a greater proportion of unique and accessory gene families per genome.
[Cover Image]
The research article, "Bryophytes hold a larger gene family space than vascular plants," published in Nature Genetics as cover story.
Genome features of 138 bryophytes across evolutionary time. Shows bryophytes maintain diverse genome architectures despite ancient origins. Establishes foundation for understanding how Earth's first land plants adapted and diversified.
The research reveals three major findings that challenge conventional views of bryophyte evolution. First, despite having smaller genomes on average, bryophytes possess a remarkably larger total number of gene families than vascular plants, with many unique to individual species or lineages. Second, bryophytes show unprecedented levels of horizontal gene transfer, acquiring an average of 229 genes from microbes compared to 163 in vascular plants. These horizontally transferred genes are often stress-responsive and may enhance ecological adaptability across diverse environments. Third, the study documents novel immune and defense systems in bryophytes, including new classes of disease-resistance genes and insect-toxic proteins with potential applications in agriculture. One highlighted example is a small protein containing an FB-lectin domain that caused up to 97.62% mortality in cotton bollworm larvae in laboratory assays, demonstrating the untapped potential of bryophyte-derived genes for pest management.
Open-access bryogenomes.org portal with 138 genome assemblies and annotations. Democratizes bryophyte genomics by providing free global access. Enables worldwide researchers to explore plant evolution and discover new applications.
The comprehensive dataset spans 47 of the 55 recognized bryophyte orders, providing unprecedented coverage across this diverse group. The team employed multiple sequencing platforms and advanced assembly techniques to generate high-quality genome assemblies, with all data made freely available through the bryogenomes.org portal and major public repositories.
Bryophyte diversity spanning 47 of 55 recognized orders with representative photos. Demonstrates comprehensive coverage across this ancient plant group's remarkable morphological diversity. Fills critical gaps in understanding early land plant evolution and adaptation strategies.
This international collaboration involves researchers from institutions across five continents, led by Shenzhen Fairy Lake Botanical Garden and BGI-Research, with key contributions from Ghent University (Belgium), Monash University (Australia), and the University of Connecticut (USA), among others.
Gene family comparison: bryophytes (637,597 families) vs vascular plants (373,581 families). Overturns assumptions that "simple" bryophytes have limited genetic diversity. Reveals small plants maintain larger genetic toolkits than trees and crops, reshaping evolutionary biology understanding.
The findings suggest that bryophytes, long viewed as evolutionarily "simple," are actually persistent genomic innovators. While applications in agriculture and biotechnology will require further development and validation, this genomic resource provides a foundation for exploring plant adaptation strategies and identifying novel genes for stress tolerance and pest resistance. All experiments adhered to institutional biosafety guidelines.
Horizontal gene transfer patterns: bryophytes acquire 229 microbial genes vs 163 in vascular plants. Shows bryophytes actively "borrow" genes from bacteria and fungi throughout evolution. Suggests new strategies for crop improvement through understanding natural gene exchange mechanisms.
These dynamics are quantified across evolutionary time, with accumulation curves indicating that many bryophyte gene families remain to be discovered as sampling grows. The findings suggest that expanding genomic coverage across under-sampled plant lineages can reshape understanding of adaptation and resilience mechanisms.
Bryophyte FBT protein kills 97.62% of cotton bollworm larvae in laboratory tests. Demonstrates bryophytes harbor potent natural pesticides derived from ancient fungal genes. Offers sustainable pest control alternatives for agriculture without synthetic chemicals.
Bryophyte disease-resistance genes trigger immune responses in tobacco plants. Reveals bryophytes evolved unique plant immunity mechanisms over 500 million years. Provides new genetic resources for developing disease-resistant crops to enhance global food security.
As a community resource developed by an international consortium, this work contributes to global scientific knowledge with potential benefits for sustainable agriculture and environmental stewardship, subject to careful validation and testing.
This study can be accessed here: https://www.nature.com/articles/s41588-025-02325-9