In a groundbreaking study that merges botanical expertise with cutting-edge genomic technologies, a multidisciplinary team of researchers has embarked on an ambitious quest to decode the DNA of ancient non-flowering seed plants. These gymnosperms, which include conifers and the enigmatic Ginkgo, represent some of the planet’s oldest living seed-bearing flora and are pivotal not only for understanding plant evolution but also for their critical ecological roles. By unlocking the genetic secrets behind seed development in these species, the team has made significant strides in unveiling the evolutionary pathways and molecular machinery that underpin seed formation, a feature that revolutionized terrestrial plant life.
Gymnosperms are distinguished by their production of “naked seeds” — ovules that are not enclosed within fruits — a trait that sets them apart from angiosperms or flowering plants. This distinctive characteristic marks a crucial juncture in plant evolution, as seeds confer remarkable advantages in terms of reproduction, dispersal, and survival. However, despite their evolutionary importance, the genetic basis of seed development in gymnosperms remained largely unexplored until now, hampered by the complexity of their genomes and the scarcity of genomic resources. This study, set to be published in Nature Communications, represents the largest and most detailed genomic effort to date to characterize those genes associated with seed evolution and development in gymnosperms.
The research initiative was spearheaded by the New York Plant Genomics Consortium, a collaboration uniting botanists, evolutionary biologists, genomic scientists, and bioinformaticians from institutions including New York University, the New York Botanical Garden, and Cold Spring Harbor Laboratory. Recognizing that genome sequencing technology is now ubiquitous, the critical challenge was to strategically select species that would illuminate the evolutionary origins of seed traits. This comprehensive approach resulted in sampling from 14 distinct gymnosperm species alongside four flowering plants and two non-seed-producing ferns for comparative analysis, thereby creating an evolutionary framework bridging vascular plant lineages.
To tackle the genomic complexity, the team employed transcriptome sequencing — capturing RNA molecules which reflect genes actively expressed during seed and leaf development stages. The samples, rigorously collected from living collections at the New York Botanical Garden, provided high-quality material for RNA extraction and sequencing. At the Cold Spring Harbor Laboratory’s DNA Sequencing Center, sophisticated sequencing platforms generated millions of transcript data points, which were subsequently assembled into over 586,000 genes. This assembly culminated in the most expansive gymnosperm ovule transcriptome database established so far, revealing an unprecedented view into the gene expression landscape that governs seed formation.
Harnessing the power of NYU’s High Performance Computing Cluster, the researchers innovatively merged phylogenomic methods with gene expression profiling. This dual-pronged analysis allowed them to identify orthologous genes — those shared across species due to common ancestry — and investigate how their differential expression patterns correlate with key evolutionary events. Building a genome-scale evolutionary tree including 20 species, the team traced the gene selection dynamics implicated in ovule and leaf development, observing how genetic innovation aligns with pivotal moments in seed plant lineage divergence.
Their findings identified a remarkable pool of over 4,000 candidate genes potentially instrumental in directing seed evolution. Intriguingly, many of these genes are homologous to those found in model plant species, yet their functions in early seed plants were previously uncharacterized. The revelation that some genes retain ancestral roles while others have diverged to mediate seed-specific adaptations underscores the complexity and plasticity within seed plant genomes. These insights not only deepen our understanding of biological innovation but also pave the way for translational applications in agriculture and conservation biology.
Functionality of these candidate genes was further corroborated through meticulous in vivo studies conducted on several gymnosperm species, including the well-studied yew (Taxus baccata). Notably, the yew’s unique aril structure—a red, fleshy growth enveloping the seed—provides a natural laboratory for exploring seed dispersal mechanisms. Gene expression analyses revealed that specific developmental genes are active not only throughout the ovule but also in the aril, suggesting that differential gene regulation has driven the evolution of novel seed structures enhancing ecological fitness, such as attracting bird dispersers. This observation elegantly connects molecular genetics with phenotypic innovations critical for survival.
The implications of this research extend far beyond academic curiosity. Decoding the genetic programs responsible for seed traits holds tremendous potential for improving crop yields by breeding or engineering plants with enhanced seed qualities such as viability, stress tolerance, and dispersal capacity. Additionally, these genetic resources may be instrumental in conserving endangered gymnosperms, some of which are considered living fossils, having persisted relatively unchanged for millions of years. Protecting and propagating these ancient species could be pivotal amid accelerating climate change and habitat loss.
The collaborative nature of the project was a cornerstone of its success, integrating the expertise of field botanists, molecular scientists, and computational biologists. The synergy between NYBG’s extensive living collections and modern sequencing laboratories provided an unparalleled platform for molecular biodiversity research. Further, the seamless integration of data analysis from transcriptome assembly to phylogenomic reconstruction exemplifies the future direction of plant evolutionary studies — combining high-throughput genomics with ecological and morphological perspectives.
This study exemplifies how evolutionary questions can be addressed using genomic and computational tools, illuminating genetic underpinnings of complex traits like seed development in a phylogenetic context. The identification of genes with lineage-specific expression patterns and their evolutionary dynamics underscores the intricate interplay between development and diversification. The work also exemplifies the power of interdisciplinary research teams in solving long-standing biological puzzles while generating resources with broad utility across scientific and applied domains.
In sum, the research not only charts a genetic roadmap of seed evolution but also underscores the enduring significance of gymnosperms in our global ecosystems. As these plants constitute about 30% of the world’s forests, understanding their biology is crucial for ecosystem management and restoration efforts. This comprehensive genomic atlas and the associated functional studies set a new benchmark in plant genomics and evolutionary biology, potentially transforming strategies in agriculture and conservation with implications reaching well into the future.
This landmark paper is funded by prominent grants from the U.S. National Science Foundation, the European Union’s Horizon 2020 program, and the National Institutes of Health, demonstrating the global commitment to advancing plant science. The publication of their findings in Nature Communications offers a rich resource for researchers and highlights the essential value of integrating biodiversity collection with next-generation genomic technologies to address evolutionary and ecological questions.
Subject of Research:
Seed evolution and gene function in gymnosperms through phylogenomics and transcriptomics
Article Title:
Developmentally regulated genes drive phylogenomic splits in ovule evolution
News Publication Date:
13-Nov-2025
Web References:
http://dx.doi.org/10.1038/s41467-025-65399-3
Image Credits:
Veronica Sondervan, NYU & New York Botanical Garden
Keywords:
Plant sciences, Botanical gardens, Horticulture, Plant biotechnology, Plant genetics, Plant evolution, Plant gene expression, Plant genes, Plant genomes
