A wealth of genes for seed improvement uncovered in living fossils

Seed plants are essential as a source of food, fuel, medicine and much more. Today, a multidisciplinary team of researchers has combined deep botanical knowledge with powerful genomic technology to decode and mine the DNA of non-flowering seed plants and discover the genes that have evolved to help plants produce seeds.

These results, published in Natural communicationscan help scientists improve seed production in agriculture and conserve these endangered ancient seed plants.

In this study led by members of the New York Plant Genomics Consortium – a multi-institutional collaboration of botanists, evolutionary and genomics scientists, and bioinformaticians – researchers isolated and studied seed genes encoded in the genomes of the oldest living seed plants: gymnosperms.

Gymnosperms, which include conifers and ginkgo, bear “naked” seeds not protected by a fruit and are one of the most endangered plant groups. Many gymnosperms are also “living fossils,” a term coined by Darwin to describe their persistence on Earth since the time of the dinosaurs.

“Now that scientists can sequence any genome, the question is which species to sequence and why?” said Gloria Coruzzi, the Carroll & Milton Petrie Professor in NYU’s Department of Biology and Center for Genomics and Systems Biology.

“By studying gymnosperms, the species in which seeds first evolved and which make up 30% of the world’s forests, we identified the genes that support the evolution of seeds.”

“Based on our studies reconstructing the evolutionary tree of life of gymnosperms, we know which species to study, where to collect them, and how to cultivate them, elucidating the origin and development of their unique structural components such as the seed,” said Dennis Stevenson, senior curator emeritus at the New York Botanical Garden (NYBG).

Collection and sequencing of gymnosperm samples

The NYBG researchers collected developing seeds, called ovules, and leaves from 14 different gymnosperms and four flowering plants, as well as spores from two species of ferns, which do not produce seeds, for comparison.

Working with Cold Spring Harbor Laboratory (CSHL), they extracted transcripts from these samples and used powerful DNA sequencing technology. The team at NYU’s Center for Genomics and Systems Biology then assembled more than 586,000 genes for these species, creating the largest collection of gymnosperm egg transcriptomes to date.

“This study highlights the power of biodiversity to answer fundamental questions,” said Barbara Ambrose, curator of plant genomics and director of laboratory research at NYBG.

“The breadth of our living collections as well as a modern laboratory close to our collections to process samples are essential for research into molecular biodiversity.”

Discover genes linked to seed evolution

To identify how these genes play a role in seed development, NYU researchers used a new two-pronged analysis combining evolutionary history and gene expression data using NYU’s high-performance computing cluster.

To do this, they identified genes shared between species, called orthologs, and integrated information about how the genes are activated or expressed in different tissues and how they influence the evolutionary history of these plants.

By creating a genome-wide evolutionary tree of these 20 species, the researchers identified more than 22,000 genes containing information about the history of these seed plants. Furthermore, they observed for the first time that major evolutionary changes in the history of seed plants are driven by the selection of genes whose expression changes during leaf and ovule development in seed plants.

The research team ultimately discovered 4,076 candidate genes that may play a specific role in seed evolution, including genes from model species whose function was previously unknown.

Testing gene function in living plants

“Model plants are species whose genomes have been extensively studied to answer fundamental scientific questions,” said Veronica Sondervan, who led the phylogenomic analysis at NYU and conducted plant studies at NYBG.

“The fact that we can still discover new roles for these genes in model species using genomic information from these early seeds is very exciting.”

“This is an interdisciplinary team that has been working together for a long time, and this study shows the very important advances that this approach can make,” said team member W. Richard McCombie, the Davis Family Professor of Human Genetics at CSHL.

To confirm whether the newly identified genes play a functional role in seed development, the NYBG team conducted experiments on several gymnosperms. In one example, they tested how two candidate genes were expressed in the ovules of a gymnosperm, the yew Taxus baccata first described in 1753 by Carl Linnaeus in his Species Plantarum.

Yews are distinguished by the unique cup-shaped red “fruits” that surround their seeds, called arils – the plant’s only non-toxic organ – which are eaten by birds to enable seed dispersal.

The results confirmed the evolutionary importance of these genes in seed dispersal by showing that the genes were expressed throughout the ovules. They also demonstrated expression patterns different from those seen in other gymnosperm species, including expression in single arils.

This suggests that sequence changes in developmentally regulated genes may play an important role in how seed structures are created to enhance dispersal and facilitate persistence in plant evolution.

“This genetic resource for understanding seed development across plant species can not only help scientists improve the traits of seeds from a variety of crops, but could also provide tools to protect and propagate endangered plants, including these valuable living fossils,” notes Sondervan.