Researchers Create the Largest Seed Plant Tree of Life

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This rendering illustrates the phylogenomic reconstruction of the evolutionary diversification of seed plants (E.K. Lee et al.)

Working with colleagues at Cold Spring Harbor Laboratory, the New York Botanical Garden, and New York University, Museum scientists have created the largest genome-based tree of life for seed plants. Their findings plot the evolutionary relationships of 150 different species of plants based on advanced genome-wide analysis of gene structure and function. This new approach, called “functional phylogenomics,” allows scientists to reconstruct the pattern of events that led to the vast number of plant species we see today and could help identify genes used to improve seed quality for agriculture.

The research, performed by members of the New York Plant Genomics Consortium, was funded by the National Science Foundation Plant Genome Program to identify the genes that caused the evolution of seeds, a trait of important economic interest.

The species the group studied span from the flowering variety—peanuts and dandelions, for example—to non-flowering cone plants like spruce and pine. The sequences of the plants’ genomes—all of the biological information needed to build and maintain an organism, encoded in DNA—were either culled from pre-existing databases or generated, in the field and at the New York Botanical Garden in the Bronx, from live specimens.

With the processing power of supercomputers, the sequences—nearly 23,000 sets of genes (specific sections of DNA that code for certain proteins)—were grouped, ordered, and organized in a tree according to their evolutionary relationships. Algorithms that determine similarities of biological processes were used to identify the genes underlying species diversity.

The results support major hypotheses about evolutionary relationships in seed plants. The most interesting finding is that gnetophytes, a group that consists mostly of shrubs and woody vines, are the most primitive living non-flowering seed plants—present since the late Mesozoic era, the “age of dinosaurs.”

In addition, the researchers made predictions about genes that caused the evolution of important plant characteristics. One such evolutionary signal is RNA interference, a process that cells use to turn down or silence the activity of specific genes. Based on their new phylogenomic maps, the researchers believe that RNA interference played a large role in the separation of monocots—plants that have a single seed leaf, including orchids, rice, and sugar cane—from other flowering plants. Even more surprising, RNA interference also played a major role in the emergence of flowering plants themselves.

For more information, see the Museum press release.