Developmentally regulated genes drive phylogenomic splits in ovule evolution

Veronica M. Sondervan, Gil Eshel, Kranthi Varala, Samantha Frangos, Manpreet S. Katari, Tim L. Jeffers, Cecilia Zumajo-Cardona, Sebastiano Nigris, Lisa DeGironimo, Tynisha Smalls, W. Richard McCombie, Damon P. Little (), Barbara Ambrose (), Dennis Wm. Stevenson () and Gloria M. Coruzzi ()
Additional contact information
Veronica M. Sondervan: New York University
Gil Eshel: New York University
Kranthi Varala: Purdue University
Samantha Frangos: New York University
Manpreet S. Katari: New York University
Tim L. Jeffers: New York University
Cecilia Zumajo-Cardona: New York Botanical Garden
Sebastiano Nigris: Università degli studi di Padova
Lisa DeGironimo: New York Botanical Garden
Tynisha Smalls: New York Botanical Garden
W. Richard McCombie: Cold Spring Harbor Laboratory
Damon P. Little: New York Botanical Garden
Barbara Ambrose: New York Botanical Garden
Dennis Wm. Stevenson: New York Botanical Garden
Gloria M. Coruzzi: New York University

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract The evolution of seeds transformed life on earth and is responsible for our most important food crops. Gymnosperms, the oldest living seed plants, are an untapped genomic reservoir for genes involved in seed evolution. To tap this resource, we assemble deep transcriptomes of 14 gymnosperms, four angiosperms, and two ferns and identified 22,429 phylogenetically informative ortholog groups. We observe that genes differentially expressed in ovules or leaves provide the majority of phylogenomic support for the evolutionary splits between 1) seed and non-seed plants; 2) gymnosperms and angiosperms; and/or 3) within gymnosperms (conifers vs. “ancient” gymnosperms). Our gymnosperm data identifies unreported candidate ovule regulated genes in Arabidopsis. Moreover, prior knowledge from Arabidopsis helps uncover 4,076 candidate ovule genes that influence these evolutionary splits. We validate the expression of candidate ovule genes in gymnosperm-specific ovule structures. Our work provides a resource for seed gene discovery, conservation, and crop improvement.

Date: 2025
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DOI: 10.1038/s41467-025-65399-3

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