Developmentally regulated genes drive phylogenomic splits in ovule evolution

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.