Genomic analyses of a “living fossil”: The endangered dove‐tree

Davidia involucrata Baill, also known as the dove-tree, is a living fossil and an endangered species currently restricted to the mountains of southwestern and central China. It has a beautiful and innovative trait of high horticultural value: two white bracts covering the flower caputila. Here, we report on the chromosome-scale genome of this species using single-molecule real-time long reads and chromosome conformation capture (Hi-C) techniques. This species has a larger genome size of 1,169 Mb and contains relatively more genes (42,554) than the closely related species Camptotheca acuminata (397 Mb and 31,825 genes). Both species shared one recent whole genome duplication before their divergence. The expansion of the repetitive elements after their divergence contributed greatly to the increase in the genome size of the dove-tree. Photosynthesis-related genes were almost absent or showed reduced expression in the bracts of the dove-tree, while defence- and chemical-related genes increased greatly, highlighting the important roles of the bracts in protecting flowers and attracting pollinators. The effective population size of the dove-tree continuously decreased during the climate changes of the Quaternary. Such climate sensitivity should be fully considered in conservation efforts for this relict endangered species in the context of continuous climate warming in the future.