A deep-time landscape of plant cis-regulatory sequence evolution
Summary
Developmental gene function is often conserved over deep time, but cis-regulatory sequence conservation is difficult to identify. Rapid sequence turnover, paleopolyploidy, structural variation, and limited phylogenomic sampling have impeded conserved noncoding sequence (CNS) discovery. Using Conservatory, an algorithm that leverages microsynteny and iterative alignments to map CNS-gene associations over evolution, we uncovered ~2.3 million CNSs, including more than 3000 predating angiosper
Content
# A deep-time landscape of plant cis-regulatory sequence evolution
*Published: 2026 May 21*
Developmental gene function is often conserved over deep time, but
cis-regulatory sequence conservation is difficult to identify. Rapid sequence
turnover, paleopolyploidy, structural variation, and limited phylogenomic
sampling have impeded conserved noncoding sequence (CNS) discovery. Using
Conservatory, an algorithm that leverages microsynteny and iterative alignments
to map CNS-gene associations over evolution, we uncovered ~2.3 million CNSs,
including more than 3000 predating angiosperms, from 284 plant species spanning
300 million years of diversification. Ancient CNSs were enriched near
developmental regulators, and mutating CNSs near HOMEOBOX genes produced strong
phenotypes. Tracing CNS evolution uncovered key principles: CNS spacing varies,
but order is conserved; genomic rearrangements form new CNS-gene associations;
and ancient CNSs are preferentially retained among paralogs but are often lost
as cohorts or evolve into lineage-specific CNSs.
DOI: 10.1126/science.adt8983