A deep-time landscape of plant cis-regulatory sequence evolution

Amundson, Kirk R, Hendelman, Anat, Ciren, Danielle, Yang, Hailong, de Neve, Amber E, Tal, Shai, Sulema, Adar, Jackson, David, Bartlett, Madelaine E, Lippman, Zachary B, Efroni, Idan (September 2025) A deep-time landscape of plant cis-regulatory sequence evolution. bioRxiv. ISSN 2692-8205 (Submitted)

PDF 10.1101.2025.09.17.676453.pdf - Submitted Version Available under License Creative Commons Attribution. Download (27MB)

Abstract

Developmental gene function is conserved over deep time, but cis-regulatory sequence conservation is rarely found. Rapid sequence turnover, paleopolyploidy, structural variation, and limited phylogenomic sampling have impeded conserved non-coding sequence (CNS) discovery. Using Conservatory, an algorithm that leverages microsynteny and iterative alignments to map CNS-gene associations over evolution, we uncovered ∼2.3M CNSs, including over 3,000 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.

Item Type:	Paper
Subjects:	organism description > plant
CSHL Authors:	Hendelman, Anat Ciren, Danielle Jackson, David P. Lippman, Zachary B.
Communities:	CSHL labs > Jackson lab CSHL labs > Lippman lab CSHL Post Doctoral Fellows School of Biological Sciences > Publications
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	19 September 2025
Date Deposited:	09 Dec 2025 18:31
Last Modified:	09 Dec 2025 18:31
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42032

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