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

Area of Science:

• Evolutionary biology
• Genomics
• Developmental biology

Background:

• Conserved non-coding sequences (CNSs) are crucial for gene regulation but challenging to identify due to rapid sequence evolution and genomic changes.
• Previous methods struggled to discover CNSs across vast evolutionary timescales and diverse plant species.

Purpose of the Study:

• To develop and apply a novel computational approach for discovering ancient CNSs and their associated genes across plant evolution.
• To investigate the evolutionary dynamics and functional significance of conserved cis-regulatory elements.

Main Methods:

• Developed the Conservatory algorithm, utilizing microsynteny and iterative alignments to map CNS-gene associations.
• Analyzed genomic data from 284 plant species spanning 300 million years of diversification.
• Performed experimental validation by mutating CNSs near HOMEOBOX genes.

Main Results:

• Identified approximately 2.3 million CNSs, including over 3,000 ancient CNSs predating angiosperms.
• Ancient CNSs were found to be significantly enriched near developmental regulator genes.
• Mutations in CNSs near HOMEOBOX genes resulted in pronounced developmental phenotypes.

Conclusions:

• The order of CNSs is conserved, though spacing varies, and genomic rearrangements can create new CNS-gene links.
• Ancient CNSs show preferential retention in paralogs but can be lost or evolve into lineage-specific elements.
• This study provides a powerful framework for discovering ancient regulatory elements and understanding their evolutionary roles.