Widespread turnover of a conserved cis-regulatory code across 589 grass species

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Comparative genomics facilitates identifying functional loci for trait variation using non-model organisms.
• Cis-regulatory regions are key drivers of phenotypic evolution, but linking them to specific functions is difficult.

Purpose of the Study:

• To identify conserved cis-regulatory motifs and their evolutionary dynamics across grass species.
• To investigate the relationship between cis-regulatory element evolution and ecological niche transitions.

Main Methods:

• Identification of 514 cis-regulatory motifs enriched in regulatory regions of five grass species.
• Quantification of motif instance occupancy across 589 grass species using new genome assemblies.
• Application of phylogenetic mixed models to associate motif evolution with environmental factors.

Main Results:

• 73% of identified motifs were conserved across all five diverse grass species, indicating a conserved regulatory code.
• Widespread gain and loss of motif instances occurred over evolutionary time, with rapid decline post-divergence but significant ancient conservation.
• Convergent gains of HSF/GARP motifs were linked to temperate environments and an Alpha-N-acetylglucosaminidase gene.

Conclusions:

• Cis-regulatory evolution in grasses follows a "stable motifs, variable binding sites" model, characterized by turnover of individual binding sites.
• Comparative genomics and phylogenetic modeling are powerful tools for uncovering the genetic basis of complex traits and evolutionary adaptations.