Amazing stuff!
"The study ... reveals that the power of plant genomes lies not only in their protein-coding genes, but also in ancient regulatory DNA sequences that control where, when and how strongly to turn on gene expression. ...
Scientists have long searched for similar ancient regulatory sequences in plants, but with limited success. Now, The Conservatory Project team has revealed the hidden ancient regulatory sequences that have been hiding in plain sight. ...
Plant genes are continually shuffling themselves around, which makes the links between genes and their master switches extremely hard to spot. ...
They identified over two million ancient gene master switches, which control gene expression across 284 plant species from 73 plant families. This includes DNA switches that pre-date the emergence of flowering plants over 300 million years ago. ..."
From the abstract:
"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 non-coding sequence (CNS) discovery.
Using Conservatory, an algorithm that leverages microsynteny and iterative alignments to map CNS-gene associations over evolution, we uncovered ~2.3 million 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."
A deep-time landscape of plant cis-regulatory sequence evolution (no public access)
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