Genome-wide identification of conserved RNA structure in plastids

The systematic discovery of functional RNA structure directly from sequence remains a central challenge in genomics. Plastid genomes, with their deep evolutionary history and extensive data availability, provide an ideal system to address this challenge. Here, we developed a stringent, covariation-based pipeline that integrates well-established and novel tools to perform an unbiased screen for conserved secondary structures across ∼14,000 plastid genomes. Our analysis identified a repertoire of 57 conserved RNA motifs. Beyond recovering known functional classes, we uncovered cis -acting novel structures within the UTRs and introns of key photosynthetic genes, including psbN, clpP, and atpF, as well as trans -acting antisense RNAs to petB and psbT, pointing to previously unknown regulatory elements. This work provides a stringent atlas of conserved plastid RNA structures, reveals an extensive layer of post-transcriptional regulation, and establishes a robust framework for structural genomics in other systems, including nuclear genomes.