The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, evidence of massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well-defined due to the sparse sequence data available from early-diverging land plant lineages. We exploit the comprehensive OneKP dataset of over 1,000 transcriptomes from diverse plants and algae to establish a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterise over 2,250,000 PPR motifs in over 400,000 proteins. In lycophytes, polypod ferns and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity. We identify sequence variation that implies functional differences between PPR proteins in seed plants versus non-seed plants and which we propose to be linked to seed-plant-specific editing cofactors. Finally, using the sequence variation across the dataset, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA editing factors, given their phylogenetic distribution and sequence characteristics.
|Date made available||11 Dec 2019|