Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants

MicroRNA (miRNA)‐directed posttranscriptional gene silencing (miR‐PTGS) is an integral component of gene regulatory networks governing plant development and responses to the environment. The sequence homology between Sly‐miR4376, a miRNA common to Solanaceae and reported to target autoinhibited Ca(2+)‐ATPase 10 (ACA10) messenger RNA (mRNA) in tomato, and Arabidopsis miR391 (Ath‐miR391), previously annotated as a nonconserved member of the deeply conserved miR390 family, has prompted us to revisit the function of Ath‐miR391, as well as its regulatory conservation. A combination of genetic, molecular, and bioinformatic analyses revealed a hidden conservation for miR‐PTGS of ACA10 homologs in spermatophytes. We found that the Arabidopsis ACA10 mRNA undergoes miR391‐directed cleavage in vivo. Furthermore, transgenic overexpression of miR391 recapitulated the compact inflorescence (cif) phenotypes characteristic of ACA10 loss‐of‐function mutants, due to miR391‐directed PTGS of ACA10. Significantly, comprehensive data mining revealed robust evidence for widespread PTGS of ACA10 homologs directed by a superfamily of related miRNAs sharing a conserved sequence core. Intriguingly, the ACA‐targeting miRNAs in Poaceae also direct PTGS for calmodulin‐like proteins which are putative Ca(2+) sensors. The PTGS of ACA10 homologs is therefore directed by a miRNA superfamily that is of ancient origin and has undergone rapid sequence diversification associated with functional innovation.