Identification of the target genes of AqAPETALA3‐3 (AqAP3‐3) in Aquilegia coerulea (Ranunculaceae) helps understand the molecular bases of the conserved and nonconserved features of petals

Abstract

Identification and comparison of the conserved and variable downstream genes of floral organ identity regulators are critical to understanding the mechanisms underlying the commonalities and peculiarities of floral organs. Yet, because of the lack of studies in non‐model species, a general picture of the regulatory evolution between floral organ identity genes and their targets is still lacking. Here, by conducting extensive chromatin immunoprecipitation followed by high‐throughput sequencing (ChIP‐seq), electrophoretic mobility shift assay (EMSA) and bioinformatic analyses, we identify and predict the target genes of a petal identity gene, AqAPETALA3‐3 (AqAP3‐3), in Aquilegia coerulea (Ranunculaceae) and compare them with those of its counterpart in Arabidopsis thaliana, AP3. A total of 7,049 direct target genes are identified for AqAP3‐3, of which 2,394 are highly confident and 1,085 are shared with AP3. Gene Ontology (GO) enrichment analyses further indicate that conserved targets are largely involved in the formation of identity‐related features, whereas non‐conserved targets are mostly required for the formation of species‐specific features. These results not only help understand the molecular bases of the conserved and non‐conserved features of petals, but also pave the way to studying the regulatory evolution between floral organ identity genes and their targets.