Interspecies transcriptomic comparisons reveal potential molecular genetic mechanisms underlying the evolutionary development of dimorphic flowers in <i>Viola</i>

Abstract Viola philippica develops chasmogamous (CH) and cleistogamous (CL) flowers under different photoperiods, while Viola cornuta only forms CH flowers. Gene expression variations driven by photoperiods that contribute to the CH–CL transition remain largely unknown. Here, we performed comparative transcriptomics between V . philippica and V . cornuta during flower development and revealed differentially expressed genes (DEGs) between CL and CH flowers. Compared to CL flowers in V . philippica under 16‐h daylight conditions, DEGs, including auxin response factor (ARF) genes and floral MADS‐box genes, were identified in CH flowers under 12‐h daylight conditions; however, their homologous genes in V . cornuta were equivalently expressed in CH flowers across both photoperiods. Genes in the modules most significantly correlated with floral types were DEGs between CH and CL flowers in V . philippica , but they were not altered in V . cornuta CH flowers under either photoperiod. Moreover, genes related to fatty acid, flavonoid, and anthocyanin biosynthesis were upregulated in CH flowers, whereas defense response genes were upregulated in CL flowers. Furthermore, the genes co‐expressed with the floral B‐class MADS‐box gene APETALA3 included ARFs , CRABS CLAW , BIGPETALp , TCP14 , and UGT87A , whose homologous genes are involved in nectary and floral organ development, including organ identity, size, and coloration. Thus, the putative coordination of genes involved in defense response and auxin signaling pathways, floral organ identity determination and growth, and fatty acid and flavonol biosynthesis in response to photoperiod might regulate CH–CL development in V . philippica , thus providing new insights into the evolution of dimorphic flower development in Viola .