Cleistogenes songorica is a cultivated turfgrass species that employs a mixed breeding system. To determine the morphological differences and molecular mechanisms of the chasmogamous (CH) and cleistogamous (CL) flowers of this species, we evaluated seed traits and analyzed six transcription factor (TF) families related to floral development. The seed traits from the CH and CL flowers were significantly different. In total, 12 CsAP2, 13 CsSPL, 9 CsGRF, 21 CsMYB, 15 CsMADS, and 1 CsLFY differentially expressed genes were identified from the transcriptome of the C. songorica flowers, which was further supported by evolutionary relationships and conserved motifs. All collinear gene pairs had a Ka/Ks ratio <1. Analysis of the promoters and miRNAs of the TFs revealed that the members of the six TF families may coregulate the divergence of CH and CL flowers during evolution. Two CsAP2, 8 CsSPL, 6 CsGRF, 3 CsMYB (targeted by miR172s, miR156s, miR396a/b and miR159a/b, respectively), and 15 CsMADS genes as well as 1 CsLFY gene may be involved in the development of CH and CL flowers. This study is the first to analyze the differences between CH and CL flowers at the TF-family level, which will help in the understanding of dimorphic turfgrasses.
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