Comparative analysis of NF-Y transcription factors in four orchids with expression insights from Gastrodia elata

The NUCLEAR FACTOR Y (NF-Y) transcription factor family plays a crucial regulatory role in various aspects of plant development, physiological responses, and light signaling pathways. Nevertheless, there are limited reports on the characteristics and functions of NF-Ys in orchids. This study identified the NF-Y gene family in four orchids (Gastrodia elata, Gastrodia menghaiensis, Platanthera guangdongensis, and Platanthera zijinensis) and analyzed their structural domains, physicochemical properties, phylogenetic relationships, gene collinearity, and the cis-elements in their promoter region. A total of 91 NF-Ys were identified from four orchids, among which NF-Y gene numbers varied among orchid species, with relatively fewer NF-Y genes identified in fully mycoheterotrophic orchids compared with partially mycoheterotrophic taxa. Phylogenetic analysis classified these genes into three subfamilies, and the protein domains and gene structures of the same branch exhibited high similarity. The promoters of these NF-Ys are enriched with photoresponsive cis-elements. During floral organ development in G. elata, GelNFY2, GelNFY6, and GelNFY14 were significantly downregulated at the large bud stage (S2) but significantly upregulated in the lip of flowering stage (S4), suggesting their potential involvement in lip development. In conclusion, this study provides a valuable resource for further investigation into the regulatory functions of the NF-Y gene family in orchids.