Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Phalaenopsis equestris

The SQUAMOSA promoter-binding protein-like (SPL/SBP) family plays crucial roles in multiple developmental processes. Phalaenopsis equestris is a key ornamental and breeding species known for producing abundant colorful flowers on a single inflorescence. The SPL gene family in this species remains largely uncharacterized. In this study, 15 SPL genes were identified, all encoding proteins that are bioinformatically predicted to be nuclear-localized, hydrophilic, and unstable, with conserved SBP domains. Phylogenetic and collinearity analyses revealed a closer evolutionary relationship with rice SPLs than Arabidopsis SPLs. Conserved motif and gene structure analyses showed that subfamily II members possess more motifs and introns, implying functional complexity. Five PeqSPLs contained transmembrane domains, suggesting potential dual nuclear/cytoplasmic roles. Promoter analysis revealed abundant cis-elements responsive to light, stress, and phytohormones. Expression profiling across tissues showed that PeqSPL2, PeqSPL3, and PeqSPL5 exhibited broad expression and PeqSPL10 exhibited predominantly high expression in flowers, indicating possible roles in normal growth and floral development. This study provides a foundation for further functional exploration of PeqSPL genes in P. equestris.