Evolutionary dynamics of Orchid DL paralogs: gene duplication, functional divergence, and expression patterns across Orchid subfamilies

Background Orchids are known for their extraordinarily diversified floral structures and evolutionary adaptations. The study of transcription factor genes, such as the YABBY gene DROOPING LEAF, is crucial for understanding the molecular mechanisms underlying orchid development and evolution. This study aims to elucidate the evolutionary dynamics and expression patterns of DL genes across orchid subfamilies. Results Through genomic and transcriptomic analyses, we identified 25 full-length DL genes in orchids, with two paralogs (DL1 and DL2-like genes) observed in Epidendroideae, Orchidoideae, Cypripedioideae, and Vanilloideae, while the most ancestral Apostasioideae retained a single-copy gene. In addition to the functional DL, genomic features reveal the presence of a DL pseudogene within Apostasioideae. Evolutionary analyses revealed relaxed selection pressures acting on orchid DL2 paralogs. Sequence comparison and expression analyses uncovered potential pseudogenization events affecting DL2 paralogs of Vanilloideae and Cypripedioideae, while in the most recent subfamily Epidendroideae, differential expression of DL2 in inner perianth tissues suggests the possible acquisition of a new function in the development of the lip callus. Conclusions Our study provides insights into the evolutionary trajectory of DL genes in orchids. The relaxed selection on DL2 paralogs might be related to pseudogenization or functional divergence. Pseudogenization of DL2 in most ancestral orchids and possible neofunctionalization in Epidendroideae indicate a dynamic evolutionary process shaping the functional repertoire of DL genes. These findings contribute to our understanding of the genetic basis of orchid diversity and evolution, with implications for future studies on the role of transcription factors in plant development and adaptation.