Land-plant Phylogenomic and Pomegranate Transcriptomic Analyses Reveal an Evolutionary Scenario of CYP75 Genes Subsequent to Whole Genome Duplications

Regulatory and developmental genes are retained following whole-genome duplication (WGD) events, and, thus, are central to elucidating the evolution of the gene family subsequent to WGDs. Among these genes, the CYP75 gene family is a key member of the biggest enzyme superfamily in land-plant lineages. Although the molecular genetics of the biological progress involved with CYP75 genes have been partly elucidated, the evolution after WGDs in landplant lineages are still largely unknown. Here, we identified CYP75 orthologues in pomegranate (Punica granatum) and other twenty-five representative species to explore the gene evolution under WGD shaping on a broad evolutionary scale. Phylogenomic analyses identified genome-wide CYP75 candidates and suggested that a recent duplication of the CYP75 genes in seed plants occurred prior to the split of gymnosperms and angiosperms approximately 400 million years ago. Molecular evolution analyses revealed that CYP75 gene lineages evolved under a different purifying selection pressure, and slight relaxations occurred in the recent duplication groups in gymnosperms and angiosperms. The syntenic analyses showed that WGDs together with segmental duplications contributed to the CYP75 gene evolution in pomegranate. RT-PCR, qRT-PCR and RNA-Seq verification suggested that pomegranate CYP75 genes evolved through exon fusion and had a fruit-specific expression pattern. Neo- or sub-functionalization is the main fate of CYP75 genes following duplication. The expression pattern of homologous copies of CYP75 in pomegranate supports the CYP75 family evolution contributing to species reproduction that showy fruit colours attracted birds and other animals to spread seeds. Integration of the above analyses generated a putative evolutionary scenario of the CYP75 family in land plants. Our data provided a potential reference model to further elucidate the evolution of the regulatory and developmental gene families after WGDs.