Genome-wide identification, molecular evolution and expression analyses of the phospholipase D gene family in three Rosaceae species

Phospholipase D (PLD) and its product phosphatidic acid play important roles in plants response to various stresses. In this study, totally 40 putative PLD genes were identified in three Rosaceae species: 15 from apple (Malus × domestica), 14 from strawberry (Fragaria vesca) and 11 from Chinese plum (Prunus mume). Two MdPLD genes were identified as pseudogenes. These PLD genes can be divided into six groups (α, β/γ, δ, ɛ, ζ, and φ) through phylogenetic analysis. Three pairs of segmental PLD gene duplications were identified in the apple, along with four pairs in the strawberry and three pairs in the Chinese plum. In addition, two tandem PLD gene duplications were identified in the strawberry. Thirty-three out of the 40 PLD genes were observed within conserved synteny blocks, suggesting that PLD genes in these species may have originated from a common ancestor. The primary driving force behind the evolution of these PLD genes was found to be purifying selection. Gene expression analysis showed that PmPLDs were expressed differentially in various organs. Five PmPLD genes were significantly up-regulated by ABA or salt treatment.

► 15, 14 and 11 PLD members were identified in apple, strawberry and Chinese plum, respectively.
► The identified PLD genes were divided into six subgroups.
► PLD genes in these three species may have originated from common ancestor.
► We examine the expression level of PLD in five Chinese plum organs and under stresses.