Genome-Wide Identification and Expression Analyses of the PP2C Gene Family in Paulownia fortunei

We explored the composition and roles of the protein phosphatase 2C (PP2C) family in Paulownia fortunei. The genome P. fortunei harbored 91 PfPP2C genes, encoding proteins with 120–1107 amino acids (molecular weight range, 13.51–124.81 kDa). The 91 PfPP2Cs were distributed in 12 subfamilies, with 1–15 PfPP2Cs per subfamily. The number and types of conserved structure domains differed among PP2Cs, but the distribution of conserved motifs within each subfamily was similar, with the main motif structure being motifs 3, 16, 13, 10, 2, 6, 12, 4, 14, 1, 18, and 8. The PfPP2C genes had 2 to 20 exons. There were ABA-response elements in the promoters of 42 PfPP2C genes, response elements to phytohormones, and stress in the promoters of other PfPP2C genes. A covariance analysis revealed that gene fragment duplication has played an important role in the evolution of the PfPP2C family. There were significant differences in the transcript levels of some PfPP2C genes in P. fortunei affected by witches’ broom (PaWB) and after treatment with rifampicin and methyl methanesulfonate. PfPP2C02, PfPP2C12, PfPP2C19, and PfPP2C80 were strongly related to PaWB. These findings provide a foundation for further studies on the roles of PP2Cs in PaWB.