Genome-Wide Identification, Evolution and Expression Profiling of the Pentatricopeptide Repeat (PPR) Gene Family in Woodland Strawberry (Fragaria vesca) and Cultivated Strawberry (Fragaria × ananassa)

Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in plants and play important roles in organellar RNA metabolism, plant growth and development, and stress responses. In strawberry (Fragaria spp.), an economically important crop of the Rosaceae, the composition, evolutionary history and expression patterns of this family have not been characterized systematically. Using the genome assemblies of diploid woodland strawberry (Fragaria vesca) and octoploid cultivated strawberry (Fragaria × ananassa), we identified PPR genes genome-wide with HMMER and integrated subfamily classification, chromosomal mapping, phylogeny, gene duplication, selection pressure and transcriptome expression analyses. A total of 603 and 1785 PPR genes were identified in F. vesca and F. × ananassa, respectively, with P:PLS ratios of 1.29 and 1.27 that agree closely with the value of 1.20 obtained for the positive control Arabidopsis thaliana. Most PPR genes lacked introns, and single-exon genes accounted for 61.5% and 42.3% of the two repertoires. F. vesca PPR genes were unevenly distributed among the seven chromosomes, with the largest number on Fvb6 (121), whereas F. × ananassa PPR genes were distributed among 28 chromosomes (43 to 105 genes per chromosome). Phylogenetic analysis resolved the P and PLS subfamilies into two clearly separated clades and revealed numerous species-specific expansion clusters at the tips of the Fragaria branches. Duplication analysis showed that expansion of the F. vesca PPR family depended mainly on tandem duplications and intra-chromosomal segmental duplications, whereas expansion in F. × ananassa proceeded mainly through inter-chromosomal segmental duplications (retention of subgenome homeologs, 96.4%). Selection pressure analysis showed that 97.1% of duplicated pairs had Ka/Ks < 1 and 71.75% had Ka/Ks < 0.5, indicating strong purifying selection; the mean Ks of F. vesca (1.02) was much higher than that of F. × ananassa (0.116), reflecting differences in the timing of duplication. Transcriptome analysis showed pronounced differential expression of PPR genes among tissues and across fruit developmental stages. Under cold stress, 45 differentially expressed PPR genes were identified in F. vesca (23 down-regulated and 22 up-regulated), whereas no gene passed the stringent threshold under ABA treatment in F. × ananassa and only 29 candidate genes were obtained. This study provides the first systematic characterization of the strawberry PPR gene family and a resource of candidate genes for dissecting PPR function in the Rosaceae and for genetic improvement of stress tolerance and fruit quality in strawberry.