A Genome-Wide Analysis of Pentatricopeptide Repeat Protein (PPR) Genes in Cotton

Pentatricopeptide repeat (PPR) proteins are encoded by genes from one of the largest families in higher plants. In this study, 513, 558, 990 and 1054 PPR genes were identified in sequenced genomes of G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. The two cultivated allotetraploid species have similar numbers of PPR genes, which are almost the sum of these from the two diploid progenitors. PPR genes can be further divided into P subfamily and PLS subfamily based on the P motif variation and a series of conserved C-terminal domains. The P subfamily contained roughly half of the identified PPR genes in the four species. With TargetP software, 295 (57.5%), 345 (61.8%), 600 (60.6%), and 544 (51.6%) PPR proteins were predicted to be targeted to mitochondria or chloroplasts in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. Phylogenetic trees indicated a small portion of subfamily members were not clustered to the same group, and genetic variations might have happened in the C-terminal motifs during the natural or artificial selection in cotton. A comparative physical map of PPR genes in the four Gossypium species showed that most of the PPR genes in G. raimondii, G. hirsutum and G. barbadense except for G. arboreum had good collinear relationships. By comparing with the published linkage maps of CMS fertility restorer genes (Wang et al. 2009; Wu et al. 2014), we found l1 PPR proteins located in the target region of Rf genes, but four of them were targeted to chloroplasts. The sequence variation and expression variation of these genes between sterile line, fertile maintainer line and fertility restorer line will be identified and analyzed. In addition, an transcriptomic analysis of PPR genes in various tissues and environmental conditions will be performed.