Genome-Wide Identification and Expression Analysis of the PME and PMEI Gene Families in Diospyros kaki: A Bioinformatics Study

Pectins are major components of cell walls in plants. Pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs) play crucial roles in pectin synthesis and metabolism. Overall, 28 putative DkPMEs and 29 putative DkPMEIs were identified from the D. kaki genome. According to phylogenetic analysis, DkPME/DkPMEI proteins can be classified into four and five clades, respectively. Motif and gene structure analysis showed that DkPME/DkPMEI are highly conserved in the same clades, which indicates that the function of these DkPME/DkPMEI were similar. Besides, DkPME/DkPMEI genes were distributed unevenly on their corresponding chromosomes. Synteny analysis showed that PME or PMEI gene usually matched with more than one DkPME/DkPMEI in D. oleifera, D. lotus, and A. thaliana, implying that the function of these genes in D. kaki may be diverse. Expression analysis showed that DkPME/DkPMEI from the same clade exhibited diverse expression patterns, indicating that these genes might have diverse functions. Functional protein-protein interaction network analysis showed that DkPMEI21 and DkPMEI15 were core nodes and were, respectively, positive and negative regulators for carbohydrate metabolism, stress responses, and sugar signaling. This study provides a theoretical basis for the functional characteristics, evolutionary relationship, and role of these gene families in developing persimmon fruit.

Automated summary

Pectins are important components of plant cell walls. This study identified multiple putative DkPMEs and DkPMEIs in the persimmon genome and classified them into different clades based on phylogenetic analysis. These genes were found to be highly conserved within the same clades, indicating similar functions. Furthermore, the distribution of these genes on chromosomes was uneven. Expression analysis showed diverse expression patterns within the same clade, suggesting diverse functions. Protein-protein interaction network analysis revealed core nodes involved in carbohydrate metabolism, stress responses, and sugar signaling. This study provides important insights into the functional characteristics, evolutionary relationship, and role of these gene families in persimmon fruit development.