Unveiling the architecture variability of coding regions in Prunus persica: Identification and characterization of key gene families impacting plant development

Abstract

This study aimed to investigate gene families related to Prunus persica (peach) and their evolutionary relationships. Gene identification and sequence alignment methods were used to characterize Homeobox, MADS-box, NAC, and Receptor-kinase-like gene families. Gene expression data analysis was conducted to assess gene activity and regulatory mechanisms in peach plant development. Gene identification involved a local BLASTp analysis using protein sequences from Arabidopsis thaliana gene families as queries against the peach proteome. Multiple sequence alignment and phylogenetic tree construction were performed using ClustalW and iToL, respectively. Gene expression analysis utilized the GEO2R online tool and focused on two datasets, GSE71561 and GSE71460. Gene identification revealed 593 genes in total, with varying gene counts and sequence lengths among the different families. Phylogenetic analysis demonstrated distinct clusters within each gene family. Protein-protein interaction analysis showed significant interconnectivity among Homeobox transcription factors, while MADS-box and NAC gene families displayed lower connectivity. Enrichment analysis highlighted developmental processes associated with these gene families. Gene expression analysis provided insights into peach fruit development, ripening, and postharvest changes, revealing differential gene expression patterns and regulatory mechanisms. This study provides valuable insights into the gene families related to Prunus persica, their evolutionary relationships, and regulatory mechanisms. The identified genes and their functional characteristics contribute to a better understanding of peach development and fruit phenotypes. Further research is required to elucidate the implications of gene variations and interactions in the studied system