A comprehensive update on genome-wide analysis of autophagy-related genes in wheat (Triticum aestivum L.)

Autophagy is a highly conserved cellular process that plays essential roles in plant growth, development, and responses to environmental stresses. In this study, we performed a genome-wide analysis and characterization of autophagy related genes (ATGs) in wheat. A total of 100 proteins were identified, including 94 ATGs and 6 NBR1s, grouped into 19 subfamilies. Gene structure analysis revealed conserved intron–exon arrangements within families, while motif analysis showed diversity, especially in scaffold proteins such as ATG2, ATG9, and ATG11. Phylogenetic analysis with rice, maize, and Arabidopsis confirmed evolutionary conservation, along with expansions of certain gene families like ATG18 and ATG8 in wheat. Chromosomal mapping indicated a broad distribution across the 21 wheat chromosomes, with clustering in subtelomeric regions that may contribute to gene expansion and functional diversification. Promoter analysis revealed abundant cis-regulatory elements responsive to hormones, abiotic stresses, and developmental cues, suggesting complex transcriptional control. Expression profiling demonstrated that core genes such as ATG3, ATG8, and NBR1 are constitutively expressed across tissues, while several ATG18 members showed stress- or tissue-specific expression. Notably, autophagy genes responded strongly to phosphorus starvation, cold, heat, and drought stresses, with distinct patterns indicating both general and stress-specific roles. Overall, this study provides an advanced and comprehensive overview of wheat ATGs, offering valuable insights into their evolutionary conservation, regulatory networks, and functional roles in development and stress adaptation. It also represents an improved analysis of wheat autophagy genes, incorporating the identification of 100 ATGs, evidence of their conserved domain structures and protein–protein interaction networks.