Genome-wide sequence and expressional analysis of autophagy Gene family in bread wheat (Triticum aestivum L.)

Autophagy, a highly conserved intracellular degradation system, is regarded to be responsible for self-defense and protect cells from abiotic stress. Extensive studies have demonstrated that autophagy plays a crucial role in regulating plant growth and development as well as in response to diverse stresses. However, little is known about autophagy-associated genes (ATGs) in wheat, especially those involved in the regulatory network of stress processes. In this study, a total of 108 putative wheat ATGs (TaATG) were obtained based on a genome-wide search approach. Phylogenetic analysis classified them into 13 subfamilies, of which the TaAtg16 subfamily consisted of 29 members, ranking it the largest subfamily. The conserved motif compositions as well as their exon-intron structures were systematically analyzed and strongly supported the classification. The homoeologous genes tended to have similar gene features during wheat polyploidization. Furthermore, a total of 114 putative cis-elements were found, and those related to hormone, stress, and light responsiveness were abundantly presented in the promoter regions. Co-expression network analysis revealed that orthologous VAMP727 was the hub node of the whole network, and complex interactions were also found. Finally, the expression profiles of TaATGs among different tissues and under abiotic stresses were investigated to identify tissue-specific or stress-responsive candidates, and then 14 were validated by wet-lab analysis. Results showed that the TaAtg8 subfamily played a crucial role in tissue autophagy and stress defense, which could be considered as processes that are candidates for further functional study. This was the first study to comprehensively investigate the ATG family in wheat, which ultimately provided important clues for further functional analysis and also took a step toward uncovering the evolutionary mechanism of ATG genes in wheat and beyond.