Genome-wide Identification and Expression Analysis of Autophagy-Related Genes (ATG) in Gossypium Spp. Reveals Their Crucial Role in Stress Tolerance

Autophagy is an evolutionarily conserved process mediated by AuTophaGy (ATG) genes, in which cellular components are degraded and recycled within vacuoles or lysosome. Yeast ATG was extensively studied; their homologs are reported in plants including Arabidopsis. However, they have not been reported in cotton. In the present study, the ATG cascade genes were studied in four Gossypium species, namely G. hirsutum, G. arboreum, G. herbaceum, and G. raimondii. A total of 40 GhirATG, 33 GaATG, 34 GherbATG, and 25 GrATG genes were identified in these species. These ATG sequences exhibited conserved ATG domains and other overlapping domains, including Ras, Pkinase, Snf7, WD40, Glyco_hydro_17, and bZIP_1, and were named based on their phylogenetic relationships with Arabidopsis ATGs. A phylogenetic analysis revealed evolutionary relationships among ATG genes among these species, as well as significant sub-clades indicating patterns of gene retention. Based on synonymous and non-synonymous substitutions, cotton groups diverged at different times from Arabidopsis. Gene structure analysis and chromosome localization showed exon-intron patterns and locations. Expression analysis of ATGs in different tissues during development and under stress conditions indicated their functional specificity. The ATG8 subclass genes were significantly expressed under abiotic stress conditions, indicating their role in stress response. In addition, qRT-PCR analysis of selected 12 GhirATGs in leaves treated with stress elicitors, MeJA, SA, NaCl, and PEG for varying time intervals showed a pattern of their significant upregulation. The findings contribute to our understanding of autophagy-related processes in cotton, including their potential role in stress response and development.