Genome-wide identification and expression analysis of Autophagy-Related Genes in eggplant (Solanum melongena L.)

Autophagy, a highly conserved cellular process in plants, plays a vital role in regulating abiotic stress responses and senescence. Eggplant is a widely cultivated vegetable crop, its fruit is susceptible to cold damage, and its molecular mechanisms underlying stress tolerance, fruit ripening, and senescence remain largely uncharacterized. In this study, we systematically identified 41 Autophagy-Related Genes (ATGs) in eggplant and through bioinformatics methods, we analyzed their gene structures, evolutionary features, chromosomal locations, and promoter elements. Additionally, we conducted RNA-seq transcriptome analysis of various eggplant organs as well as under different stress conditions, and assessed the expression patterns of the SmATG8 under cold stress in eggplant fruit. Our analysis results show that the SmATGs promoters have diverse cis-regulatory elements, with most SmATGs exhibiting low and stable expression levels in different tissues. Some genes displayed tissue-specific expression patterns. Under 4 °C low-temperature stress, the expression of the SmATG8 family was continuously upregulated, indicating that autophagy plays a crucial role in defending against cold damage in eggplant. Furthermore, we found that ATGs in dicots and monocots exhibit distinct homology patterns. Within the dicots, eggplant and pepper, both being Solanaceae plants, their ATGs exhibit high homology, suggesting that SmATGs in Solanaceae plants have unique homologous relationships. The analysis of SmATGs unveiled their potential contributions to plant stress responses, fruit ripening, and senescence, thus offering a theoretical foundation for further exploration of stress resistance and senescence mechanisms in eggplant.