Genome-Wide Identification, Characterization, and Expression Analysis of the DnaJ/HSP40 Gene Family in Response to Heat, Drought, and Salt Stress in Tomato (Solanum lycopersicum)

Heat shock protein 40 (DnaJ/HSP40) co-chaperones are key regulators of protein folding, cellular homeostasis, and stress adaptation in plants. Although individual HSP40 proteins have been functionally characterized in tomato and HSP40 members have also been examined within broader HSP chaperone networks, an integrated characterization of the tomato HSP40 family combining evolutionary relationships, structural features, promoter regulation, tissue-specific expression, multi-stress transcriptomic profiling, and experimental expression validation remains limited. In this study, a systematic genome-wide analysis identified 95 tomato HSP40 genes, which were classified into three phylogenetic groups. The encoded proteins contained conserved J-domains, and distinct conserved motif distributions, while the genes exhibited variable exon–intron organization. Chromosomal mapping revealed an uneven distribution across the 12 tomato chromosomes, with segmental duplication representing the predominant duplication pattern contributing to HSP40 family expansion. Promoter analysis identified 37 distinct types of cis-regulatory elements associated with hormone signaling, growth and development, and abiotic stress responses, indicating complex transcriptional regulation. Tissue-specific expression analysis showed that the majority of HSP40 genes were expressed across multiple tissues and developmental stages, whereas several members exhibited preferential or limited expression patterns. Transcriptomic profiling under drought, salinity, and heat stress revealed dynamic and stress-dependent regulation, with some genes showing consistent induction across multiple stresses and others being markedly repressed. qRT-PCR analysis of selected HSP40 genes further confirmed distinct temporal responses to drought, salinity, and heat stress, supporting their potential involvement in abiotic stress adaptation. Collectively, these findings provide an integrated genomic, evolutionary, structural, and transcriptional framework for the tomato HSP40 family and identify candidate genes for future functional validation and molecular breeding strategies aimed at improving tomato resilience to abiotic stress.