Termotolerância em Arracacia xanthorrhiza: RNA-seq e análise de famílias gênicas com estratégias computacionais

Abstract

Climate change has increased the frequency of extreme heat events and imposed significant challenges on agricultural production, especially for temperature-sensitive species. Arracacia xanthorrhiza Bancroft, known as mandioquinha-salsa, is an Andean vegetable of high socioeconomic importance, yet remains poorly studied at the genomic and molecular levels. This work investigated the molecular basis of the heat-stress response in A. xanthorrhiza and in closely related Apiaceae species, integrating bibliometric analysis, a bioinformatic pipeline for gene-family identification, and de novo transcriptome data. The bibliometric analysis showed that research on A. xanthorrhiza is concentrated in a few countries, mainly Brazil and Andean regions, and is primarily focused on food science and technology, starch properties, and nutritional composition. Agronomic, genomic, physiological, and abiotic-stress studies are less frequent, revealing important gaps for biotechnology and climate-adaptation strategies. Nevertheless, there has been recent growth in studies connecting the species to sustainability and resilient cropping systems. In the comparative stage, the pipeline based on conserved domains enabled the identification of HSF and HSP families (HSP20, HSP40, HSP60, HSP70, HSP90, and HSP100) in Arabidopsis thaliana and in four cultivated Apiaceae species. All families were detected in all species, with variation in gene counts, exon–intron structure, and predicted subcellular localization. Phylogenetic trees grouped the genes according to the functional classification of A. thaliana and revealed expansions and duplications in specific subfamilies. Conserved motifs confirmed the preservation of critical functional domains, providing a comparative perspective on the evolution of these families in heat-stress response. In the de novo transcriptome of A. xanthorrhhiza, assembled from Pavão cultivar plants under control and heat-stress conditions, libraries contained 20–24 million reads with over 96% mapping. The assembly generated 280,571 transcripts (mean length 884 nt; N50 = 1,393 nt; Ex90N50 = 1,465 nt), with 30.8% exceeding 1 kb. BUSCO analysis indicated 86.9% complete orthologs, reflecting good gene-space recovery and the complexity associated with the species’ tetraploid genome. Twelve differentially expressed genes were identified, including HSP20, HSP100/ClpB chaperones, and proteins involved in regulation and proteome remodeling. Functional annotation highlighted protein folding, heat response, and proteostasis. GO categories and the predominant KEGG pathway, protein processing and folding, reinforced the central role of chaperones in cellular protection. The absence of HSFs among the DEGs suggests that the sampled time-point captured a specific phase of the response, possibly regulated by post-transcriptional mechanisms. Taken together, the results demonstrate that A. xanthorrhiza responds to heat primarily through chaperones and protein-integrity maintenance, supported by conserved HSP/HSF families across Apiaceae, with evidence of subfamily-specific expansions. The integration of bibliometric, comparative, and transcriptomic analyses provides the first systematic overview of thermotolerance in mandioquinha-salsa and establishes a foundation for advances in breeding, biotechnology, and crop management under global warming scenarios.