Comparative Analysis of the Transcriptomes of Three Varieties Provides Insights Into the Diversity of the Heat Response Mechanisms in Clematis Species

Abstract Background: Clematis species are commonly grown in western and Japanese gardens. Heat stress can inhibit many physiological processes mediating plant growth and development. The mechanism regulating responses to heat has been well characterized in Arabidopsis thaliana and some crops, but not in horticultural plants, including Clematis species. Results: In this study, we identified a heat-sensitive Clematis variety (Clematis alpina ‘Stolwijk Gold’) and two heat-tolerant Clematis varieties (Clematis vitalba and Clematis viticella ‘Polish Spirit’) based on heat-related physiological indices. The leaf transcriptomes under normal and heat stress conditions were analyzed by RNA sequencing. Additionally, heat tolerance-related genes (HTGs) were identified and their expression levels were analyzed. Following heat treatments, 41.67% of the differentially expressed HTGs in Stolwijk Gold had down-regulated expression levels, whereas only 9.80% and 21.36% of the differentially expressed HTGs in C. vitalba and Polish Spirit, respectively, had the same trend. The HTGs’ co-expression and protein–protein interaction networks revealed that the hub genes regulating Clematis resistance to heat stress encode heat shock transcription factors (HSFs) and heat shock proteins (HSPs). Moreover, the sensitivity of Stolwijk Gold to heat is mainly due to the heat-induced down-regulated expression of these genes. On the basis of phylogenetic and expression analyses, the differentially expressed HSF and HSP genes in the three examined varieties were divided into three and four clades, respectively, with similar expression profiles common among orthologous family members. Furthermore, we identified two HSF classes in C. vitalba that may have diverse functions influencing heat resistance. Conclusions: Our study provides insights into the diversity of the heat response mechanisms among Clematis species and may be useful for breeding new heat-resistant ornamental Clematis varieties.