Natural regeneration is deemed essential for maintaining biodiversity and ecosystem stability. Previous studies, however, have primarily concentrated on regions exhibiting limited environmental and climatic variability, overlooking the classification of natural regeneration based on age and source. Research conducted at the mesoscale, characterized by increased environmental variability and the incorporation of neighborhood competition and understory-associated vegetation, enhances our comprehension of the multifaceted influences on natural regeneration. To comprehend this issue, this study implemented 60 plots, each measuring 20 m × 20 m, across five distinct areas of Chongqing, China. Twenty explanatory variables were chosen from five diverse categories: understory vegetation, neighborhood competition, stand structure, climatic factors, and environmental factors. And the naturally regenerated species were classified into seedlings and saplings, as well as endogenous and exogenous species, based on their age and origin. We examined the response of the different categories of natural regeneration to various factors and constructed a structural equation model (SEM) for significant factors to investigate their direct and indirect effects on natural regeneration. A total of 61 regenerated tree species belonging to 29 families and 42 genera were found in the study area, and the naturally regenerating species with high importance values were Quercus fabri, Robinia pseudoacacia, Alangium chinense, Cunninghamia lanceolata, and Ligustrum lucidum. It was found that neighborhood competition and understory-associated vegetation explained the largest proportion (more than 50%) of the variation in the different categories of natural regeneration, and forests with clumped distribution (W), a high mingling index (M) and strong competition (H) had a reduced natural regeneration capacity. Understory-associated herbs significantly reduced natural regeneration and the crowdedness index (C) significantly inhibited the understory-associated herbs, thus indirectly promoting natural regeneration. The shrub cover is significantly and positively correlated with the number of naturally regenerated plants and can be used as an indicator of a forest community’s regeneration potential. Understanding the differences in the importance of various factors at the mesoscale, as well as their direct and indirect impacts, can help us further comprehend the mechanisms of natural regeneration and provide a foundation for the sustainable development of forests.

R. platypodum (Rhododendron platypodum) is an endangered alpine species with a highly restricted distribution in the southwestern region of China, which possesses significant ornamental and horticultural value. In this study, the high-quality genome assembly of R. platypodum at the chromosomal level is reported. The total genome size was determined to be 642.25 Mb, with a contig N50 of 25.64 Mb, and it contains 36,522 predicted genes. Comparative genomic analysis between R. platypodum and other species revealed the expansion of gene families, such as those related to transition metal ion binding and sodium ion transport, as well as the contraction of gene families involved in the recognition of pollen and pollen–pistil interaction. These findings might explain the adaptation of R. platypodum to rocky habitats and contribute to its endangered status. Furthermore, a heat stress experiment was conducted on R. platypodum, followed by transcriptome sequencing and physiological co-analysis to construct a co-expression network. This analysis identified the candidate gene TAR1-A and other transcription factors exhibiting differential expression under heat stress. The whole-genome sequencing, transcriptome analysis, and physiological co-analysis of R. platypodum provide valuable resources for its conservation and offer insights into its mechanisms of heat stress.