Background: Kinesins are ATP-dependent molecular motors that mediate intracellular transport, cytoskeleton remodeling, and abiotic stress responses in plants. The KIN gene family remains poorly characterized in Prunus mume. This study aimed to explore the evolutionary features and cold-responsive functions of the PmKIN gene family. Methods: A systematic genome‑wide analysis was performed in P. mume. We performed phylogenetic classification, conserved domain detection, gene duplication and selection pressure analysis, cis-element prediction, tissue expression profiling, cold stress expression assay, and protein interaction network prediction. Results: Fifty PmKIN family members were defined and grouped into 10 subfamilies. K14 subfamily contained the largest number of members. All members harbor conserved motor domains, and segmental duplication drove the expansion of this gene family, which was overall constrained by purifying selection. The PmKIN homologous genes were highly conserved among Rosaceae species, including Prunus persica, Prunus armeniaca, Prunus avium, and Malus domestica. Our promoter analysis detected abundant cis-elements for light, hormone, cold, and drought signals in PmKIN genes, especially in the K14 and K7 subfamilies. These genes displayed tissue-biased expression, with roots and stems showing much higher transcript levels than fruits. Under low-temperature stress, the tolerant cultivar appeared to mount a relatively rapid PmKIN upregulation, whereas the sensitive one seemed to show a sluggish response and poor recovery. Three members (PmKIN22/27/35) were suggested to be potentially critical in low-temperature-response regulation. A 285-pair interaction network predicted PmKIN45 as the central hub, and functional predictions imply that PmKIN proteins may be linked to microtubules, hormone pathways, and stress signaling, possibly coordinating growth and low-temperature responses. Conclusions: This work screens candidate genes associated with low-temperature responses in P. mume, providing genetic resources for the molecular breeding of cold-resistant cultivars and expanded cultivation of P. mume and other ornamental horticultural species.

The basic Helix-Loop-Helix (bHLH) transcription factor family is crucial for plant growth, development, and stress response regulation. Despite previous studies on the bHLH gene family in Lagerstroemia indica, many bHLH genes remain unidentified, hindering further research on LibHLHs. Here, we identified 150 LibHLHs from the genome of L. indica and categorized them into 12 subfamilies (comprising 25 subgroups) showing conservation within subgroups. Cis-acting element analysis suggests roles in plant development, and responses to light, hormones, and stress. Examination of gene expression patterns highlighted the potential involvement of specific genes, such as LibHLH25 in subgroup IIIf, LibHLH68, LibHLH106, and LibHLH142 in subgroup IIIb, and LibHLH112 in subgroup VIIa, in anthocyanin biosynthesis in leaves of L. indica. This investigation enhances our comprehension of the complexity of the bHLH gene family and highlights the potential roles of LibHLHs in anthocyanin biosynthesis in L. indica, offering valuable insights for future genetic breeding endeavors.