The plant mitochondrial genome (mitogenome) has a complex organization and carries genetic traits of value in exploiting genetic resources. In this study, the Ilex macrocarpa mitogenome was sequenced and assembled to understand the genetic diversity and phylogenetic relationship. The mitogenome has a cyclic molecular structure and is 539,461 bp long with a GC content of 45.53%. It contained 39 protein-coding proteins, 19 tRNA genes, and 3 rRNA genes. The 146 simple sequence repeats and 591 dispersed repeat sequences were identified in the mitogenome. Codon usage analysis revealed a preference for codons ending in A/T. A total of 517 C to U RNA editing sites were predicted, with nad4 and ccmB being edited most frequently (39 times). Phylogenetic analysis via mitochondrial protein-coding genes showed that the Aquifoliales order contains sister plants to Lamiales, Solanales, and Gentianales. In addition, the conflicts between chloroplast and mitochondrial phylogeny were also observed. This study provides a theoretical framework for understanding the evolution, classification, and identification of the Ilex genus, which lays an important foundation for future molecular breeding investigations.

Ilex × altaclerensis ‘Belgica Aurea’ is an attractive ornamental plant bearing yellow-green variegated leaves. However, the mechanisms underlying the formation of leaf variegation in this species are still unclear. Here, the juvenile yellow leaves and mature variegated leaves of I. altaclerensis ‘Belgica Aurea’ were compared in terms of leaf structure, pigment content and transcriptomics. The results showed that no obvious differences in histology were noticed between yellow and variegated leaves, however, ruptured thylakoid membranes and altered ultrastructure of chloroplasts were found in yellow leaves (yellow) and yellow sectors of the variegated leaves (variegation). Moreover, the yellow leaves and the yellow sectors of variegated leaves had significantly lower chlorophyll compared to green sectors of the variegated leaves (green). In addition, transcriptomic sequencing identified 1675 differentially expressed genes (DEGs) among the three pairwise comparisons (yellow vs. green, variegation vs. green, yellow vs. variegation). Expression of magnesium-protoporphyrin IX monomethyl ester (MgPME) [oxidative] cyclase, monogalactosyldiacylglycerol (MGDG) synthase and digalactosyldiacylglycerol (DGDG) synthase were decreased in the yellow leaves. Altogether, chlorophyll deficiency might be the main factors driving the formation of leaf variegation in I.altaclerensis ‘Belgica Aurea’.

The cut branches of Ilex verticillata are highly ornamental and have high economic value. Since its introduction to China, it has received widespread attention. In the context of climate change today, ensuring its promotion and sustainable production in China is of great significance. In this study we evaluated the habitat suitability of the species using MaxEnt, combined with climate and soil variables, to assess the impact of climate change on its potential suitable habitat. We used 121 I. verticillata occurrence data and validated the model prediction using extensive field testing (12 test sites located in areas from 23.19° N to 42.91° N and 76.17° E to 125.14° E). The habitat suitability model (AUC = 0.854) performed well. Among them, three precipitation variables and one temperature variable were the main factors determining the distribution of I. verticillata in China. Field trial tests and model predictions of the suitability of I. verticillata were consistent, indicating that our model predictions are biologically meaningful and economically valuable. Under the Shared Socioeconomic Pathways (SSPs) climate change scenario, the high and medium suitable habitats for this species will be reduced in the future climate. This study helps to better understand the impact of climate change on I. verticillata and provides suggestions for the introduction and cultivation areas and protection of this species in China.

Ilex rotunda Thunb. is a prestigious ornamental tree renowned for its vibrant red fruits, yet the molecular mechanisms governing its fruit color variation remain poorly understood. The discovery of a rare yellow-fruited natural bud sport cultivar, ‘Peace Time’, provides an ideal model to investigate these processes compared to the wild-type red fruit. In this study, we integrated physiological evaluations, untargeted metabolomics, and de novo transcriptomics across multiple fruit developmental stages to elucidate the basis of this color transition. Our results demonstrated that the yellow phenotype is characterized by high lightness and yellowness values, driven by the profound suppression of anthocyanin biosynthesis. Biochemical and transcriptomic profiling revealed that DFR (dihydroflavonol 4-reductase), a critical “gatekeeper” gene, experiences severe transcriptional silencing in the yellow-fruited cultivar. This enzymatic bottleneck triggers a “passive substrate overflow,” redirecting shared precursors toward the parallel flavonol branch, resulting in the substantial accumulation of specific flavonols, including rutin and isoquercitrin. Furthermore, correlation network analysis highlighted a putative dual regulatory module associated with this metabolic reprogramming: the down-regulation of the putative activator bHLH30 coupled with the robust up-regulation of the putative repressor bHLH51, together likely contributing to the silencing of DFR transcription. These findings provide a comprehensive “dual-module” and “passive overflow” framework for fruit coloration in I. rotunda, highlighting a remarkable metabolic plasticity that reshapes this cultivar’s phytochemical profile and offers vital insights for future ornamental breeding.

Winterberry (Ilex verticillata) is a deciduous shrub within the Aquifoliaceae family that holds significant ornamental and medicinal value. However, the lack of systematic research on the genetic background and phylogenetic relationships among its cultivars has hindered germplasm conservation and breeding efforts. This study marks the first application of genotyping-by-sequencing (GBS) technology to analyze winterberry germplasm resources. Sequencing was performed on 79 samples from eight representative cultivars, and 3,411,968 high-quality single-nucleotide polymorphism (SNP) markers were developed using a de novo assembly strategy. Population structure analysis based on STRUCTURE indicated K = 8 as the statistically optimal number of genetic components according to the delta K statistic. However, when STRUCTURE results were interpreted together with principal component analysis (PCA) and phylogenetic reconstruction, the winterberry cultivars were consistently summarized into five major genetic clusters. Ilex verticillata ‘Winter Gold’ and I. verticillata ‘Winter Red’ shared highly consistent genetic backgrounds, indicating extremely close kinship; I. verticillata ‘Citronella’ and I. verticillata ‘Oosterwijk’ clustered closely together; I. verticillata ‘Red Sprite’ (Rizhao) and I. verticillata ‘Red Sprite’ (Dezhou), despite differing geographical origins, clustered together, demonstrating good genetic stability; and I. verticillata ‘Golden Verboom’ and I. verticillata ‘Little Goblin Red’ each formed independent genetic branches, possessing unique genetic backgrounds. This study concludes that GBS effectively reveals the complex genetic structure among winterberry cultivars. The findings not only provide accurate molecular evidence for cultivar identification and intellectual property protection but also lay a solid foundation for future hybrid breeding, including parent selection, identification of superior genes, and advancement of marker-assisted breeding.