Background: Ilex metabaptista is a woody tree species with strong waterlogging tolerance and is also admired as a landscape plant with high development prospects and scientific research value. Unfortunately, populations of this species have declined due to habitat loss. Thus, it is a great challenge for us to efficiently protect I. metabaptista resources from extinction. Molecular biology research can provide the scientific basis for the conservation of species. However, the study of I. metabaptista genetics is still in its infancy. To date, no mitochondrial genome (mitogenome) in the genus Ilex has been analysed in detail. Results: The mitogenome of I. metabaptista was assembled based on the reads from Illumina and Nanopore sequencing platforms; it was a typical circular DNA molecule of 529,560 bp with a GC content of 45.61% and contained 67 genes, including 42 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 286 dispersed repeats, 140 simple repeats, 18 tandem repeats, and 543 RNA editing sites. Analysis of codon usage showed that codons ending in A/T were preferred. Gene migration was observed to occur between the mitogenome and chloroplast genome via the detection of homologous fragments. In addition, Ka/Ks analysis revealed that most of the protein-coding genes in the mitogenome had undergone negative selection, and only the ccmB gene had undergone potential positive selection in most asterids. Nucleotide polymorphism analysis revealed the variation in each gene, with atp9 being the most notable. Furthermore, comparative analysis showed that the GC contents were conserved, but the sizes and structure of mitogenomes varied greatly among asterids. Phylogenetic analysis based on the mitogenomes reflected the exact evolutionary and taxonomic status of I. metabaptista. Conclusion: In this study, we sequenced and annotated the mitogenome of I. metabaptista and compared it with the mitogenomes of other asterids, which provided essential background information for further understanding of the genetics of this plant and helped lay the foundation for future studies on molecular breeding of I. metabaptista.

Background: Ilex pubescens is an important traditional Chinese medicinal plant with many naturally occurring compounds and multiple pharmacological effects. However, the lack of reference genomic information has led to tardiness in molecular biology research and breeding programs of this plant. Results: To obtain knowledge on the genomic information of I. pubescens, a genome survey was performed for the first time by next generation sequencing (NGS) together with genome size estimation using flow cytometry. The whole genome survey of I. pubescens generated 46.472 Gb of sequence data with approximately 82.2 × coverage. K-mer analysis indicated that I. pubescens has a small genome of approximately 553 Mb with 1.93% heterozygosity rate and 39.1% repeat rate. Meanwhile, the genome size was estimated to be 722 Mb using flow cytometry, which was possibly more precise for assessment of genome size than k-mer analysis. A total of 45.842 Gb clean reads were assembled into 808,938 scaffolds with a relatively short N50 of 760 bp. The average guanine and cytosine (GC) content was 37.52%. In total, 197,429 microsatellite motifs were detected with a frequency of 2.8 kb, among which mononucleotide motifs were the most abundant (up to 62.47% of the total microsatellite motifs), followed by dinucleotide and trinucleotide motifs. Conclusion: In summary, the genome of I. pubescens is small but complex with a high level of heterozygosity. Even though not successfully applied for estimation of genome size due to its complex genome, the survey sequences will help to design whole genome sequencing strategies and provide genetic information support for resource protection, genetic diversity analysis, genetic improvement and artificial breeding of I. pubescens.

Anthocyanin biosynthesis and accumulation is closely associated with tissue/organ coloring in plants. To gain insight into the physiological and molecular mechanisms of leaf coloring in Acer palmatum, a deciduous tree during autumnal senescence, we first investigated concentration dynamics of pigments (i.e., chlorophyll, carotenoid and anthocyanin) in leaves with differential coloring. It was found that compared to green leaves (GN), anthocyanins were accumulated actively in semi-red (SR) and total-red (TR) leaves, accompanied with chlorophyll and carotenoid degradation. Then transcriptional profiling on GN and SR leaves identified thousands of transcripts with differential expression in SR compared to GN leaves. An annotation search showed that the entire flavonoid/anthocyanin biosynthesis pathway from the production of naringenin chalcone to modification of flavonoid backbone was extensively activated at the transcriptional level in SR leaves. Phylogenetic analysis of putative MYB proteins identified ApMYB1 as a putative regulator promoting anthocyanin biosynthesis. Expression of ApMYB1 in leaves was induced by exogenous hormones including abscisic acid. Stable overexpression of ApMYB1 in tobacco resulted in leaves with higher accumulation of anthocyanins. Collectively, our results identified ApMYB1 as a positive regulator associated with leaf coloring in Acer palmatum during autumnal senescence, which may be regarded a potential target for breeding color-leafed plants.

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’.

Vaccinium mandarinorum Diels, a wild blueberry species distributed in the south of the Yangtze River in China, holds significant ecological and commercial value. Understanding its potential distribution and response to climate change is crucial for effective resource utilization and scientific introduction. By using the Maximum Entropy (MaxEnt) model, we evaluated V. mandarinorum’s potential distribution under current (1970–2000) and future climate change scenarios (2041–2060, 2061–2080, and 2081–2100) based on 216 modern distribution records and seven bioclimatic variables. The results showed that the MaxEnt model could effectively simulate the historical distribution and suitability degree of V. mandarinorum. The top two major environmental variables were precipitation of the driest quarter and annual precipitation, considering their contribution rates of 61.3% and 23.4%, respectively. Currently, the high suitability areas were mainly concentrated in central and northern Jiangxi province, central and southern Zhejiang province, southern Anhui province, central and northern Fujian province, and the border areas of Hunan and Guangxi provinces, covering 21.5% of the total suitable area. Future projections indicate that habitat will shift to higher latitudes and altitudes and that habitat quality will decline. Strategies are required to protect current V. mandarinorum populations and their habitats. The study results could provide an important theoretical reference for the optimization of planting distribution and ensure the sustainable production of the blueberry industry.