Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.

Mongolian oak (Quercus mongolica) is a common building material and landscaping tree species in northern China, with significant economic and ecological value. Its seedling growth is inhibited by high light intensity, but the mechanism by which light stress affects the growth and development of its seedlings remains unclear. In this study, we investigated the phenotypes, physiological processes, and molecular responses of 3-year-old Mongolian oak seedlings under different light treatments: full light (Sck), light shading (S1; 40% light), moderate shading (S2; 20% light), and severe shading (S3; 3% light). Compared to Sck, the S1 and S2 treatments resulted in higher leaf area, photosynthetic pigment content, photosynthesis rates, soluble sugar contents, and soluble protein contents in Mongolian oak seedlings. The S1 and S2 treatments also promoted seedling height and diameter growth and resulted in lower degrees of membrane lipid peroxidation, cell membrane permeability, and antioxidant enzyme activity. In contrast, severe shading (S3) significantly inhibited seedling height and diameter growth due to the lower net photosynthetic rate, and exhibiting higher degrees of membrane lipid peroxidation and cell membrane permeability. Shading treatments (S1 and S2) alleviated the negative effects of strong light on the growth and development of Mongolian oak seedlings, with the S2 treatment having the greatest effect. However, severe shading (S3) inhibited growth and development. A total of 3726 differentially expressed genes (DEGs) were detected in leaves under different shading treatments in RNA sequencing analysis. Among these, 1691, 3150, and 824 DEGs were detected in the Sck-S1, Sck-S2, and S1-S2 comparison groups, respectively. The different shading treatments determined common expression regulation pathways, including carotenoid biosynthesis, photosynthetic antenna proteins, and mitogen activated protein kinase (MAPK) signal transduction. Shading induced increases in gene expression levels in light harvesting complexes, which are related to changes in gene expression in the photosynthetic system, leading to changes in photosynthetic physiology. The expression levels of genes related to reactive oxygen species signal perception and activation enzymes were upregulated in Sck. Together, these findings revealed the response mechanisms of Mongolian oak seedlings to different shading levels at the physiological and molecular levels, providing a scientific basis and technical support for the cultivation and large-scale production of Mongolian oak seedlings.

Circular RNAs (circRNAs) are important regulatory molecules involved in various biological processes. However, the potential function of circRNAs in the turning red process of Quercus mongolica leaves is unclear. This study used RNA-seq data to identify 6228 circRNAs in leaf samples from four different developmental stages and showed that 88 circRNAs were differentially expressed. A correlation analysis was performed between anthocyanins and the circRNAs. A total of 16 circRNAs that may be involved in regulating the colour of Mongolian oak leaves were identified. CircRNAs may affect the colour of Q. mongolica leaves by regulating auxin, cytokinin, gibberellin, ethylene, and abscisic acid. This study revealed the potential role of circRNAs in the colour change of Q. mongolica leaves.