Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus.

Abscisic acid (ABA) is a plant hormone that regulates tolerance to abiotic stress. In this study, we evaluated the effect of exogenous different concentrations of ABA (0, 0.5, 1, 10, 100 and 200 μM) to mitigate oxidative stress in Platycladus orientalis (L.) Franco exposed to 100 mM hydrogen peroxide (H₂O₂), and its effects on reactive oxygen metabolism. Results indicated that exposure to 100 mM H₂O₂ significantly increased the contents of H₂O₂, malondialdehyde (MDA), ascorbic acid, total glutathione, and proline, and the activities of superoxide dismutase (SOD) and catalase (CAT) in P. orientalis leaves, while peroxidase (POD) activity decreased. The transcript levels of Cu/Zn-SOD, CAT, GR, APX, MDAR, and GST were upregulated in P. orientalis after 48 h of H₂O₂-induced stress. Compared with 100 and 200 μM ABA, lower ABA concentrations (0.5, 1, and 10 μM) significantly enhanced the activities of SOD, POD and CAT, and increased the contents of ascorbic acid, total glutathione, and proline in H₂O₂-treated seedlings at 48 h, accompanied by reduced H₂O₂ and MDA contents. Among the three lower concentrations of ABA, the 1 μM ABA concentration had the strongest effect on enzyme activities and the contents of antioxidant compounds. Among all the ABA concentrations, 1 μM ABA had the strongest effect to increase the transcript levels of Cu/Zn-SOD, CAT, GR, APX and MDAR in P. orientalis under H₂O₂-induced stress. This study revealed that an appropriate concentration of ABA effectively mitigated the damage caused by reactive oxygen species to P. orientalis via regulating the antioxidant defense system.

Platycladus orientalis (i.e., Chinese thuja) is famous for its lifespan spanning hundreds, and even thousands, of years. Most ancient P. orientalis populations are widely distributed in China, with accessible historical records, making them valuable genetic resources. In this study, the distribution pattern of ancient P. orientalis in China was analyzed based on 13 bioclimatic factors. Additionally, a specific-locus amplified fragment (SLAF) sequencing method was applied to detect single nucleotide polymorphisms (SNPs) in the genomes of 100 accessions from 13 populations. The resulting data revealed that the suitable areas for the distribution of ancient P. orientalis populations were accurately predicted with four main climatic factors. A total of 81,722 SNPs were identified from 461,867 SLAFs for 100 individuals, with an average sequencing depth of 10.11-fold and a Q30 value of 82.75%. The pair-wise genetic distance and genetic differentiation of 13 populations indicated that the BT-T population exhibited the largest divergence from the other populations. A neighbor-joining phylogenetic tree suggested the relationship between many individuals was inconsistent with the geographical location, possibly indicative of a history of transplantation and cultivation. All individuals were clustered into nine genotypes according to a structural analysis and the relationships between individuals were clarified in phylogenetic trees. This study highlights the importance of the de novo genome sequencing of ancient P. orientalis and may provide the basis for the conservation of P. orientalis genetic resources, the identification of supergene families, and the evaluation of related genetic resources.

Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.

To evaluate the effects of donor ages on growth and stress resistance of 6-year-old seedlings propagated from 5-, 2000-, and 3000-year-old Platycladus orientalis donors with grafting, cutting, and seed sowing, growth indicators and physiological and transcriptomic analyses were performed in 6-year-old seedlings in winter. Results showed that basal stem diameters and plant heights of seedlings of the three propagation methods decreased with the age of the donors, and the sown seedlings were the thickest and tallest. The contents of soluble sugar, chlorophyll, and free fatty acid in apical leaves of the three propagation methods were negatively correlated with donor ages in winter, while the opposite was true for flavonoid and total phenolic. The contents of flavonoid, total phenolic, and free fatty acid in cutting seedlings were highest in the seedlings propagated in the three methods in winter. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis of differentially expressed genes showed phenylpropanoid biosynthesis and fatty acid metabolism pathways, and their expression levels were up-regulated in apical leaves from 6-year-old seedlings propagated from 3000-year-old P. orientalis donors. In addition, hub genes analysis presented that C4H, OMT1, CCR2, PAL, PRX52, ACP1, AtPDAT2, and FAD3 were up-regulated in cutting seedlings, and the gene expression levels decreased in seedlings propagated from 2000- and 3000-year-old donors. These findings demonstrate the resistance stability of cuttings of P. orientalis and provide insights into the regulatory mechanisms of seedlings of P. orientalis propagated from donors at different ages in different propagation methods against low-temperature stress.