Transcriptome and Metabolome Based Mechanisms Revealing the Accumulation and Transformation of Sugars and Fats in Pinus armandii Seed Kernels during the Harvesting Period.

Pinus armandii seed kernel is a nutrient-rich and widely consumed nut whose yield and quality are affected by, among other things, harvesting time and climatic conditions, which reduce economic benefits. To investigate the optimal harvesting period of P. armandii seed kernels, this study determined the nutrient composition and seed kernel morphology and analyzed the gene expression and metabolic differences of P. armandii seed kernels during the harvesting period by transcriptomics and metabolomics. The results revealed that during the maturation of P. armandii seed kernels, there was a significant increase in the width, thickness, and weight of the seed kernels, as well as a significant accumulation of sucrose, soluble sugars, proteins, starch, flavonoids, and polyphenols and a significant decrease in lipid content. In addition, transcriptomic and metabolomic analyses of P. armandii seed kernels during the harvesting period screened and identified 103 differential metabolites (DEMs) and 8899 differential genes (DEGs). Analysis of these DEMs and DEGs revealed that P. armandii seed kernel harvesting exhibited gene-metabolite differences in sugar- and lipid-related pathways. Among them, starch and sucrose metabolism, glycolysis, and gluconeogenesis were associated with the synthesis and catabolism of sugars, whereas fatty acid degradation, glyoxylate and dicarboxylic acid metabolism, and glycerophospholipid metabolism were associated with the synthesis and catabolism of lipids. Therefore, the present study hypothesized that these differences in genes and metabolites exhibited during the harvesting period of P. armandii seed kernels might be related to the accumulation and transformation of sugars and lipids. This study may provide a theoretical basis for determining the optimal harvesting time of P. armandii seed kernels, changes in the molecular mechanisms of nutrient accumulation, and quality directed breeding.

Chromosome-scale genome assembly of Docynia delavayi provides new insights into the α-farnesene biosynthesis.

Docynia delavayi is an economically significant fruit species with a high market potential due to the special aroma of its fruit. Here, a 653.34 Mb high-quality genome of D. delavayi was first reported, of which 93.8 % of the sequences (612.98 Mb) could be anchored to 17 chromosomes, containing 48,325 protein-coding genes. Ks analysis proved that two whole genome duplication (WGD) events occurred in D. delavayi, resulting in the expansion of genes associated with terpene biosynthesis, which promoted its fruit-specific aroma production. Combined multi-omics analysis, α-farnesene was detected as the most abundant aroma substance emitted by D. delavayi fruit during storage, meanwhile one α-farnesene synthase gene (AFS) and 15 transcription factors (TFs) were identified as the candidate genes potentially involved in α-farnesene biosynthesis. Further studies for the regulation network of α-farnesene biosynthesis revealed that DdebHLH, DdeERF1 and DdeMYB could activate the transcription of DdeAFS. To our knowledge, it is the first report that MYB TF plays a regulatory role in α-farnesene biosynthesis, which will greatly facilitate future breeding programs for D. delavayi.

[Research Advances of Groundwater Nitrate Pollution and Source Apportionment in China].

Groundwater nitrate (NO3-) contamination in China has become a serious environmental problem, especially in agricultural production areas, which greatly affects the safety of drinking groundwater and requires urgent attention. In this study, the main sources of groundwater nitrate in China were reviewed, including atmospheric deposition, soil nitrogen, agricultural fertilization, and fecal sewage, among which fecal sewage and agricultural fertilization were the main reasons for the excessive groundwater nitrate. The application of hydrochemical analysis, multivariate statistical analysis, stable isotope tracer method, and microbial source tracking in the source apportionment of groundwater nitrate was summarized. All types of source apportionment methods had certain limitations. It is suggested that a variety of methods should be used to identify the source of groundwater nitrate, and the contribution rate of different pollution sources should be calculated using multivariate statistical analysis and isotope quantitative analysis models. The source apportionment of nitrate pollution has undergone a process from qualitative to quantitative research. At present, the SIAR and MixSIAR models based on δ15N-NO3-and δ18O-NO3- have been used widely to analyze the source of nitrate. However, due to the overlap of isotope characteristic values of different input end-members, the difference in δ15N-NO3-and δ18O-NO3- values under different spatial and temporal changes, and the influence of isotope fractionation in the process of nitrogen migration and transformation, the results calculated by the model remain uncertain. It is necessary to further optimize the analytical method of the model to obtain the source of nitrate pollution and its contribution rate more accurately to further aid in the scientific management of groundwater resources.

Urease-producing bacteria with plant growth-promoting ability that may tolerate and remove cadmium from aqueous solution.

Urease-producing bacteria (UPB) are widely present in soil and play an important role in soil ecosystems. In this study, 65 UPB strains were isolated from cadmium (Cd)-polluted soil around a lead-zinc mine in Yunnan Province, China. The Cd tolerance, removal of Cd from aqueous solution, production of indoleacetic acid (IAA) and plant growth-promoting effects of these materials were investigated. The results indicate that among the 65 UPB strains, four strains with IAA-producing ability were screened and identified as Bacillus thuringiensis W6-11, B. cereus C7-4, Serratia marcescens W11-10, and S. marcescens C5-6. Among the four strains, B. cereus C7-4 had the highest Cd tolerance, median effect concentration (EC50) of 59.94 mg/L. Under Cd 5 mg/L, S. marcescens C5-6 had the highest Cd removal from aqueous solution, up to 69.83%. Under Cd 25 mg/kg, inoculation with B. cereus C7-4 significantly promoted maize growth in a sand pot by increasing the root volume, root surface area, and number of root branches by 22%, 29%, and 20%, respectively, and plant height and biomass by 16% and 36%, respectively, and significantly increasing Cd uptake in the maize roots. Therefore, UPB is a potential resource for enhancing plant adaptability to Cd stress in plants with Cd-polluted habitats.

This study utilized urease-producing bacteria screened from the soil of lead zinc mining areas in Yunnan, China as the research object, enriching the microbial resources in Yunnan. In addition, this article verified the IAA production ability and cadmium removal ability of urease-producing bacteria, and screened out bifunctional urease-producing bacteria that have potential in cadmium pollution control and plant growth promotion.

DNA Methylation Analysis of Growth Differences between Upright and Inverted Cuttings of Populus yunnanensis.

DNA methylation is an important mechanism for epigenetic modifications that have been shown to be associated with responses to plant development. Previous studies found that inverted Populus yunnanensis cuttings were still viable and could develop into complete plants. However, the growth status of inverted cuttings was weaker than that of upright cuttings, and the sprouting time of inverted cuttings was later than that of upright cuttings. There is currently no research on DNA methylation patterns in inverted cuttings of Populus yunnanensis. In this study, we detected genome-wide methylation patterns of stem tips of Populus yunnanensis at the early growth stage and the rapid growth stage by Oxford Nanopore Technologies (ONT) methylation sequencing. We found that the methylation levels of CpG, CHG, CHH, and 6mA were 41.34%, 33.79%, 17.27%, and 12.90%, respectively, in the genome of inverted poplar cuttings, while the methylation levels of the four methylation types were higher in the genome of upright poplar cuttings than in inverted cuttings, 41.90%, 34.57%, 18.09%, and 14.11%, suggesting important roles for DNA methylation in poplar cells. In all comparison groups, CpG-type methylation genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were annotated to pathways associated with carbon metabolism, ribosome biogenesis in eukaryotes, glycolysis/gluconeogenesis, pyruvate metabolism, and mRNA detection pathways, suggesting that different biological processes are activated in upright and inverted cuttings. The results show that methylation genes are commonly present in the poplar genome, but only a few of them are involved in the regulation of expression in the growth and development of inverted cuttings. From this, we screened the DET2 gene for significant differences in methylation levels in upright or inverted cuttings. The DET2 gene is a key gene in the Brassinolide (BRs) synthesis pathway, and BRs have an important influence on the growth and development process of plants. These results provide important clues for studying DNA methylation patterns in P. yunnanensis.

Genome-Wide Identification, Expression Analysis, and Subcellular Localization of DET2 Gene Family in Populus yunnanensis.

(1) Background: Brassinosteroids (BRs) are important hormones involved in almost all stages of plant growth and development, and sterol dehydrogenase is a key enzyme involved in BRs biosynthesis. However, the sterol dehydrogenase gene family of Populus yunnanensis Dode (P. yunnanensis) has not been studied. (2) Methods: The PyDET2 (DEETIOLATED2) gene family was identified and analyzed. Three genes were screened based on RNA-seq of the stem tips, and the PyDET2e was further investigated via qRT-PCR (quantitative real-time polymerase chain reaction) and subcellular localization. (3) Results: The 14 DET2 family genes in P. yunnanensis were categorized into four groups, and 10 conserved protein motifs were identified. The gene structure, chromosome distribution, collinearity, and codon preference of all PyDET2 genes in the P. yunnanensis genome were analyzed. The codon preference of this family is towards the A/U ending, which is strongly influenced by natural selection. The PyDET2e gene was expressed at a higher level in September than in July, and it was significantly expressed in stems, stem tips, and leaves. The PyDET2e protein was localized in chloroplasts. (4) Conclusions: The PyDET2e plays an important role in the rapid growth period of P. yunnanensis. This systematic analysis provides a basis for the genome-wide identification of genes related to the brassinolide biosynthesis process in P. yunnanensis, and lays a foundation for the study of the rapid growth mechanism of P. yunnanensis.

Chromosomal-scale genomes of two Rosa species provide insights into genome evolution and ascorbate accumulation.

Rosa roxburghii and Rosa sterilis, two species belonging to the Rosaceae family, are widespread in the southwest of China. These species have gained recognition for their remarkable abundance of ascorbate in their fresh fruits, making them an ideal vitamin C resource. In this study, we generated two high-quality chromosome-scale genome assemblies for R. roxburghii and R. sterilis, with genome sizes of 504 and 981.2 Mb, respectively. Notably, we present a haplotype-resolved, chromosome-scale assembly for diploid R. sterilis. Our results indicated that R. sterilis originated from the hybridization of R. roxburghii and R. longicuspis. Genome analysis revealed the absence of recent whole-genome duplications in both species and identified a series of duplicated genes that possibly contributing to the accumulation of flavonoids. We identified two genes in the ascorbate synthesis pathway, GGP and GalLDH, that show signs of positive selection, along with high expression levels of GDP-d-mannose 3', 5'-epimerase (GME) and GDP-l-galactose phosphorylase (GGP) during fruit development. Furthermore, through co-expression network analysis, we identified key hub genes (MYB5 and bZIP) that likely regulate genes in the ascorbate synthesis pathway, promoting ascorbate biosynthesis. Additionally, we observed the expansion of terpene synthase genes in these two species and tissue expression patterns, suggesting their involvement in terpenoid biosynthesis. Our research provides valuable insights into genome evolution and the molecular basis of the high concentration of ascorbate in these two Rosa species.

[Hydrochemical Characteristics and Control Factors of Surface Water in Kuaize River Basin at the Upper Pearl River].

The Kuaize River is a small typical karst watershed in the source area of the Pearl River as well as an important coal mining area in Eastern Yunnan with a fragile ecological environment. Strengthening the research on the water environment in the region plays an important role in supporting the comprehensive management of the ecological environment and water resources in the source region of the Pearl River. Through the systematic collection of surface water, karst groundwater, and mine water samples, mathematical statistics analysis, correlation analysis, ion ratio analysis, absolute principal component scores multiple linear regression(APCS-MLR), and other methods were used to study the characteristics of hydrochemical evolution and control factors in Kuaize River Basin. The results showed that the average pH value of surface water in Kuaize River Basin was 7.8, which was weakly alkaline. The main cations were Ca2+ and Na+, showing the characteristics of Ca2+>Na+>Mg2+>K+. The main anions were HCO3- and SO42-, showing the characteristics of HCO3->SO42->NO3->Cl-. The variation coefficients of Na+, SO42-, and NO3- in surface water were high, showing strong spatial variability. The water chemical type of the trunk stream was mainly HCO3-Ca, whereas the water chemical type of the tributary was relatively complex, mainly HCO3-Ca, HCO3-Ca·Na, and HCO3·SO4-Ca·Na. The chemical composition of surface water was mainly affected by rock weathering, cation exchange, and human activities. Ca2+, Mg2+, Na+, and HCO3- in surface water mainly came from the weathering of carbonate rock and silicate rock; SO42- mainly came from the oxidation of sulfide, such as pyrite in coal seams; K+, Cl-, and NO3- mainly came from domestic sewage and agricultural activities. The APCS-MLR receptor model analysis results showed that the surface water in the Kuaize River Basin was mainly affected by sulfide oxidation, carbonate weathering, weathering of silicate rock in mine water, domestic sewage, agricultural activities, and unknown sources. In general, the contribution rate of human activities such as mining, domestic sewage, and agricultural activities to the surface water reached 47.17%, indicating that human activities were the key driving factor of surface water chemistry in the Kuaize River Basin.

Chromosome-scale genomes of commercially important mahoganies, Swietenia macrophylla and Khaya senegalensis.

Mahogany species (family Meliaceae) are highly valued for their aesthetic and durable wood. Despite their economic and ecological importance, genomic resources for mahogany species are limited, hindering genetic improvement and conservation efforts. Here we perform chromosome-scale genome assemblies of two commercially important mahogany species: Swietenia macrophylla and Khaya senegalensis. By combining 10X sequencing and Hi-C data, we assemble high-quality genomes of 274.49 Mb (S. macrophylla) and 406.50 Mb (K. senegalensis), with scaffold N50 lengths of 8.51 Mb and 7.85 Mb, respectively. A total of 99.38% and 98.05% of the assembled sequences are anchored to 28 pseudo-chromosomes in S. macrophylla and K. senegalensis, respectively. We predict 34,129 and 31,908 protein-coding genes in S. macrophylla and K. senegalensis, respectively, of which 97.44% and 98.49% are functionally annotated. The chromosome-scale genome assemblies of these mahogany species could serve as a vital genetic resource, especially in understanding the properties of non-model woody plants. These high-quality genomes could support the development of molecular markers for breeding programs, conservation efforts, and the sustainable management of these valuable forest resources.

[Hydrochemical Characteristics and Controlling Factors in Wudu River Basin of Guizhou Province].

TheWudu River is a typical mining-type watershed in the karst mountainous area of western Guizhou Province. Based on the collection of the main stream, tributaries, spring water, and mine water samples in Wudu River Basin, the hydrochemical characteristics and control factors of Wudu River Basin were studied using Gibbs diagram, Piper diagram, and mathematical statistics analysis, and the solute contribution rate of different sources was calculated. The results revealed that the pH value of the water in the Wudu River Basin ranged from 7.87 to 8.52, with an average of 8.14. The TDS values ranged from 135 to 243 mg·L-1, with an average of 191.7 mg·L-1. The major cations in natural river and spring water were Ca2+ and Mg2+, the major anion was HCO3-, and the hydrochemical type was HCO3-Ca. However, owing to the influence of mining activities, the major cations in some tributaries were Ca2+ and Na+, and the hydrochemical types transitioned to HCO3·SO4-Ca and HCO3·SO4-Ca·Na. The ion components of river water in Wudu River Basin were affected by mine water discharge and cation exchange, carbonate rock weathering, silicate rock weathering, and agricultural fertilization. The high concentration of SO42- and Na+in mine water was the primary source of SO42- and Na+in the tributaries of the Wudu River. The method for calculating chemical material balance showed that the contribution rate of carbonate rock weathering ranged from 44.12% to 86.92%, with an average of 74.32%. The contribution rate of mining activities ranged from 3.28% to 37.07%, with an average of 11.61%. Carbonate rock weathering was the main controlling factor of hydrochemical components in the Wudu River Basin; meanwhile, mining activities also had a certain impact on river water chemistry but they showed spatial heterogeneity. The average contribution rates of atmospheric precipitation, silicate rock weathering, agricultural activities, and domestic sewage were 3.75%, 4.67%, 2.85%, and 2.81%, respectively, which had a limited impact on the hydrochemical components of the basin.

Comparative Transcriptomic and Metabolomic Analyses of Differences in Trunk Spiral Grain in Pinus yunnanensis.

Having a spiral grain is considered to be one of the most important wood properties influencing wood quality. Here, transcriptome profiles and metabolome data were analyzed in the straight grain and twist grain of Pinus yunnanensis. A total of 6644 differential expression genes were found between the straight type and the twist type. A total of 126 differentially accumulated metabolites were detected. There were 24 common differential pathways identified from the transcriptome and metabolome, and these pathways were mainly annotated in ABC transporters, arginine and proline metabolism, flavonoid biosynthesis, isoquinoline alkaloid biosynthesis, linoleic acid metabolism, phenylpropanoid, tryptophan metabolism, etc. A weighted gene coexpression network analysis showed that the lightblue4 module was significantly correlated with 2'-deoxyuridine and that transcription factors (basic leucine zipper (bZIP), homeodomain leucine zipper (HD-ZIP), basic helix-loop-helix (bHLH), p-coumarate 3-hydroxylase (C3H), and N-acetylcysteine (NAC)) play important roles in regulating 2'-deoxyuridine, which may be involved in the formation of spiral grains. Meanwhile, the signal transduction of hormones may be related to spiral grain, as previously reported. ARF7 and MKK4_5, as indoleacetic acid (IAA)- and ethylene (ET)-related receptors, may explain the contribution of plant hormones in spiral grain. This study provided useful information on spiral grain in P. yunnanensis by transcriptome and metabolome analyses and could lay the foundation for future molecular breeding.

Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis).

Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species.

Genome-Wide Characterization of PEBP Gene Family and Functional Analysis of TERMINAL FLOWER 1 Homologs in Macadamia integrifolia.

Edible Macadamia is one of the most important commercial nut trees cultivated in many countries, but its large tree size and long juvenile period pose barriers to commercial cultivation. The short domestication period and well-annotated genome of Macadamia integrifolia create great opportunities to breed commercial varieties with superior traits. Recent studies have shown that members of the phosphatidylethanolamine binding protein (PEBP) family play pivotal roles in regulating plant architecture and flowering time in various plants. In this study, thirteen members of MiPEBP were identified in the genome of M. integrifolia, and they are highly similarity in both motif and gene structure. A phylogenetic analysis divided the MiPEBP genes into three subfamilies: MFT-like, FT-like and TFL1-like. We subsequently identified two TERMINAL FLOWER 1 homologues from the TFL1-like subfamily, MiTFL1 and MiTFL1-like, both of which were highly expressed in stems and vegetative shoots, while MiTFL1-like was highly expressed in young leaves and early flowers. A subcellular location analysis revealed that both MiTFL1 and MiTFL1-like are localized in the cytoplasm and nucleus. The ectopic expression of MiTFL1 can rescue the early-flowering and terminal-flower phenotypes in the tfl1-14 mutant of Arabidopsis thaliana, and it indicates the conserved functions in controlling the inflorescence architecture and flowering time. This study will provide insight into the isolation of PEBP family members and the key targets for breeding M. integrifolia with improved traits in plant architecture and flowering time.

Comparison of the diversity and structure of the rhizosphere microbial community between the straight and twisted trunk types of Pinus yunnanensis.

Background: Pinus yunnanensis is a major silvicultural species in Southwest China. Currently, large areas of twisted-trunk Pinus yunnanensis stands severely restrict its productivity. Different categories of rhizosphere microbes evolve alongside plants and environments and play an important role in the growth and ecological fitness of their host plant. However, the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types-straight and twisted-remain unclear. Methods: We collected the rhizosphere soil of 5 trees with the straight and 5 trees with the twisted trunk type in each of three sites in Yunnan province. We assessed and compared the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types by Illumina sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions. Results: The available phosphorus in soil differed significantly between P. yunnanensis with straight and twisted trunks. Available potassium had a significant effect on fungi. Chloroflexi dominated the rhizosphere soils of the straight trunk type, while Proteobacteria was predominant in the rhizosphere soils of the twisted trunk type. Trunk types significantly explained 6.79% of the variance in bacterial communities. Conclusion: This study revealed the composition and diversity of bacterial and fungal groups in the rhizosphere soil of P. yunnanensis with straight and twisted trunk types, providing proper microbial information for different plant phenotypes.

[Characteristics and Driving Factors of Hydrochemical Evolution in Tuochangjiang River Basin, Western Guizhou Province].

Tuochangjiang River is a typical mining-type watershed in the karst mountainous area of western Guizhou province. The study of its hydrochemical evolution characteristics and driving factors is of great significance to the local economic development and the scientific management of water resources. The samples of river water, spring water, and mine water in the Tuochangjiang River Basin were collected, and the sources of solutes and their contribution to the chemical components of river water were discussed by means of hydrochemical diagrams, mathematical statistics, and the absolute principal component scores-multivariate linear regression model (APCS-MLR). The results showed that the pH of the river water ranged between 7.30 to 8.31, and the TDS value ranged between 40 to 520 mg·L-1, which was mainly contributed by Ca2+, Na+, HCO3-, and SO42-. The dominant cations in river water were Ca2+ and Na+, the dominant anions were HCO3- and SO42-, and the main water chemistry transitioned from HCO3-Ca to HCO3-Ca·Na and HCO3·SO4-Ca·Na type, whereas that of the mine water was mainly the HCO3-Na and HCO3·SO4-Na types. The chemical composition of river water was affected by rock weathering, exchange adsorption of anions, mineral dissolution and precipitation, and human activities, in which Ca2+, Mg2+, and HCO3- were mainly derived from the weathering and dissolution of carbonate and silicate rocks, Na+and SO42- were mainly from the discharge of mining wastewater, and Cl- and NO3- were affected by domestic sewage and agricultural activities, respectively. APCS-MLR analysis further showed that the river water solutes mainly included five sources:discharge of mining wastewater, dissolution of soil minerals, geological background, agricultural activities, and unknown sources, and their contribution rates to river water were 23.49%, 35.04%, 13.87%, 7.96%, and 20.63%, respectively. Mining factors and soil factors were the most important sources of solutes in the river water, and they were the main driving factors for the hydrochemical evolution of the Tuochangjiang River Basin.

PyuARF16/33 Are Involved in the Regulation of Lignin Synthesis and Rapid Growth in Populus yunnanensis.

(1) Background: Lignin is a unique component of the secondary cell wall, which provides structural support for perennial woody plants. ARFs are the core factors of the auxin-signaling pathway, which plays an important role in promoting plant growth, but the specific relationship between auxin response factors (ARFs) and lignin has not been fully elucidated with regard to rapid plant growth in forest trees. (2) Objectives: This study aimed to investigate the relationship between ARFs and lignin with regard to rapid plant growth in forest trees. (3) Methods: We used bioinformatics analysis to investigate the PyuARF family, find genes homologous to ARF6 and ARF8 in Populus yunnanensis, and explore the changes in gene expression and lignin content under light treatment. (4) Results: We identified and characterized 35 PyuARFs based on chromosome-level genome data from P. yunnanensis. In total, we identified 92 ARF genes in P. yunnanensis, Arabidopsis thaliana, and Populus trichocarpa, which were subsequently divided into three subgroups based on phylogenetic analysis and classified the conserved exon-intron structures and motif compositions of the ARFs into the same subgroups. Collinearity analysis suggested that segmental duplication and whole-genome duplication events were majorly responsible for the expansion of the PyuARF family, and the analysis of Ka/Ks indicated that the majority of the duplicated PyuARFs underwent purifying selection. The analysis of cis-acting elements showed that PyuARFs were sensitive to light, plant hormones, and stress. We analyzed the tissue-specific transcription profiles of PyuARFs with transcriptional activation function and the transcription profiles of PyuARFs with high expression under light in the stem. We also measured the lignin content under light treatment. The data showed that the lignin content was lower, and the gene transcription profiles were more limited under red light than under white light on days 1, 7, and 14 of the light treatments. The results suggest that PyuARF16/33 may be involved in the regulation of lignin synthesis, thereby promoting the rapid growth of P. yunnanensis. (5) Conclusions: Collectively, this study firstly reports that PyuARF16/33 may be involved in the regulation of lignin synthesis and in promoting the rapid growth in P. yunnanensis.

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes.

BACKGROUND: Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important commercial arbor species, which can provide us with the raw lacquer, an excellent adhesive and painting material used to make lacquer ware. Compared with diploid, triploid lacquer tree has a higher yield of raw lacquer and stronger resistance to stress. Triploid T. vernicifluum was a newly discovered natural triploid lacquer tree. However, the taxonomy of triploid T. vernicifluum has remained uncertain. Here, we sequenced and analyzed the complete chloroplast (cp) genome of triploid T. vernicifluum and compared it with related species of Toxicodendron genus based on chloroplast genome and SSR markers. RESULTS: The plastome of triploid T. vernicifluum is 158,221 bp in length, including a pair of inverted repeats (IRs) of 26,462 bp, separated by a large single-copy region of 86,951 bp and a small single-copy region of 18,346 bp. In total, 132 genes including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified in the triploid T. vernicifluum. Among these, 16 genes were duplicated in the IR regions, 14 genes contain one intron, while three genes contain two introns. After nucleotide substitutions, seven small inversions were analyzed in the chloroplast genomes, eight hotspot regions were found, which could be useful molecular genetic markers for future population genetics. Phylogenetic analyses showed that triploid T. vernicifluum was a sister to T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi. Moreover, phylogenetic clustering based on the SSR markers showed that all the samples of triploid T. vernicifluum, T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi in one group, while the samples of T. vernicifluum and T. succedaneum in another group, which is consistent with the cp genome and morphological analysis. CONCLUSIONS: The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, variety identification, breeding and resource exploitation, and future genetic diversity-related studies of T. vernicifluum.

Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum.

Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. succedaneum to date. In this study, the expression of 10 candidate RGs was analyzed by RT-qPCR in different tissues (roots, stems, leaves), stress treatments (high/low temperature, drought), and hormone stimulation (jasmonic acid, JA). Then, the stability ranking of 10 candidate genes was evaluated by ∆Ct analysis and three software programs: geNorm, NormFinder, and BestKeeper. Finally, RefFinder was used to comprehensively analyze the expression stability of 10 candidate genes. The comprehensive analysis showed that TsRG05/06, TsRG01/06, and TsRG03/ACT were stable under high/low-temperature stress, drought stress, and JA treatment, respectively. TsRG03 and ACT had stable expression in different tissues. While the TsRG03 and ACT were recommended as the suitable RGs for T. succedaneum in all samples. Meanwhile, UBQ was the least suitable as a reference gene for T. succedaneum. In addition, the results of geNorm showed that the combination of two stable RGs could make the results of gene expression more accurate. These results provide alternative RGs for the study of gene function, correction, and normalization of target gene expression and directed molecular breeding in T. succedaneum.

PyunBBX18 Is Involved in the Regulation of Anthocyanins Biosynthesis under UV-B Stress.

(1) Background: Populus yunnanensis Dode (P. yunnanensis) grows in the low-latitude and high-altitude areas of southwest China. In low-latitude and high-altitude areas, plants suffer from the high intensity of UV-B (ultraviolet-b) radiation, and they have a complete regulation system to adapt to the environment of the high UV-B radiation. As natural antioxidants, anthocyanins play an important role in scavenging free radicals. BBX (B-box) genes are involved in anthocyanins biosynthesis. (2) Methods: By exploring the gene structure and motifs of PyunBBX genes (genes of P. yunnanensis BBX family) and the evolutionary relationship between PyunBBX genes and other species BBX genes, six PyunBBX genes that responded to UV-B and participated in anthocyanins biosynthesis were screened. BBX, with the potential to regulate anthocyanins biosynthesis, was further investigated by anthocyanins content determination and RT-qPCR (real-time quantitative polymerase chain reaction); (3) Results: After 7 days of UV-B treatment, anthocyanins were significantly accumulated, and the expression of PyunBBX18 was up-regulated for 7 days. The expression of PyunBBX12 was inhibited by UV-B treatment. By analyzing the RNA-seq data of leaves and bark of P. yunnanensis, we found that PyunBBX18 was highly expressed in leaves and young bark; (4) Conclusions: These results showed that PyunBBX18 and PyunBBX12 may be involved in the response process of UV-B stress, in which PyunBBX18 may regulate the anthocyanins biosynthesis to resist UV damage.