Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness.

Quercus variabilis is a deciduous woody species with high ecological and economic value, and is a major source of cork in East Asia. Cork from thick softwood sheets have higher commercial value than those from thin sheets. It is extremely difficult to genetically improve Q. variabilis to produce high quality softwood due to the lack of genomic information. Here, we present a high-quality chromosomal genome assembly for Q. variabilis with length of 791,89 Mb and 54,606 predicted genes. Comparative analysis of protein sequences of Q. variabilis with 11 other species revealed that specific and expanded gene families were significantly enriched in the "fatty acid biosynthesis" pathway in Q. variabilis, which may contribute to the formation of its unique cork. Based on weighted correlation network analysis of time-course (i.e., five important developmental ages) gene expression data in thick-cork versus thin-cork genotypes of Q. variabilis, we identified one co-expression gene module associated with the thick-cork trait. Within this co-expression gene module, 10 hub genes were associated with suberin biosynthesis. Furthermore, we identified a total of 198 suberin biosynthesis-related new candidate genes that were up-regulated in trees with a thick cork layer relative to those with a thin cork layer. Also, we found that some genes related to cell expansion and cell division were highly expressed in trees with a thick cork layer. Collectively, our results revealed that two metabolic pathways (i.e., suberin biosynthesis, fatty acid biosynthesis), along with other genes involved in cell expansion, cell division, and transcriptional regulation, were associated with the thick-cork trait in Q. variabilis, providing insights into the molecular basis of cork development and knowledge for informing genetic improvement of cork thickness in Q. variabilis and closely related species.

Metabolic profiling reveals key metabolites regulating adventitious root formation in ancient Platycladus orientalis cuttings.

Platycladus orientalis, a common horticultural tree species, has an extremely long life span and forms a graceful canopy. Its branches, leaves, and cones have been used in traditional Chinese medicine. However, difficulty in rooting is the main limiting factor for the conservation of germplasm resources. This study shows that the rooting rates and root numbers of cuttings were significantly reduced in ancient P. orientalis donors compared to 5-year-old P. orientalis donors. The contents of differentially accumulated metabolites (DAMs) in phenylpropanoid (caffeic acid and coniferyl alcohol) and flavonoid biosynthesis (cinnamoyl-CoA and isoliquiritigenin) pathways increased significantly in cuttings propagated from ancient P. orientalis donors compared to 5-year-old P. orientalis donors during adventitious root (AR) formation. These DAMs may prevent the ancient P. orientalis cuttings from rooting, and gradual lignification of callus was one of the main reasons for the failed rooting of ancient P. orientalis cuttings. The rooting rates of ancient P. orientalis cuttings were improved by wounding the callus to identify wounding-induced rooting-promoting metabolites. After wounding, the contents of DAMs in zeatin (5'-methylthioadenosine, cis-zeatin-O-glucoside, and adenine) and aminoacyl-tRNA biosynthesis (l-glutamine, l-histidine, l-isoleucine, l-leucine, and l-arginine) pathways increased, which might promote cell division and provided energy for the rooting process. The findings of our study suggest that breaking down the lignification of callus via wounding can eventually improve the rooting rates of ancient P. orientalis cuttings, which provides a new solution for cuttings of other difficult-to-root horticultural and woody plants.

Effects of Different Donor Ages on the Growth of Cutting Seedlings Propagated from Ancient Platycladus orientalis.

The effects of tree age on the growth of cutting seedlings propagated from ancient trees have been an important issue in plant breeding and cultivation. In order to understand seedling growth and stress resistance stability, phenotypic measurements, physiological assays, and high-throughput transcriptome sequencing were performed on sown seedlings propagated from 5-year-old donors and cutting seedlings propagated from 5-, 300-, and 700-year-old Platycladus orientalis donors. In this study, the growth of cutting seedlings propagated from ancient trees was significantly slower; the soluble sugar and chlorophyll contents gradually decreased with the increase in the age of donors, and the flavonoid and total phenolic contents of sown seedlings were higher than those of cutting seedlings. Enrichment analysis of differential genes showed that plant hormone signal transduction, the plant-pathogen interaction, and the flavone and flavonol biosynthesis pathways were significantly up-regulated with the increasing age of cutting seedlings propagated from 300- and 700-year-old donors. A total of 104,764 differentially expressed genes were calculated using weighted gene co-expression network analysis, and 8 gene modules were obtained. Further, 10 hub genes in the blue module were identified, which revealed that the expression levels of JAZ, FLS, RPM1/RPS3, CML, and RPS2 increased with the increase in tree age. The results demonstrated that the age of the donors seriously affected the growth of P. orientalis cutting seedlings and that cutting propagation can preserve the resistance of ancient trees. The results of this study provide important insights into the effects of age on asexually propagated seedlings, reveal potential molecular mechanisms, and contribute to an improvement in the level of breeding and conservation of ancient germplasm resources of P. orientalis trees.

Effects of Donor Ages and Propagation Methods on Seedling Growth of Platycladus orientalis (L.) Franco in Winter.

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.

Population Structure, Genetic Diversity and Candidate Genes for the Adaptation to Environmental Stress in Picea koraiensis.

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.

Interspecific Gene Flow and Selective Sweeps in Picea wilsonii, P. neoveitchii and P. likiangensis.

Genome-wide single nucleotide polymorphism (SNP) markers were obtained by genotyping-by-sequencing (GBS) technology to study the genetic relationships, population structure, gene flow and selective sweeps during species differentiation of Picea wilsonii, P. neoveitchii and P. likiangensis from a genome-wide perspective. We used P. jezoensis and P. pungens as outgroups, and three evolutionary branches were obtained: P. likiangensis was located on one branch, two P. wilsonii populations were grouped onto a second branch, and two P. neoveitchii populations were grouped onto a third branch. The relationship of P. wilsonii with P. likiangensis was closer than that with P. neoveitchii. ABBA-BABA analysis revealed that the gene flow between P. neoveitchii and P. wilsonii was greater than that between P. neoveitchii and P. likiangensis. Compared with the background population of P. neoveitchii, the genes that were selected in the P. wilsonii population were mainly related to plant stress resistance, stomatal regulation, plant morphology and flowering. The genes selected in the P. likiangensis population were mainly related to plant stress resistance, leaf morphology and flowering. Selective sweeps were beneficial for improving the adaptability of spruce species to different habitats as well as to accelerate species differentiation. The frequent gene flow between spruce species makes their evolutionary relationships complicated. Insight into gene flow and selection pressure in spruce species will help us further understand their phylogenetic relationships and provide a scientific basis for their introduction, domestication and genetic improvement.

Exploring the Phylogeography of Ancient Platycladus orientalis in China by Specific-Locus Amplified Fragment Sequencing.

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.

Inhibition of α-ketoglutarate dehydrogenase activity affects adventitious root growth in poplar via changes in GABA shunt.

MAIN CONCLUSION: Blocking α-ketoglutarate dehydrogenase results in up-regulation of γ-aminobutyric acid (GABA) shunt activity, and inhibits the growth of poplar adventitious roots (ARs), indicating that AR growth is closely associated with GABA shunt. γ-Aminobutyric acid (GABA) shunt starts from α-ketoglutarate in the tricarboxylic acid cycle, which is thought to represent the cross road between carbon and nitrogen metabolism. Previous studies (Araújo et al. 2012b, Plant Cell 24: 2328-2351) have shown that blocking α-ketoglutarate dehydrogenase (α-KGDH) affects the GABA shunt activity, and inhibits growth. However, its effects on the growth of adventitious roots (ARs) are unclear. In this study, the growth of ARs in tissue-cultured 84K poplar (Populus alba × Populus glandulosa cv. '84K') was significantly inhibited when succinyl phosphate (SP), a specific inhibitor of α-KGDH, was supplied. The inhibition of ARs was associated with significant changes in the levels of soluble sugars, organic acids, and amino acids, and was coupled with the up-regulation of the GABA shunt activity at the transcriptional and translational levels. Exogenous GABA also inhibited AR growth following the increase of the endogenous GABA level. Transcriptomic analyses further showed that genes related to cell wall carbon metabolism and phytohormone (indoleacetic acid, ABA, and ethylene) signaling were affected by the changes of GABA shunt activity, resulting from the α-KGDH inhibition. Thus, our study indicates that the inhibition of poplar AR growth by blocking α-KGDH is closely associated with GABA shunt, which would benefit a better understanding of GABA's roles in plant development and stress response.

Roles of γ-aminobutyric acid on salinity-responsive genes at transcriptomic level in poplar: involving in abscisic acid and ethylene-signalling pathways.

MAIN CONCLUSION: γ-Aminobutyric acid (GABA) affected ABA and ethylene metabolic genes and signal components in salt-treated poplar, indicating its potential role in signal pathways of ABA and ethylene during salt stress. GABA is a small signalling molecule that accumulates rapidly in plants exposed to various stresses. However, the relationship between GABA and other signalling molecules, such as hormones, remains unclear. Here, in the poplar woody plant under 200-mM NaCl conditions, the application of low (0.25 mM) and high (10 mM) exogenous GABA, compared to 0 mM, affected the accumulation of hydrogen peroxide and hormones, including ABA and ethylene, in different manners. Transcriptomic analysis demonstrated that 1025 differentially expressed genes (DEGs; |log2Ratio| ≥ 1.5) were widely affected by exogenous GABA under salt stress. A clustering analysis revealed that GABA could rescue or promote the effects of salt stress on gene expression. Among them, 146 genes involved in six hormone-signalling pathways were enriched, including 22 ABA- and 50 ethylene-related genes. Quantitative expression of selected genes involved in hormone-related pathways showed that ABA metabolic genes (ABAG, ABAH2, and ABAH4), ethylene biosynthetic genes (ACO1, ACO2, ACO5, ACOH1, ACS1, and ACS7) and receptor genes (PYL1, PYL2, PYL4, and PYL6) were regulated by exogenous GABA, even at a 0.1 mM level. The production of ABA was negatively correlated with ABAH expression levels at different GABA concentrations. The increase of endogenous GABA, resulting from inhibitor (succinyl phosphonate) of α-ketoglutarate dehydrogenase, affected the PYLs levels. Thus, GABA may be involved in ABA- and ethylene-signalling pathways. Our data provide a better understanding of GABA's roles in the plant responses to environmental stresses.

Proteome-Level Analysis of Metabolism- and Stress-Related Proteins during Seed Dormancy and Germination in Gnetum parvifolium.

Gnetum parvifolium is a rich source of materials for traditional medicines, food, and oil, but little is known about the mechanism underlying its seed dormancy and germination. In this study, we analyzed the proteome-level changes in its seeds during germination using isobaric tags for relative and absolute quantitation. In total, 1,040 differentially expressed proteins were identified, and cluster analysis revealed the distinct time points during which signal transduction and oxidation-reduction activity changed. Gene Ontology analysis showed that "carbohydrate metabolic process" and "response to oxidative stress" were the main enriched terms. Proteins associated with starch degradation and antioxidant enzymes were important for dormancy-release, while proteins associated with energy metabolism and protein synthesis were up-regulated during germination. Moreover, protein-interaction networks were mainly associated with heat-shock proteins. Furthermore, in accord with changes in the energy metabolism- and antioxidant-related proteins, indole-3-acetic acid, Peroxidase, and soluble sugar content increased, and the starch content decreased in almost all six stages of dormancy and germination analyzed (S1-S6). The activity of superoxide dismutase, abscisic acid, and malondialdehyde content increased in the dormancy stages (S1-S3) and then decreased in the germination stages (S4-S6). Our results provide new insights into G. parvifolium seed dormancy and germination at the proteome and physiological levels, with implications for improving seed propagation.

Transcriptome differences between 20- and 3, 000-year-old Platycladus orientalis reveal that ROS are involved in senescence regulation

Background: Platycladus orientalis has an extremely long life span of several thousands of years, attracting great interests in the mechanisms involved in such successful senescence regulation and resistance at physiological and molecular levels. Results: The levels of reactive oxygen species (ROS) were higher in 3,000-year-old than in 20-year-old P. orientalis, and the activities of GR and GSH demonstrated the same trend. We produced and analyzed massive sequence information from pooled samples of P. orientalis through transcriptome sequencing, which generated 51,664 unigenes with an average length of 475 bp. We then used RNA-seq analysis to obtain a high-resolution age­course profile of gene expression in 20- and 3,000-year-old P. orientalis individuals. Totally, 106 differentially expressed genes were obtained, of which 47 genes were downregulated and 59 upregulated in the old tree. These genes were involved in transcription factors, hormone-related responses, ROS scavengers, senescence-related responses, stress response, and defense and possibly play crucial roles in tackling various stresses in the 3,000-year-old P. orientalis during its life time. The expression patterns of genes related to ROS homeostasis further indicated that the high ability of ROS scavenging could be helpful for the 3,000-year-old P. orientalis to resist senescence. Conclusions: This study provides a foundation for the elucidation of senescence resistance through molecular studies and the discovery of useful genes in P. orientalis.

Expression and integrated network analyses revealed functional divergence of NHX-type Na+/H+ exchanger genes in poplar.

The Na+/H+ antiporters (NHXs) are secondary ion transporters to exchange H+ and transfer the Na+ or K+ across membrane, they play crucial roles during plant development and stress responses. To gain insight into the functional divergence of NHX genes in poplar, eight PtNHX were identified from Populus trichocarpa genome. PtNHXs containing 10 transmembrane helices (TMH) and a hydrophilic C-terminal domain, the TMH compose a hollow cylinder to provide the channel for Na+ and H+ transport. The expression patterns and cis-acting elements showed that all the PtNHXs were response to single or multiple stresses including drought, heat, cold, salinity, MV, and ABA. Both the co-expression network and protein-protein interaction network of PtNHXs implying their functional divergence. Interestingly, although PtNHX7 and PtNHX8 were generated by whole genome duplication event, they showed significant differences in expression pattern, protein structure, co-expressed genes, and interacted proteins. Only PtNHX7 interact with CBL and CIPK, indicating PtNHX7 is the primary NHX involved in CBL-CIPK pathway during salt stress responses. Natural variation analysis based on 549 P. trichocarpa individuals indicated the frequency of SNPs in PtNHX7 was significantly higher than other PtNHXs. Our findings provide new insights into the functional divergence of NHX genes in poplar.

Identification of two CiGADs from Caragana intermedia and their transcriptional responses to abiotic stresses and exogenous abscisic acid.

BACKGROUND: Glutamate decarboxylase (GAD), as a key enzyme in the γ -aminobutyric acid (GABA) shunt, catalyzes the decarboxylation of L-glutamate to form GABA. This pathway has attracted much interest because of its roles in carbon and nitrogen metabolism, stress responses, and signaling in higher plants. The aim of this study was to isolate and characterize genes encoding GADs from Caragana intermedia, an important nitrogen-fixing leguminous shrub. METHODS: Two full-length cDNAs encoding GADs (designated as CiGAD1 and CiGAD2) were isolated and characterized. Multiple alignment and phylogenetic analyses were conducted to evaluate their structures and identities to each other and to homologs in other plants. Tissue expression analyses were conducted to evaluate their transcriptional responses to stress (NaCl, ZnSO4, CdCl2, high/low temperature, and dehydration) and exogenous abscisic acid. RESULTS: The CiGADs contained the conserved PLP domain and calmodulin (CaM)-binding domain in the C-terminal region. The phylogenetic analysis showed that they were more closely related to the GADs of soybean, another legume, than to GADs of other model plants. According to Southern blotting analysis, CiGAD1 had one copy and CiGAD2-related genes were present as two copies in C. intermedia. In the tissue expression analyses, there were much higher transcript levels of CiGAD2 than CiGAD1 in bark, suggesting that CiGAD2 might play a role in secondary growth of woody plants. Several stress treatments (NaCl, ZnSO4, CdCl2, high/low temperature, and dehydration) significantly increased the transcript levels of both CiGADs, except for CiGAD2 under Cd stress. The CiGAD1 transcript levels strongly increased in response to Zn stress (74.3-fold increase in roots) and heat stress (218.1-fold increase in leaves). The transcript levels of both CiGADs significantly increased as GABA accumulated during a 24-h salt treatment. Abscisic acid was involved in regulating the expression of these two CiGADs under salt stress. DISCUSSION: This study showed that two CiGADs cloned from C. intermedia are closely related to homologs in another legume, soybean. CiGAD2 expression was much higher than that of CiGAD1 in bark, indicating that CiGAD2 might participate in the process of secondary growth in woody plants. Multiple stresses, interestingly, showed that Zn and heat stresses had the strongest effects on CiGAD1 expression, suggesting that CiGAD1 plays important roles in the responses to Zn and heat stresses. Additionally, these two genes might be involved in ABA dependent pathway during stress. This result provides important information about the role of GADs in woody plants' responses to environmental stresses.

High temperature and UV-C treatments affect stilbenoid accumulation and related gene expression levels in Gnetum parvifolium

Background: Gnetum parvifolium stems and roots have been used for a long time in traditional Chinese medicines. Stilbenes are bioactive compounds present in G. parvifolium plants, and they possess antioxidative and anticancer properties. However, little is known about the responses of G. parvifolium stilbene biosynthetic pathways to stress conditions. Therefore, we investigated stilbene biosynthesis, including the expression of relevant genes, in G. parvifolium exposed to high-temperature and ultraviolet-C treatments. Results: High temperatures did not influence the accumulation of total stilbenes in stems but decreased stilbene concentrations in roots at 3 h, with a subsequent restoration to control levels. In contrast, ultraviolet irradiation induced the accumulation of total stilbenes in stems but not in roots. We also observed that high temperatures inhibited the production of resveratrol and piceatannol in G. parvifolium stems and roots, whereas ultraviolet treatments initially inhibited their accumulation (up to 6 h) but induced their production at later time points. Analyses of specific genes (i.e., PAL, C4H, 4CL, STS, and CYP) revealed that their expression levels generally increased in stress-treated stems and roots, although there was some variability in the expression profiles during treatments. Conclusions: Our results indicated that high temperatures and ultraviolet irradiation differentially affect the biosynthesis of specific stilbenes in G. parvifolium stems and roots. Therefore, cultivating G. parvifolium seedlings under optimal stress conditions may increase the biosynthesis of specific stilbene compounds.

Isolation of high-quality RNA from Platycladus orientalis and other Cupressaceae plants

Platycladus orientalis has a lifespan of several thousand years in China, making it a good plant in which to study aging at the molecular level, but this requires sufficient quantities of high-quality P. orientalis RNA. However, no appropriate methods have been reported for total RNA isolation from P. orientalis leaves. The TRIzol method did not extract RNA, while cetyltrimethylammonium bromide, sodium dodecyl sulfate-phenol, and plant RNAout kit (Tianz, Inc., China) protocols resulted in low yields of poor quality RNA. Isolating total RNA using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) resulted in a high-quality product but a low yield. However, the two-step removal of polyphenols and polysaccharides in the improved plant RNAout kit protocol resulted in the isolation of RNA with a 28S:18S rRNA ratio of band intensities that was ~2:1, the A260/A280 absorbance ratio was 2.03, and the total RNA yield from P. orientalis leaves was high. This protocol was tested on different P. orientalis tissues of different ages and on leaves of five other Cupressaceae plants. The total RNAs were successfully used in complementary DNA synthesis for transcriptome sequencing and would be suitable to use in additional experiments. The results of this study will benefit future studies in Cupressaceae plants.

Transcriptome Characterization of Gnetum parvifolium Reveals Candidate Genes Involved in Important Secondary Metabolic Pathways of Flavonoids and Stilbenoids.

Gnetum is a small, unique group of Gnetophyta with a controversial phylogenetic position. Gnetum parvifolium is an important Chinese traditional medicinal plant, which is rich in bioactive compounds such as flavonoids and stilbenoids. These compounds provide significant medicinal effects, mostly as antioxidant, anticancer, and antibacterial agents. However, the mechanisms involved in the biosynthesis and regulation of these compounds in G. parvifolium are still unknown. In this study, we found that flavonoids and stilbene compounds accumulated at different levels in various tissues of G. parvifolium. We further obtained and analyzed massive sequence information from pooled samples of G. parvifolium by transcriptome sequencing, which generated 94,816 unigenes with an average length of 724 bp. Functional annotation of all these unigenes revealed that many of them were associated with several important secondary metabolism pathways including flavonoids and stilbenoids. In particular, several candidate unigenes (PAL-, C4H-, 4CL-, and STS-like genes) involved in stilbenoids biosynthesis were highly expressed in leaves and mature fruits. Furthermore, high temperature and UV-C strongly induced the expression of these genes and enhanced stilbene production (i.e., resveratrol and piceatannol) in leaves of young seedlings. Our present transcriptomic and biochemical data on secondary metabolites in G. parvifolium should encourage further investigation on evolution, ecology, functional genomics, and breeding of this plant with strong pharmaceutical potential.

Transcriptomic analysis reveals importance of ROS and phytohormones in response to short-term salinity stress in Populus tomentosa.

Populus tomentosa (Chinese white poplar) is well adapted to various extreme environments, and is considered an important species to study the effects of salinity stress on poplar trees. To decipher the mechanism of poplar's rapid response to short-term salinity stress, we firstly detected the changes in H2O2 and hormone, and then profiled the gene expression pattern of 10-week-old seedling roots treated with 200 mM NaCl for 0, 6, 12, and 24 h (h) by RNA-seq on the Illumina-Solexa platform. Physiological determination showed that the significant increase in H2O2 began at 6 h, while that in hormone ABA was at 24 h, under salt stress. Compared with controls (0 h), 3991, 4603, and 4903 genes were up regulated, and 1408, 2206, and 3461 genes were down regulated (adjusted P ≤ 0.05 and |log2Ratio|≥1) at 6, 12, and 24 h time points, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in hormone- and reactive oxygen species-related biological processes, including "response to oxidative stress or abiotic stimulus," "peroxidase activity," "regulation of transcription," "hormone synthetic and metabolic process," "hormone signal transduction," "antioxidant activity," and "transcription factor activity." Moreover, K-means clustering demonstrated that DEGs (total RPKM value>12 from four time points) could be categorized into four kinds of expression trends: quick up/down over 6 or 12 h, and slow up/down over 24 h. Of these, DEGs involved in H2O2- and hormone- producing and signal-related genes were further enriched in this analysis, which indicated that the two kinds of small molecules, hormones and H2O2, play pivotal roles in the short-term salt stress response in poplar. This study provides a basis for future studies of the molecular adaptation of poplar and other tree species to salinity stress.

Comparative proteomic analysis in Miscanthus sinensis exposed to antimony stress.

To explore the molecular basis of Sb tolerance mechanism in plant, a comparative proteomic analysis of both roots and leaves in Miscanthus sinensis has been conducted in combination with physiological and biochemical analyses. M. sinensis seedlings were exposed to different doses of Sb, and both roots and leaves were collected after 3 days of treatment. Two-dimensional gel electrophoresis (2-DE) and image analyses found that 29 protein spots showed 1.5-fold change in abundance in leaves and 19 spots in roots, of which 31 were identified by MALDI-TOF-MS and MALDI-TOF-TOF-MS. Proteins involved in antioxidant defense and stress response generally increased their expression all over the Sb treatments. In addition, proteins relative to transcription, signal transduction, energy metabolism and cell division and cell structure showed a variable expression pattern over Sb concentrations. Overall these findings provide new insights into the probable survival mechanisms by which M. sinensis could be adapting to Sb phytotoxicity.

Responses and acclimation of Chinese cork oak (Quercus variabilis Bl.) to metal stress: the inducible antimony tolerance in oak trees.

Antimony (Sb) pollution has become a pressing environmental problem in recent years. Trees have been proven to have great potential for the feasible phytomanagement; however, little is known about Sb retention and tolerance in trees. The Chinese cork oak (Quercus variabilis Bl.) is known to be capable of growth in soils containing high concentrations of Sb. This study explored in detail the retention and acclimation of Q. variabilis under moderate and high external Sb levels. Results revealed that Q. variabilis could tolerate and accumulate high Sb (1623.39 mg kg(-1) DW) in roots. Dynamics of Sb retention in leaves, stems, and roots of Q. variabilis were different. Leaf Sb remained at a certain level for several weeks, while in roots and stems, Sb concentrations continued to increase. Sb damaged tree's PSII reaction cores but elicited defense mechanism at the donor side of PSII. It affected the electron transport flow after QA (-) more strongly than the oxygen-evolving complex and light-harvesting pigment-protein complex II. Sb also decreased leaf chlorophyll concentrations and therefore inhibited plant growth. During acclimation to Sb toxicity, Sb concentrations in leaves, stems, and roots decreased, with photosynthetic activity and pigments recovering to normal levels by the end of the experiment. These findings suggest that Sb tolerance in Q. variabilis is inducible. Acclimation seems to be related to homeostasis of Sb in plants. Results of this study can provide useful information for trees breeding and selection of Sb phytomanagement strategies, exploiting the established ability of Q. variabilis to transport, delocalize in the leaves, and tolerate Sb pollutions.

The evaluation of heavy metal accumulation and application of a comprehensive bio-concentration index for woody species on contaminated sites in Hunan, China.

Fast-growing metal-accumulating woody plants are considered potential candidates for phytoextraction of metals. Shuikoushan mining, one of the biggest Pb and Zn production bases in China, presents an important source of the pollution of environment during the last 100 years. Over 150 km(2) of fertile soil have been contaminated by the dust, slag, and tailings from this mining. The goal of the present work has been to determine the content of Pb, Zn, Cd, and Cu in wild woody plants (18 species) naturally growing in this area. Two hundred five plant and soil samples from 11 contaminated sites were collected and analyzed. In addition, to assess the ability of multi-metal accumulation of these trees, we proposed a predictive comprehensive bio-concentration index (CBCI) based on fuzzy synthetic assessment. Our data suggest some adult trees could also accumulate a large amount of metals. Pb concentrations in leaves of Paulownia fortunei (Seem.) Hemsl. (1,179 mg/kg) exceeded the hyperaccumulation threshold (1,000 mg/kg). Elevated Pb concentrations (973.38 mg/kg) were also found in the leaves of Broussonetia papyrifera (L.) Vent., with a Pb bio-concentration factor of up to 0.701. Endemic species, Zenia insignis Chun exhibited huge potential for Zn and Cd phytoextraction, with the highest concentrations of Zn (1,968 mg/kg) and Cd (44.40 mg/kg), characteristic root nodules, and fast growth rates in poor soils. As for multi-metal accumulation ability, native species B. papyrifera was calculated to have the most exceptional ability to accumulate various metals simultaneously (CBCI 2.93), followed by Amorpha fruticosa L. (CBCI 2.72) and Lagerstroemia indica L. (CBCI 2.53). A trend of increasing metal from trunks to leaves (trunks < branches < leaves) and towards fine roots has been shown by metal partitioning between tissues. The proposed CBCI would allow for the selection of suitable trees for phytoremediation in the future.