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Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.

Background and Aims The East Asian–Tethyan disjunction pattern and its mechanisms of formation have long been of interest to researchers. Here, we studied the biogeographical history of Asteraceae tribe Cardueae, with a particular focus on the temperate East Asian genus Atractylodes DC., to understand the role of tectonic and climatic events in driving the diversification and disjunctions of the genus. Methods A total of 76 samples of Atractylodes from 36 locations were collected for RAD-sequencing. Three single nucleotide polymorphism (SNP) datasets based on different filtering strategies were used for phylogenetic analyses. Molecular dating and ancestral distribution reconstruction were performed using both chloroplast DNA sequences (127 Cardueae samples) and SNP (36 Atractylodes samples) datasets. Key Results Six species of Atractylodes were well resolved as individually monophyletic, although some introgression was identified among accessions of A. chinensis, A. lancea and A. koreana. Dispersal of the subtribe Carlininae from the Mediterranean to East Asia occurred after divergence between Atractylodes and Carlina L. + Atractylis L. + Thevenotia DC. at ~31.57 Ma, resulting in an East Asian–Tethyan disjunction. Diversification of Atractylodes in East Asia mainly occurred from the Late Miocene to the Early Pleistocene. Conclusions Aridification of Asia and the closure of the Turgai Strait in the Late Oligocene promoted the dispersal of Cardueae from the Mediterranean to East China. Subsequent uplift of the Qinghai–Tibet Plateau as well as changes in Asian monsoon systems resulted in an East Asian–Tethyan disjunction between Atractylodes and Carlina + Atractylis + Thevenotia. In addition, Late Miocene to Quaternary climates and sea level fluctuations played major roles in the diversification of Atractylodes. Through this study of different taxonomic levels using genomic data, we have revealed an overlooked dispersal route between the Mediterranean and far East Asia (Japan/Korea) via Central Asia and East China.

The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai–Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.

Menispermum dauricum is a woody liana with great medicinal value. In the current study, we assembled the first chloroplast (cp) genome of M. dauricum. The whole chloroplast genome is 158,623 bp in length, with one large copy region (LSC: 88,879 bp), a small single copy region (SSC: 20,644 bp), and two inverted repeats (IR: 24,550 bp). The cp genome contains 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. In our phylogeny of Ranunculales, Papaveraceae is found to be the basal group of Ranunculales and M. dauricum is sister to Stephania japonica.

Gymnocarpos przewalskii (Caryophyllaceae) is a desert shrub, which is listed as an endangered species in the Red List of China. In this study, the complete chloroplast (cp) genome of G. przewalskii is reported. The genome size is 150,636 bp, with an average GC content of 36.5%, containing a pair of inverted repeat (IR, 25,350 bp) regions, separated by a large single copy (LSC, 83,114 bp) and a small single copy (SSC, 16,822 bp) region. There are 111 genes, including 77 protein coding genes, 30 tRNA genes and 4 rRNA genes. We also reconstructed the phylogeny of Caryophyllaceae based on all published cp genomes. The maximum likelihood (ML) trees supported Gymnocarpos as the basal taxon of Caryophyllaceae.

Polyploidization plays an important role in plant adaption to adverse environments, but the mechanism by which polyploidization confers adaptation to cold stress remains elusive. Here, autotetraploid strawberry (2n = 4x = 28) was successfully synthesized from wild strawberry (Fragaria nilgerrensis; 2n = 2x = 14) using a primary meristem processing technique. The autotetraploid plants exhibited a higher resistance to cold stress compared to their parental diploids, revealed by a series of physiological-biochemical examinations. Transcriptome analysis showed that expression pattern changes of genes in several pathways were the key contributors to the high cold resistance of autotetraploid strawberry. These main players included Ca2+ signal transduction, transcription factors (TFs), reactive oxygen species (ROS) scavenging enzyme, phenylpropanoid biosynthesis, abscisic acid (ABA) signaling and carbohydrate metabolism. The coordinate action of these factors enhanced the antioxidant defense system and protected the integrity of membranes and cellular organelles. Notably, gene co-expression network analysis (WGCNA) demonstrated that four hub genes (regulating cinnamyl-alcohol dehydrogenase (CAD), peroxidase (POD), caffeoyl-CoA O-methyltransferase (CCoAMT) and calmodulin-like protein (CML)) function much importantly in the network regulating this high cold resistance. Therefore, a model is proposed to elucidate the regulatory mechanisms of high cold resistance in the autotetraploid strawberry. The present findings provide new insights into understanding the complex regulatory network responsible for enhancing cold resistance in ployploid plants.

Visible-light photodegradation test revealed that B and Zr co-doping can raise the photocatalytic ability of the undoped TiO 2 by a fold. XRD crystallography and Raman phonon spectroscopy measurements suggest that the Zr 4+ ions replace the Ti 4+ ions while the B 3+ ions occupy the interstitial sites, expanding the unit-cell volume and reducing crystallite size. The incorporation of interstitial boron dopants creates oxygen vacancies (Ov ) and reduce Ti 4+ to Ti 3+ to form [Ov -Ti 3+ ] + , which traps the carriers and prolongs carrier lifetime. Moreover, Zr 4+ ions replace Ti 4+ ions and form impurity levels, which could improve visible light response. The co-doped samples are benefited from both B interstitials and Zr substitutes.

Aiming to improve the photocatalytic activity, boron and tantalum co-doped TiO2 nanocrystals were prepared by a sol–gel method. Pure and doped titania samples were characterized by X-ray diffraction (XRD) measurements, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and UV–vis diffuse reflectance spectroscopy. The results revealed that all the samples have highly crystalline anatase structure, and no any other second phase was observed. It is found that the incorporation of dopants inhibits the growth of TiO2 nanocrystal. Moreover, XPS observations showed that Ta are in the form of Ta5+ while the majority of B species are present at interstitial sites. Finally, photocatalytic activities of all the samples were evaluated by degradation of methylene blue (MB) solutions under simulated solar light irradiation. Ta-doped and (B, Ta)-codoped catalysts exhibit enhanced photocatalytic activities in comparison with pure TiO2, with the codoped sample exhibiting the best photodegradation performance. This indicates that B and Ta co-doping is an effective way to improve photocatalytic performance of TiO2. The catalytic activity of B-doped TiO2 becomes slightly worse than pure TiO2 nanocrystals, which is plausible due to increased charge carrier recombination centers induced by incorporation of boron species.

Table S3. Locality and voucher information for populations of Oresitrophe rupifraga and Mukdenia rossii used in this study. Voucher specimens are deposited at the herbarium of Zhejiang University (HZU), Hangzhou, Zhejiang, China. (DOCX 17 kb)

Table S1. Characteristics of the twelve nuclear primer pairs newly developed in this study based on SCNG loci identified by different approaches. Table S2. Full list of 1018 SCNG loci identified from the transcriptomes of CSE and SW lineage, with their basic information including identification approaches, substitution rates between lineages and gene annotations. '+' denotes the approaches that supported the single-copy status of the locus. Table S3. List of individuals included in this study, with corresponding sampling localities and GenBank accession numbers. (PDF 415 kb)

Figure S2. Summary of STRUCTURE analyses based on the gSSR data. (A) Mean ln posterior probabilities of each K, LnP(D). (B) The corresponding Î K statistics calculated according to Evanno et al. (2005). (PDF 354 kb)

Table S4. cpSSRs identified from comparative analysis of chloroplast genome for Oresitrophe and Mukdenia. (DOCX 22 kb)

Figure S2. Distribution of gene ontology (GO) classifications for the 3737 orthologous pairs with Ka/Ks ratios significantly < 0.5. The y-axis indicates the percent (left y-axis) or number of unigenes (right y-axis) per (sub-) category. (PDF 436 kb)

Figure S1. The distribution and presence of simple sequence repeats (SSRs) in the cp genome of Oresitrophe rupifraga-HNYD (A) and Mukdenia rossii (B). (PDF 392 kb)

Figure S3. Frequency distribution of EST-SSR unit size in the transcriptomes of CSE and SW lineages. (PDF 348 kb)

Figure S7. TCS-derived network of genealogical relationships among the identified haplotypes for each of the SCNG locus (PDF 198 kb)

Figure S6. Agarose-gel electrophoresis patterns of a subset of SCNG primer pairs for T. hemsleyanum (PDF 148 kb)

Figure S5. The pairwise identity of each SCNG pair between the two lineages. Each dot in the scatter diagram denotes a SCNG locus, and the blue colored ones represent those genes under purifying selection). (PDF 177 kb)

Figure S4. Frequency distribution of EST-SSR repeat motifs (mono- to tri-nucleotide motifs) between CSE and SW lineages. (PDF 337 kb)

Gymnospermium kiangnanense is an endangered species in the family Berberidaceae. In this study, we assembled the chloroplast (cp) genome of G. kiangnanense and reconstructed the phylogenetic tree of Berberidaceae based on the complete cp genome. The cp genome of G. kiangnanense is 160,136 bp in length, comprising a pair of inverted repeat (IR) regions (26,424 bp) separated by a large single-copy (LSC) region (87,580 bp) and a small single-copy (SSC) region (19,708bp). The genome encodes 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes, with 18 duplicated genes in the inverted repeats. Phylogenetic analysis indicates that G. kiangnanense is sister to G. microrrhynchum, and the Gymnospermium clade is closely related with Nandina.

Based on molecular data, a new species, Myriolecis altunica, is described, and Lecanora caesioalutacea is placed in the genus Myriolecis (Lecanoraceae, Ascomycota). Myriolecis altunica is characterized by having a continuous, ashy brown thallus, with lobulate margins, apothecia with blackish disc and margin, with the disc whitish pruinose, and the absence of secondary substances. Myriolecis caesioalutacea has an ashy gray thallus and heavily pruinose, almost white apothecia, and contains xanthones (2,7-dichlorlichexanthone). The species was first reported as Lecanora caesioalutacea H.Magn. from Gansu, China, but is here shown to belong in the genus Myriolecis. Phylogenetic analyses based on ITS separately and on a 6-locus combined analysis (ITS, LSU, mtSSU, RPB1, RPB2, MCM7) both support placement of these two species in Myriolecis. The taxa are described and illustrated, and their distribution and ecology are briefly discussed.

Premise of the study: Polymorphic microsatellite markers were developed for Smilax sieboldii (Smilacaceae), a member of the S. hispida group with a biogeographic disjunction between eastern Asia and North America, to study the phylogeography and incipient speciation of this species and its close relatives. Methods and Results: Transcriptome sequencing produced 47,628 unigenes. Seventeen loci were developed from 122 randomly selected primer pairs. Polymorphism and genetic variation were evaluated for 68 accessions representing five populations of S. sieboldii. The number of alleles per locus ranged from four to 18; the expected heterozygosity ranged from 0.59 to 0.92. Twelve loci were successfully amplified in five related species: S. scobinicaulis, S. californica, S. hispida, S. moranensis, and S. jalapensis. Conclusions: These novel expressed sequence tag–derived microsatellite markers will facilitate further population genetic research of S. sieboldii and its close allies of the S. hispida group.

Lycium ruthenicum is a precious desert plant with high medicinal and ecological values. It contains rich anthocyanins, which are safe natural pigments and could be used for natural food colorants. In this study, the complete chloroplast (cp) genome of L. ruthenicum was assembled on the basis of next generation sequencing. The whole genome is 154,996 bp in length, including two single copy regions (LSC: 85,993 bp and SSC: 18,213 bp) and two inverted repeat regions (IR: 25,395 bp). The overall G + C content of the genome is 37.9%. The cp genome consists of 111 unique genes, including 30 tRNA genes, 4 rRNA genes and 77 protein-coding genes. Phylogenetic analysis indicates that L. ruthenicum is closely clustered with Atropa belladonna, Przewalskia tangutica, and Scopolia parviflora.

Increases in atmospheric volatile organic compounds (VOC), especially in relation to biogenic VOC (BVOC), and haze days that affect the built-up areas are believed to be closely correlated. The present study aims to provide a spatially and temporally resolved BVOC inventory of a subtropical urbanerural complex, the Greater Hangzhou Area (GHA) in China. Urban green space was subdivided into block green space and linear green space; rural areas were classified into four primary forest types. A field survey was conducted to assess the vegetation composition (species, size) and foliar mass of each tree species. BVOC emission potentials were obtained from measurement and literature. Results showed (1) the emission intensity (annual BVOC emissions per land area) in the entire GHA is 3.37 � 10

Cryptococcus laurentii was evaluated for its activity in reducing postharvest gray mold decay of pear caused by Botrytis cinerea . Washed cell suspensions of yeast controlled gray mold better than yeast in culture broth. Treatment of wounds with autoclaved cell cultures or cell-free culture filtrate did not prevent decay. The interval between inoculation with the pathogen and application of the antagonist significantly influenced the efficacy of biocontrol. Efficacy was maintained when C. laurentii was applied simultaneously or prior to inoculation with B. cinerea but reduced if applied after inoculation with B. cinerea . The concentrations of antagonist had significant effects on biocontrol effectiveness: the higher the concentrations of the antagonist, the lower the disease incidence and the smaller the lesion diameter regardless of whether the fruit was stored at 25 °C for 7 days or 2 °C for 30 days followed by 20 °C for 7 days. The efficacy of C. laurentii was enhanced by the addition of 2% CaCl 2 . C. laurentii significantly reduced the natural development of decay and did not impair quality parameters of fruit following storage at 2 °C for 60 days followed by 20 °C for 15 days.

The potential of using microwave power alone, or in combination with antagonistic yeast, for control of Rhizopus stolonifer on peach, and its effects on the postharvest quality of peach were investigated. In in vitro tests, the growth of R. stolonifer was completely inhibited by a 2,450 MHz microwave heating for 2 min or more. The population density of R. stolonifer in surface wounds of microwave treatment fruits was significantly lower than that in the control. In vivo studies of inoculation of peach fruit with R. stolonifer followed by microwave treatment, Cryptococcus laurentii or both of them, microwave power and C. laurentii, as stand-alone treatments, were capable of reducing the percentage of decayed fruit from 95% in control, untreated fruit to 42.1% and 75%, respectively. However, in fruit treated with a combination of microwave power and C. laurentii, the percentage of decayed fruits was only 23.7%. The experiments on reducing natural decay development of fruit gave similar results. The microwave treatment, C. laurentii, or both of them did not impair the quality parameters of the fruit. Thus, the combination of microwave and C. laurentii could be an alternative to chemicals for control of postharvest Rhizopus rot on peach fruits.

The aim of this study was to investigate the anti-fibrotic effects and the possible underlying mechanisms of taxus polyprenols (TPs) isolated from the needles of Taxus chinensis var. mairei.The animals were randomly divided into normal control with vehicles only (olive oil), rat model given CCl₄ only, CCl₄+low TPs (48 mg/kg), CCl₄+medium TPs (120 mg/kg), CCl₄+high TPs (300 mg/kg), and CCl₄+Polyene phosphatidylcholine (PP, 120 mg/kg). The rat model of liver fibrosis was induced by subcutaneous injection of 40% (v/v) of CCl₄ diluted in olive oil (3 mL/kg body weight) twice per week for 8 weeks. Liver histopathological study was performed. Aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP) and albumin (ALB) of the serum were determined for evaluating the liver function. In order to reveal the possible mechanisms of the anti-fibrotic effects, oxidative stress level, hepatic collagen metabolism, and hepatic stellate cells (HSCs) activation were investigated. Furthermore, the mRNA expression of the fibrotic-related factors was measured by the quantitative real-time RT-PCR.TPs successfully attenuated liver injury induced by CCl₄ shown by histopathological sections of livers and improved liver function as indicated by decreased ALT, AST and ALP levels and increased ALB levels in serum of the rats. TPs significantly increased the hepatic Cu/Zn SOD and GSH-Px activities along with GSH content while a remarkable decrease in MDA content. Both immunohistochemical staining and mRNA expression levels of α-SMA indicated a profound suppression of HSCs activation. Furthermore, it significantly inhibited the mRNA expression of the pro-fibrotic cytokines Col α1(I), Col α1(Ш), MMP-2, TIMP-1, TIMP-2, PDGF-β, TGF-β1, CTGF and TNF-α and restored the hepatoprotective factor HGF.These results suggest that the protective effects of TPs in chronic CCl₄-induced liver fibrosis might be related with the reduction of oxidative damage, the inhibition of HSCs activation, the down-regulation of pro-fibrogenic stimuli and the protection of hepatocytes.

Summary: Rapid advances in pharmaceutical sciences have brought ever-increasing interests in combined therapies for better clinical efficacy and safety, especially in cases of complicated and refractory diseases. Innovative experimental technologies and theoretical frameworks are being actively developed for multicomponent drug research. In this work, we present the Drug Combination Database, with aims to facilitate analyses of known drug combinations, to summarize patterns of beneficial drug interactions, and to provide a basis for theoretical modeling and simulation of such drug interactions. Its current version (1.0) collected 499 approved or investigational drug combinations, including 40 unsuccessful drug combinations, involving 485 individual drugs, from >6000 references. Availability: http://www.cls.zju.edu.cn/dcdb/. Contact: xinchen@zju.edu.cn Supplementary information: Supplementary data are available at the database website and Bioinformatics online.

Actinidia macrosperma (AM) is a medicinal plant in China and has been well known for its activities against cancers, especially of lung, liver and digestive system. The immunomodulatory effects of AM aqueous extract were examined using S180-bearing mice. Young adult (20 +/- 2 g) ICR mice inoculated with S180 cells were divided randomly into six groups: S180-bearing control group, normal control group, positive control group (Ginseng Radix Rubra 2000 mg/kg) and 50, 100, 250 mg/kg AM treatment groups. Each group consisted of ten mice. Body and tumor weights were obtained after 12 consecutive days, and their humoral, cellular and nonspecific immune functions were also determined by relative assays. The results showed that the aqueous extract of AM was lack of significant inhibit on transplantable sarcoma S180, with a inhibit rate of 1.5% -14.8% (dose at 250 mg/kg was the best), but significantly increased the overall immune functions (especially at 100 and 250 mg/kg). The immunomodulatory effect was dose-dependent in a nonlinear fashion with the optimal dose of 100 mg/kg. The AM-induced antitumor effects were at least partially indirect and were associated with the modulation of immune functions.

The effects of external stress on Bi2Te3 nano-films have been investigated by first-principles calculation, including stability, electronic structure, crystal structure, and bond order. It is found that the critical thickness of nano-film is sensitive to the stress in Bi2Te3 nano-film while the band gap is near constant. The critical thickness decreases under tensile stress, whereas it increases under compressive stress. The band gap and band order of Bi2Te3 film has been affected collectively by the surface and internal crystal structures, the contraction ratio between surface bond length of nano-film and the corresponding bond length of bulk decides the band order of Bi2Te3 film.