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Restoring high-fidelity textures for 3D reconstructed models are an increasing demand in AR/VR, cultural heritage protection, entertainment, and other relevant fields. Due to geometric errors and camera pose drifting, existing texture mapping algorithms are either plagued by blurring and ghosting or suffer from undesirable visual seams. In this paper, we propose a novel tri-directional similarity texture synthesis method to eliminate the texture inconsistency in RGB-D 3D reconstruction and generate visually realistic texture mapping results. In addition to RGB color information, we incorporate a novel color image texture detail layer serving as an additional context to improve the effectiveness and robustness of the proposed method. First, we select an optimal texture image for each triangle face of the reconstructed model to avoid texture blurring and ghosting. During the selection procedure, the texture details are weighted to avoid generating texture chart partitions across high-frequency areas. Then, we optimize the camera pose of each texture image to align with the reconstructed 3D shape. Next, we propose a tri-directional similarity function to resynthesize the image context within the boundary stripe of texture charts, which can significantly diminish the occurrence of texture seams. Finally, we introduce a global color harmonization method to address the color inconsistency between texture images captured from different viewpoints. The experimental results demonstrate that the proposed method outperforms state-of-the-art texture mapping methods and effectively overcomes texture tearing, blurring, and ghosting artifacts.

Plants perceive pathogens and induce robust transcriptional reprogramming to rapidly achieve immunity. The mechanisms of how immune-related genes are transcriptionally regulated remain largely unknown. Previously, the trihelix transcriptional factor ARABIDOPSIS SH4-RELATED 3 (ASR3) was shown to negatively regulate pattern-triggered immunity (PTI) in Arabidopsis thaliana. Here, we identified another trihelix family member ASR3-Interacting Transcriptional Factor 1 (AITF1) as an interacting protein of ASR3. ASR3-Interacting Transcriptional Factor 1 and ASR3 form heterogenous and homogenous dimers in planta. Both aitf1 and asr3 single mutants exhibited increased resistance against the bacterial pathogen Pseudomonas syringae, but the double mutant showed reduced resistance, suggesting AITF1 and ASR3 interdependently regulate immune gene expression and resistance. Overexpression of AITF1 triggered autoimmunity dependently on its DNA-binding ability and the presence of ASR3. Notably, autoimmunity caused by overexpression of AITF1 was dependent on a TIR-NBS-LRR (TNL) protein suppressor of AITF1-induced autoimmunity 1 (SAA1), as well as enhanced disease susceptibility 1 (EDS1), the central regulator of TNL signaling. ASR3-Interacting Transcriptional Factor 1 and ASR3 directly activated SAA1 expression through binding to the GT-boxes in SAA1 promoter. Collectively, our results revealed a mechanism of trihelix transcription factor complex in regulating immune gene expression, thereby modulating plant disease resistance and autoimmunity.

Sclerotinia sclerotiorum is a well-known phytopathogenic fungus with a wide host range. Identifying novel mycoviruses in phytopathogenic fungi is necessary to develop novel strategies for plant health protection and contribute to understanding the origin of viruses. Six new mycoviruses with positive single-stranded RNA genomes co-infecting the hypovirulent strain SCH733 of S. sclerotiorum were identified using a metatranscriptomic approach, and their complete genome sequences were molecularly determined. These mycoviruses belong to the following five families: Narnaviridae, Mitoviridae, Deltaflexviridae, Botourmiaviridae, and Ambiguiviridae. Three of these mycoviruses belong to existing International Committee on Taxonomy of Viruses (ICTV)-recognized species. Two of these newly identified mycoviruses have unique genomic features that are significantly different from those of all known mycoviruses. Phylogenetic analysis revealed that these six mycoviruses included close as well as distant relatives of known mycoviruses, thereby providing new insight into virus evolution and classification. Mycovirus horizontal transmission and elimination experiments revealed that Sclerotinia sclerotiorum narnavirus 5 is associated with hypovirulence of S. sclerotiorum, although we have not shown that it is independently responsible for the hypovirulence phenotype. This study broadens the diversity of known mycoviruses infecting S. sclerotiorum and provides a clue toward limiting hypovirulence in S. sclerotiorum.

Locoweeds are leguminous forbs known for their toxicity to livestock caused by the endophytic fungi Alternaria sect. Undifilum. Unlike the defensive mutualisms reported in many toxin-producing endophytes and their plant hosts, the benefits that A. sect. Undifilum can confer to it host plants remains unclear. Here, we conducted physiological and genetic analyses to show that A. (sect. Undifilum) oxytropis influences growth, especially root development, in its locoweed host Oxytropis ochrocephala and Arabidopsis. The presence of A. oxytropis significantly decreased primary root length while increasing the numbers of lateral roots and root hairs, and increasing plant leaf area and fresh weight. The fungus also increased the concentrations of plant endogenous auxin, and the expression of key genes for auxin biosynthesis, signaling, and transport. These effects on root development were abolished in mutants deficient in auxin signaling and polar transport. Alternaria oxytropis down-regulated expression of PIN1 but increased expression of PIN2, PIN7, and AUX1, which might reflect alterations in the spatial accumulation of auxin responsible for the changes in root architecture. Plant growth was insensitive to A. oxytropis when naphthylphthalamic acid was applied. Our findings indicate a function of A. oxytropis in promoting the growth and development of Arabidopsis via the regulation of auxin, which in turn suggests a possible role in benefiting its locoweed hosts via a process independent of its toxin production.

Plants recognize microbe-associated molecular patterns (MAMPs) to activate immune responses and defense priming to defend against pathogen infections. Transcriptional regulation of gene expression is crucial for plant immunity and is mediated by multiple factors, including DNA methylation. However, it remains unknown whether and how DNA demethylation contributes to immune responses in MAMP-triggered immunity. Here, we report that active DNA demethylation is required for MAMP-triggered immunity to bacterial pathogens. The rdd-2 triple mutant carrying mutations in ROS1, DML2, and DML3 that encode DNA glycosylases, which are key DNA demethylation enzymes, exhibits compromised immune responses triggered by the MAMPs flg22 and elf18. Genome-wide methylome analysis reveals that flg22 induces rapid and specific DNA demethylation in an RDD-dependent manner. The expression levels of salicylic acid signaling-related and phytoalexin biosynthesis-related genes are tightly associated with the flg22-induced promoter demethylation. The compromised accumulation of priming compounds and antimicrobial metabolites ultimately leads to a defense priming defect in the rdd-2 mutant. Our results reveal the critical role of active DNA demethylation in the MAMP-triggered immune response and provide unique insight into the molecular mechanism of flg22-modulated DNA demethylation.

A significant number of mycoviruses have been identified that are related to plant viruses, but their evolutionary relationships are largely unexplored. A fusarivirus, Rhizoctonia solani fusarivirus 4 (RsFV4), was identified in phytopathogenic fungus Rhizoctonia solani (R. solani) strain XY74 co-infected by an alphaendornavirus. RsFV4 had a genome of 10,833 ​nt (excluding the poly-A tail), and consisted of four non-overlapping open reading frames (ORFs). ORF1 encodes an 825 aa protein containing a conserved helicase domain (Hel1). ORF3 encodes 1550 aa protein with two conserved domains, namely an RNA-dependent RNA polymerase (RdRp) and another helicase (Hel2). The ORF2 and ORF4 likely encode two hypothetical proteins (520 and 542 aa) with unknown functions. The phylogenetic analysis based on Hel2 and RdRp suggest that RsFV4 was positioned within the fusarivirus group, but formed an independent branch with three previously reported fusariviruses of R. solani. Notably, the Hel1 and its relatives were phylogenetically closer to helicases of potyviruses and hypoviruses than fusariviruses, suggesting fusarivirus Hel1 formed an evolutionary link between these three virus groups. This finding provides evidence of the occurrence of a horizontal gene transfer or recombination event between mycoviruses and plant viruses or between mycoviruses. Our findings are likely to enhance the understanding of virus evolution and diversity.

Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production. S. sclerotiorum , a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we discovered that S. sclerotiorum treatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root.

Ralstonia solanacearum is a devastating soil-borne bacterial pathogen capable of infecting many plant species, including tomato (Solanum lycopersicum). However, the perception of Ralstonia by the tomato immune system and the pathogen's counter-defense strategy remain largely unknown. Here, we show that PehC, a specific exo-polygalacturonase secreted by Ralstonia, acts as an elicitor that triggers typical immune responses in tomato and other Solanaceous plants. The elicitor activity of PehC depends on its N-terminal epitope, and not on its polygalacturonase activity. The recognition of PehC specifically occurs in tomato roots and relies on unknown receptor-like kinase(s). Moreover, PehC hydrolyzes plant pectin-derived oligogalacturonic acids (OGs), a type of damage-associated molecular pattern (DAMP), which leads to the release of galacturonic acid (GalA), thereby dampening DAMP-triggered immunity (DTI). Ralstonia depends on PehC for its growth and early infection and can utilize GalA as a carbon source in the xylem. Our findings demonstrate the specialized and dual functions of Ralstonia PehC, which enhance virulence by degrading DAMPs to evade DTI and produce nutrients, a strategy used by pathogens to attenuate plant immunity. Solanaceous plants have evolved to recognize PehC and induce immune responses, which highlights the significance of PehC. Overall, this study provides insight into the arms race between plants and pathogens.

Sclerotinia sclerotiorum reovirus 1 (SsReV1) was previously reported to infect hypovirulent strain SCH941 of the phytopathogenic fungus Sclerotinia sclerotiorum and to contain 11 double-stranded RNA (dsRNA) segments (S1-S11). Here, we report that SsReV1 is actually composed of 12 dsRNA segments instead of 11. The full-length nucleotide sequence of the twelfth segment (S12) was determined using a combination of RACE and high-throughput sequencing methods. S12 is 1217 nucleotides in length and has highly conserved terminal sequences that resemble those of the other 11 segments of SsReV1. S12 contains a single open reading frame encoding a protein (VP12) of 311 amino acids. Although regular BLAST analysis did not reveal any similarity of VP12 to known sequences, it was found to be homologous to the VP11 of Colorado tick fever virus of the genus Coltivirus when a hidden-Markov-model-based HHpred analysis was performed. A single-protoplast regeneration experiment suggested that S12 and S2 were maintained or lost in parallel. In summary, the SsReV1 genome consists of 12 dsRNA segments.

Kiwi is a popular fruit consumed worldwide. A number of fungal pathogens have been reported to cause postharvest rot of kiwifruit, and Botryosphaeriaceae species are the major causal agents of the disease. In this study, 18 isolates belonged to the genus Neofusicoccum (family Botryosphaeriaceae) were isolated from 247 symptomatic kiwifruits of the cultivars Jinyan, Jintao, and Jinkui collected from orchards in Hubei and Jiangxi Provinces, China. Among the isolates, three grouped with various known N. parvum isolates, whereas the remaining 15 formed two independent clades. On the basis of further phylogenetic analyses with concatenated sequences of ITS and three genes encoding translation elongation factor 1-alpha (TEF), β-tubulin (TUB), and DNA-dependent RNA polymerase II subunit (RPB2), as well as morphological characteristics, two new species, N. actinidiae and N. guttata, were proposed. Their pathogenicity to kiwi, apple, and citrus fruits was also confirmed.

Fungal segmented negative-sense RNA viruses (SNSRVs) have been frequently found. Only the large segment encoding RNA-dependent RNA polymerase (RdRp) has been reported in most fungal SNSRVs, except for a few fungal SNSRVs reported to encode nucleocapsids, nonstructural proteins, or movement proteins.

Long noncoding RNAs (lncRNAs) are crucial regulators of gene expression in many biological processes, but their biological functions remain largely unknown, especially in fungi. Fusarium graminearum is an important pathogen that causes the destructive disease Fusarium head blight (FHB) or head scab disease on wheat and barley. In our previous RNA sequencing (RNA‐Seq) study, we discovered that lncRsp1 is an lncRNA that is located +99 bp upstream of a putative sugar transporter gene, Fgsp1, with the same transcription direction. Functional studies revealed that ΔlncRsp1 and ΔFgsp1 were normal in growth and conidiation but had defects in ascospore discharge and virulence on wheat coleoptiles. Moreover, lncRsp1 and Fgsp1 were shown to negatively regulate the expression of several deoxynivalenol (DON) biosynthesis genes, TRI4, TRI5, TRI6, and TRI13, as well as DON production. Further analysis showed that the overexpression of lncRsp1 enhanced the ability of ascospore release and increased the mRNA expression level of the Fgsp1 gene, while lncRsp1‐silenced strains reduced ascospore discharge and inhibited Fgsp1 expression during the sexual reproduction stage. In addition, the lncRsp1 complementary strains lncRsp1‐LC‐1 and lncRsp1‐LC‐2 restored ascospore discharge to the level of the wild‐type strain PH‐1. Taken together, our results reveal the distinct and specific functions of lncRsp1 and Fgsp1 in F. graminearum and principally demonstrate that lncRsp1 can affect the release of ascospores by regulating the expression of Fgsp1., lncRsp1, a long noncoding RNA located +99 bp upstream of a putative sugar transporter gene Fgsp1, can affect the release of ascospores by regulating the expression of Fgsp1 in Fusarium graminearum.

Chitinase plays an important role in plant resistance against chitin containing pathogens by degrading chitin. Clubroot, caused by Plasmodiophora brassicae, is a major disease in cruciferous crops worldwide, including vegetable and rapeseed. Chitin is the main component of P. brassicae spore cell walls, chitinases can enhance the plant’s defense system as they act on chitin. However, the function of chitinases in P. brassicae has not reported. Here, we found that chitin is the functional component of P. brassicae by wheat germ agglutinin staining and commercial chitinase treatment . Chitin extracted from resting spores of P. brassicae was characterized by infrared spectroscopy, X-ray diffraction and thermo gravimetry analysis.The chitinase PbChia1 was identified by chitin pull-down assays combined with LC-MS/MS method. We also showed that PbChia1 was a typical secreted chitinase, could bind to chitin and showed chitinase activity in vitro, significantly degrade the number of resting spores of P. brassicae and significantly relieve the severity of clubroot symptom, the biocontrol effect was 61.29%. Overexpression of PbChia1 in Arabidopsis thaliana resulted in susceptibility to P. brassicae, increase host survival rate and seed yields, and transgenic plants enhanced in chitin-triggered reactive oxygen species burst, MAPK activation and expression of immune-related genes. PbChia1 transgenic plants showed resistance to other pathogens, such as biotrophic bacteria Pst DC3000, necrotrophic fungi Sclerotinia sclerotiorum 1980 and Rhizoctonia solani. The findings indicate that chitinases PbChia1 is a candidate gene with potential application for broad spectrum disease resistance in breeding plants to prevent clubroot.

Clubroot caused by the soil-borne protist pathogenPlasmodiophora brassicaeis one of the most devastating diseases of Brassica oil and vegetable crops worldwide. Understanding the pathogen infection strategy is crucial for the development of disease control. However, the molecular mechanism by which this pathogen promotes infection remains largely unknown. Here, we identified aP. brassicae-secreted effector PbE3-2 that impedes plant immunity by ubiquitinating the immune regulator RD21A for degradation. Overexpression ofPbE3-2inArabidopsis thalianaresulted in higher susceptibility toP. brassicaeand decreases in chitin-triggered reactive oxygen species burst and expression of marker genes in salicylic acid signaling. PbE3-2 interacted with and ubiquitinated RD21Ain vitroandin vivo. Mutant plants deficient inRD21Aexhibited similar susceptibility and compromsied immune responses as inPbE3-2overexpression plants. These results suggest thatP. brassicaepromotes clubroot disease through RD21A degradation mediated by the effector PbE3-2. As PbE3-2 is widely conserved across differentP. brassicaepathotypes, the degradation of RD21A by PbE3-2 might be a prevalent infection strategy in this pathogen.

Fusarium pseudograminearum is a pathogenic fungus causeing crown rot. Only two mycovirus have been reported in F. pseudograminearum thus far. Here, we report a fungal virus (mycovirus), Fusarium pseudograminearum fusarivirus 1 (FpFV1), isolated from the F. pseudograminearum strain ZZ-1. FpFV1 has a single-stranded positive-sense RNA (+ ssRNA) genome of 6622 nucleotides containing four open reading frames (ORFs). ORF1 encodes for a large 1,550 amino acids (aa) polypeptide with a conserved RNA-dependent RNA polymerase (RdRp) and two helicase domains. The ORF2, ORF3 and ORF4 have overlapping regions and encode putative proteins of 154 aa, 53aa and 429aa, respectively. All three ORFs have unknown functions. Based on the genomic structure, homology searches, and phylogenetic analysis, FpFV1 could be a new member of the proposed “Fusariviridae”. This is the first study to report a fusarivirus that infects F. pseudograminearum.

Sclerotinia sclerotiorum ourmiavirus 17 (SsOV17) was isolated from the hypovirulent strain GF3 of Sclerotinia sclerotiorum. The genome of SsOV17 is 2,802 nt in length and contains a single long open reading frame (ORF) flanked by a short structured 5'-untranslated region (5'-UTR) (28 nt) and a long 3'-UTR (788 nt), respectively. The ORF encodes a protein with 663 amino acids and a predicted molecular mass of 75.0 kDa. A BLASTp search indicated that the protein encoded by SsOV17 is closely related to the putative RNA-dependent RNA polymerase (RdRp) of Sclerotinia sclerotiorum ourmiavirus 13 (71% identity). A multiple sequence alignment indicated that eight conserved amino acid motifs were present in the RdRp conserved region of SsOV17. Phylogenetic analysis demonstrated that SsOV17 clustered with members of the genus Botoulivirus.

Fusarium graminearum is an important worldwide pathogen that causes Fusarium head blight in wheat, barley, maize and other grains. LncRNAs play important roles in many biological processes, but little is known about their functions and mechanisms in filamentous fungi. Here, we report that a natural antisense RNA, GzmetE-AS, is transcribed from the opposite strand of GzmetE. GzmetE encodes a homoserine O-acetyltransferase, which is important for sexual development and plant infection. The expression of GzmetE-AS was increased significantly during the conidiation stage, while GzmetE was upregulated in the late stage of sexual reproduction. Overexpression of GzmetE-AS inhibited the transcription of GzmetE. In contrast, the expression of GzmetE was significantly increased in GzmetE-AS transcription termination strain GzmetE-AS-T. Furthermore, GzmetE-AS-T produced more perithecia and facilitated the ascospore discharge, resembling the phenotype of GzmetE overexpressing strains. However, overexpression of GzmetE-AS in ∆dcl1/2 strain cannot inhibit the expression of GzmetE, and the GzmetE nat-siRNA is also significantly reduced in ∆dcl1/2 mutant. Taken together, we have identified a novel antisense lncRNA GzmetE-AS, which is involved in asexual and sexual reproduction by regulating its antisense gene GzmetE through RNAi pathway. Our findings reveal that the lncRNA plays critical roles in the development of F. graminearum.

Pyrimethanil is an anilinopyrimidine (AP) fungicide that is highly effective in controlling green mold caused by Penicillium digitatum but has not yet been registered in China to control postharvest diseases of citrus. In this study, baseline sensitivity of P. digitatum to pyrimethanil was established based on the effective concentrations for 50% inhibition (EC50) values of 127 isolates collected from five major citrus-growing regions of China. The distribution of these EC50 values was unimodal but with a long right tail. The mean ± SD EC50 value was 0.137 ± 0.046 μg/ml, and the minimum and maximum were 0.073 and 0.436 μg/ml, respectively. Pyrimethanil in potato dextrose agar (PDA) at 0.20 μg/ml decreased methionine production in the mycelia by 21.6% and reduced the activity of cell wall-degrading enzymes cellulase and pectinase by 9.1 and 32.8%, respectively. Twelve pyrimethanil-resistant mutants were obtained by consecutive subculturing of 12 arbitrarily selected sensitive isolates on pyrimethanil-amended PDA for four generations, and the resistance factors ranged from 69 to 3,421. There was no cross-resistance between pyrimethanil and prochloraz (r = 0.377, P = 0.123). Compared with their parental isolates, pyrimethanil-resistant mutants had reduced pathogenicity to citrus fruit but higher tolerance to hydrogen peroxide. No differences were detected in tolerance to NaCl, CaCl2, Congo red, or sodium dodecyl sulfate. The exogenous addition of methionine into PDA partially alleviated pyrimethanil toxicity to the sensitive isolates but had no significant effect on toxicity to the resistant mutants. Sequencing of cystathionine γ-synthase encoding genes CGS1 and CGS2, the potential target genes for pyrimethanil, showed that there was no nucleotide mutation in the coding region of CGS of the pyrimethanil-resistant mutants. However, the relative expression of CGS1 and CGS2 of the pyrimethanil-resistant mutants was reduced by 42.5 and 57.4%, respectively. These results have important implications for applications of pyrimethanil to control P. digitatum and for understanding the modes of action and resistance mechanisms of pyrimethanil.

In this paper, we propose a Multi-View Stereo (MVS) network which can perform efficient high-resolution depth estimation with low memory consumption. Classical learning-based MVS approaches typically construct 3D cost volumes to regress depth information, making the output resolution rather limited as the memory consumption grows cubically with the input resolution. Although recent approaches have made significant progress in scalability by introducing the coarse-to-fine fashion or sequential cost map regularization, the memory consumption still grows quadratically with input resolution and is not friendly for commodity GPU. Observing that the surfaces of most objects in real world are locally smooth, we assume that most of the depth hypotheses upsampled from a well-estimated depth map are accurate. Based on the assumption, we propose a pyramid MVS network based on the adaptive depth estimation, which gradually refines and upsamples the depth map to the desired resolution. Instead of estimating depth hypotheses for all pixels in the depth map, our method only performs prediction at adaptively selected locations, alleviating excessive computation on well-estimated positions. To estimate depth hypotheses for sparse selected locations, we propose the lightweight pixelwise depth estimation network, which can estimate depth value for each selected location independently. Experiments demonstrate that our method can generate results comparable with the state-of-the-art learning-based methods while reconstructing more geometric details and consuming less GPU memory.

The progressive loss of renal function and accumulation of collagen leads to CKD. Human BM-MSCs are considered as an ideal therapeutic strategy for renal regeneration in the CKD. Polysaccharides extracted from Poria cocos, an edible medicinal mushroom, have been in use in the traditional Chinese herbal medicine as they exhibit antidiabetic, antioxidative, antitumor, and other pharmacological effects. Whether the polysaccharides of P. cocos could ameliorate the CKD via induction of BM-MSC differentiation remains to be explored. The data presented here show that the polysaccharides of P. cocos not only induced BM-MSC proliferation and differentiation, but also reduced the levels of proinflammatory cytokines and improved renal morphology.

Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.

Background Plants maintain the steady-state balance of the mutually beneficial symbiosis relationship with their endophytic fungi through secondary metabolites. Meanwhile endophytic fungi can serve as biological inducers to promote the biosynthesis and accumulation of valuable secondary metabolites in host plants through a variety of ways. The composition and structure of endophytic fungal community are affected by many factors, including tissues, seasons and so on. In this work, we studied the community diversity, temporal and spatial pattern of endophytic fungi detected from the roots, stems and leaves of Huperzia serrata in different seasons. The correlation between endophytic fungi and huperzine A (HupA) content in plants was analyzed. Results A total of 7005 operational taxonomic units were detected, and all strains were identified as 14 phyla, 54 classes, 140 orders, 351 families and 742 genera. Alpha diversity analysis showed that the diversity of endophytic fungi in stem and leaf was higher than that in root, and the diversity in summer (August) was lower than that in other months. NMDS analysis showed that the endophytic fungal communities of leaves, stems and roots were significantly different, and the root and leaf communities were also different between four seasons. Through correlation analysis, it was found that 33 genera of the endophytic fungi of H. serrata showed a significant positive correlation with the content of HupA (p Strelitziana, Devriesia, Articulospora, Derxomyces, Cyphellophora, Trechispora, Kurtzmanomyces, Capnobotryella, Erythrobasidium, Camptophora, Stagonospora, Lachnum, Golubevia) showed a highly significant positive correlation with the content of HupA (p Conclusions This report is the first time to analyze the diversity of endophytic fungi in tissues of H. serrata in different seasons, which proves that there is variability in different tissues and seasonal distribution patterns. These findings provide references to the study of endophytic fungi of H. serrata.

Clubroot, a soil-infective disease caused by

The demethylation inhibitor (DMI) fungicide prochloraz has been widely used in China to control citrus green mold, which is caused by Penicillium digitatum. The 50% effective concentration (EC50) values of prochloraz for 129 isolates of P. digitatum collected in 2017 from citrus groves of four provinces of China ranged from 0.0032 to 0.4582 mg/liter. Analysis of the distribution of natural logarithms of EC50 values indicated that 111 isolates with EC50 values lower than 0.05 mg/liter could be considered sensitive to prochloraz. Relative baseline sensitivity was established based on the 111 sensitive isolates, and the mean EC50 value was 0.0090 ± 0.0054 mg/liter (SD). Prochloraz at 60, 100, and 140 mg/liter provided preventive efficacies of 67.8, 93.0, and 96.4%, respectively. Prochloraz at 0.005 and 0.01 mg/liter disrupted cell membrane integrity of conidia but reduced cell membrane permeability of mycelia. Prochloraz at 0.01 mg/liter reduced ergosterol content in mycelia by 41.8%. Two prochloraz-resistant isolates with EC50 values of 3.97 and 5.68 mg/liter were attained by consecutive subculturing on prochloraz-amended PDA. Studies on the expression levels of three potential target genes, CYP51A, CYP51B, and CYP51C, demonstrated that whether in the absence or presence of prochloraz, only CYP51B in the resistant isolates was overexpressed at least 10-fold higher than that of the sensitive ones. Sequencing of the three genes showed that only CYP51B in the resistant isolates had a 199-bp insertion in the promoter region. In addition, only CYP51B displayed point mutations of G405S, G389C, and Y390S in the coding regions in the resistant isolates. These results were important for understanding the resistance mechanisms of P. digitatum to prochloraz.

In the traditional Chinese medicine, polysaccharide of Hippophae rhamnoides (also known as sea buckthorn) has been widely used for the treatment of liver injuries or cardiovascular problems. The effect of the polysaccharide of H. rhamnoides on kidney injury in rats with severe acute pancreatitis induced by biliopancreatic duct injection with sodium taurocholate was examined. The rats with severe acute pancreatitis showed series of degenerative changes in pancreas and kidney including inflammatory cell infiltration, edema, and necrosis that were diminished following treatment with the polysaccharide of Hippophae rhamnoides. Furthermore, sodium taurocholate injection also aggravated renal function with enhanced levels of proinflammatory cytokines, blood urea nitrogen, serum creatinine, and serum levels of amylase and lipase that were ameliorated by the polysaccharide. There was an upregulation of cleaved caspase-3 and Bax, as well as downregulation of Bcl-2, in the rats model with SAP that diminished following polysaccharide treatment. Lastly, there was an activation of MAPK/NF-κB pathway in the rats exhibiting severe acute pancreatitis that was repressed by the polysaccharide of Hippophae rhamnoides.

Mycoviruses are viruses that infect fungi, and hypovirulence-associated mycoviruses have the potential to control fungal diseases. However, it is unclear how mycovirus-mediated hypovirulent strains live and survive in the field, and no mycovirus has been applied for field crop protection. In this study, we found that a previously identified small DNA mycovirus (SsHADV-1) can convert its host, Sclerotinia sclerotiorum, from a typical necrotrophic pathogen to a beneficial endophytic fungus. SsHADV-1 downregulates the expression of key pathogenicity factor genes in S. sclerotiorum during infection. When growing in rapeseed, the SsHADV-1-infected strain DT-8 significantly regulates the expression of rapeseed genes involved in defense, hormone signaling, and circadian rhythm pathways. As a result, plant growth is promoted and disease resistance is enhanced. Field experiments showed that spraying DT-8 at the early flowering stage can reduce the disease severity of rapeseed stem rot by 67.6% and improve yield by 14.9%. Moreover, we discovered that SsHADV-1 could also infect other S. sclerotiorum strains on DT-8-inoculated plants and that DT-8 could be recovered from dead plants. These findings suggest that the mycoviruses may have the ability to shape the origin of endophytism. Our discoveries suggest that mycoviruses may influence the origin of endophytism and may also offer a novel strategy for disease control in which mycovirus-infected strains are used to improve crop health and release mycoviruses into the field.

This paper proposes a novel approach for robust plane matching and real-time RGB-D fusion based on the representation of plane parameter space. In contrast to previous planar-based SLAM algorithms estimating correspondences for each plane-pair independently, our method instead explores the holistic topology of all relevant planes. We note that by adopting the low-dimensionality parameter space representation, the plane matching can be intuitively reformulated and solved as a point cloud registration problem. Besides estimating the plane correspondences, we contribute an efficient optimization framework, which employs both frame-to-frame and frame-to-model planar consistency constraints. We propose a global plane map to dynamically represent the reconstructed scene and alleviate accumulation errors that exist in camera pose tracking. We validate the proposed algorithm on standard benchmark datasets and additional challenging real-world environments. The experimental results demonstrate its outperformance to current state-of-the-art methods in tracking robustness and reconstruction fidelity.

Sentence modeling is a critical issue for the feature generation of some natural language processing (NLP) tasks. Recently, most works generated the sentence representation by sentence modeling based on Convolutional Neural Network (CNN), Long Short-Term Memory network (LSTM) and some attention mechanisms. However, these models have two limitations: (1) they only present sentences for one individual task by fine-tuning network parameters, and (2) sentence modeling only considers the concatenation of words and ignores the function of phrases. In this paper, we propose a Cascading Gated Self-attention and Phrase-attention Network (CGSPN) that generates the sentence embedding by considering contextual words and key phrases in a sentence. Specifically, we first present a word-interaction gating self-attention mechanism to identify some important words and build the relationship between words. Then, we cascade a phrase-attention structure by abstracting the semantic of phrases to generate the sentence representation. Experiments on different NLP tasks show that the proposed CGSPN model achieves the highest accuracy among most sentence encoding methods. It improves the latest best result by 1.76% on the Stanford Sentiment Treebank (SST), and shows the best test accuracy on different sentence classification data sets. In the Natural Language Inference (NLI) task, the performance of CGSPN without phrase-attention is better than CGSPN model itself and it obtains competitive performance against state-of-the-art baselines, which show the different applicability of the proposed model. In other NLP tasks, we also compare our model with popular methods to explore our direction.

Mycoviruses are ubiquitous in pathogenic fungi including

Rhabdoviruses are ubiquitous and diverse viruses that propagate owing to bidirectional interactions with their vertebrate, arthropod, and plant hosts, and some of them could pose global health or agricultural threats. However, rhabdoviruses have rarely been reported in fungi. Here, two newly identified fungal rhabdoviruses, Rhizoctonia solani rhabdovirus 1 (RsRhV1) and RsRhV2, were discovered and molecularly characterized from the phytopathogenic fungus Rhizoctonia solani. The genomic organizations of RsRhV1 and RsRhV2 are 11,716 and 11,496 nucleotides (nt) in length, respectively, and consist of five open reading frames (ORFs) (ORFs I to V). ORF I, ORF IV, and ORF V encode the viral nucleocapsid (N), glycoprotein (G), and RNA polymerase (L), respectively. The putative protein encoded by ORF III has a lower level of identity with the matrix protein of rhabdoviruses. ORF II encodes a hypothetical protein with unknown function. Phylogenetic trees based on multiple alignments of N, L, and G proteins revealed that RsRhV1 and RsRhV2 are new members of the family Rhabdoviridae, but they form an independent evolutionary branch significantly distinct from other known nonfungal rhabdoviruses, suggesting that they represent a novel viral evolutionary lineage within Rhabdoviridae. Compared to strains lacking rhabdoviruses, strains harboring RsRhV2 and RsRhV1 showed hypervirulence, suggesting that RsRhV1 and RsRhV2 might be associated with the virulence of R. solani. Taken together, this study enriches our understanding of the diversity and host range of rhabdoviruses. IMPORTANCE Mycoviruses have been attracting an increasing amount of attention due to their impact on important medical, agricultural, and industrial fungi. Rhabdoviruses are prevalent across a wide spectrum of hosts, from plants to invertebrates and vertebrates. This study molecularly characterized two novel rhabdoviruses from four Rhizoctonia solani strains, based on their genomic structures, transcription strategy, phylogenetic relationships, and biological impact on their host. Our study makes a significant contribution to the literature because it not only enriches the mycovirus database but also expands the known host range of rhabdoviruses. It also offers insight into the evolutionary linkage between animal viruses and mycoviruses and the transmission of viruses from one host to another. Our study will also help expand the contemporary knowledge of the classification of rhabdoviruses, as well as providing a new model to study rhabdovirus-host interactions, which will benefit the agriculture and medical areas of human welfare.

Endornaviruses are capsidless linear (+) ssRNA viruses in the family

Integrating dissolving microneedles (DMNs) and nanocarriers (NC) holds great potential in transdermal drug delivery because it can simultaneously overcome the stratum corneum barrier and achieve efficient and controlled drug delivery. However, different skin sites with different thicknesses and compositions can affect the transdermal diffusion of NC-loaded DMNs. There are few reports on the biological fate (especially transdermal diffusion) of NC-loaded DMNs, and inaccurate bioimaging information of intact NC limits the accurate understanding of the in vivo fate of NC-loaded DMNs. The aggregation-caused quenching (ACQ) probes P4 emitted intense fluorescence signals in intact NC while quenched after the degradation of NC, had been demonstrated the feasibility of label intact NC. In this study, P4 was loaded in solid lipid nanoparticles (SLNs), and further encapsulated into DMNs, to track the transdermal diffusion of SLNs delivered at different skin sites. The results showed that SLNs had excellent stability after being loaded into DMNs with no significant changes in morphology and fluorescence properties. The in vivo live and ex vivo imaging showed that the transdermal diffusion rate of NC-loaded DMNs was positively correlated with skin thickness, with the order ear > abdomen > back. In conclusion, this study confirmed the site-dependency of transdermal diffusion in NC-loaded DMNs.

A novel positive single-stranded RNA virus, Sclerotinia sclerotiorum hypovirus 9 (SsHV9), was identified in the plant-pathogenic Sclerotinia sclerotiorum strain GB375, which was associated with a garden bean plant in the United States. The complete genome of SsHV9 is 14,067 nucleotides in length, excluding the poly(A) tail. It has a single large open reading frame encoding a putative polyprotein (4,196 amino acids), which is predicted to contain a papain-like protease, a protein of unknown function, an RNA-dependent RNA polymerase, and an RNA helicase. Phylogenetic analysis based on a multiple alignment of amino acid sequences of polyproteins that suggested SsHV9 belongs to the proposed genus "Alphahypovirus" in the family Hypoviridae.

A novel mycovirus named Fusarium oxysporum alternavirus 1(FoAV1) was identified as infecting Fusarium oxysporum strain BH19, which was isolated from a fusarium wilt diseased stem of Lilium brownii. The genome of FoAV1 contains four double-stranded RNA (dsRNA) segments (dsRNA1, dsRNA 2, dsRNA 3 and dsRNA 4, with lengths of 3.3, 2.6, 2.3 and 1.8 kbp, respectively). Additionally, dsRNA1 encodes RNA-dependent RNA polymerase (RdRp), and dsRNA2- dsRNA3- and dsRNA4-encoded hypothetical proteins (ORF2, ORF3 and ORF4), respectively. A homology BLAST search, along with multiple alignments based on RdRp, ORF2 and ORF3 sequences, identified FoAV1 as a novel member of the proposed family “Alternaviridae”. Evolutionary relation analyses indicated that FoAV1 may be related to alternaviruses, thus dividing the family “Alternaviridae” members into four clades. In addition, we determined that dsRNA4 was dispensable for replication and may be a satellite-like RNA of FoAV1—and could perhaps play a role in the evolution of alternaviruses. Our results provided evidence for potential genera establishment within the proposed family “Alternaviridae”. Additionally, FoAV1 exhibited biological control of Fusarium wilt. Our results also laid the foundations for the further study of mycoviruses within the family “Alternaviridae”, and provide a potential agent for the biocontrol of diseases caused by F. oxysporum.

Sentiment analysis aimed to automate the task of discriminating the sentiment tendency of a textual review, which expresses a simple sentiment as positive, negative, or neutral. In general, the basic sentiment analysis solution used for feature extraction is the word embedding technique, which only focuses on the contextual or global semantic information and ignores the sentiment polarity of text. Thus, the word embedding technique leads to biased analysis results, especially for some words that have the same semantic context but an opposite sentiment. In this paper, we propose an integrated sentiment embedding method to combine context and sentiment information using a dual-task learning algorithm to perform sentiment analysis. First, we propose three sentiment language models by encoding the sentiment information of texts into word embedding based on three existing semantic models, namely, continuous bag-of-words, prediction, and log-bilinear. Next, based on semantic language models and the proposed sentiment language models, we propose a dual-task learning algorithm to generate hybrid word embedding named integrated sentiment embedding, in which the joint learning method and parallel learning method are applied to jointly process tasks. Experiments on sentence-level and document-level sentiment classification tasks demonstrate that the proposed integrated sentiment embedding has better classification performances compared with basic word embedding methods.

Huperzia serrata ( H. serrata ) produces various types of effective lycopodium alkaloids, especially Huperzine A (HupA), which is a promising drug for the treatment of Alzheimer's disease. Numerous studies focused on the chemistry, bioactivities, toxicology, and clinical trials of HupA; however, the public genomic and transcriptomic resources are very limited for H. serrata research, especially for the selection of optimum reference genes. Based on the full‐length transcriptome datasets and previous studies, 10 traditional and three new candidate reference genes were selected in different tissue of H. serrata . Then, two optimal reference genes GAPDHB and HisH2A were confirmed by four analysis methods. In order to further verify the accuracy of the two reference genes, they were used to analyze the expression patterns of four HupA‐biosynthetic genes (lysine decarboxylas, RS‐norcoclaurine 6‐O‐methyltransferase, cytochrome P45072A1, and copper amine oxidase). The data suggested that the expression pattern of HupA‐biosynthetic genes was consistent with them in transcriptome sequencing in different tissue of H. serrata . This study identified that GAPDHB and HisH2A provides the reliable normalization for analyzing the HupA biosynthetic gene expression in different tissues of H. serrata on the transcriptional level.

Background Huperzia serrata (H. serrata) produces various types of effectively lycopodium alkaloids, especially Huperzine A (HupA), which is a promising drug for the treatment of Alzheimer’s disease. Numerous studies focused on the chemistry, bioactivities, toxicology, and clinical trials of HupA, however, the public genomic and transcriptomic resources are very limited for H. serrata research, especially for the selection of optimum reference genes. Results Based on the full-length transcriptome datasets and previous studies, thirteen candidate reference genes were selected in different tissue of H. serrata. Then, two optimal reference genes GAPDHB and HisH2A were confirmed by various analysis softwares. In order to further verify the accuracy of the two reference genes, they were used to analyze the expression patterns of four HupA-biosynthetic related genes (lysine decarboxylas, RS-norcoclaurine 6-O-methyltransferase, cytochrome P45072A1 and copper amine oxidase). The data suggested that the expression trends of HupA-biosynthetic related genes were consistent with them in transcriptome sequencing in different tissue of H. serrata. Conclusions This study screened the best reference genes GAPDHB and HisH2A in different tissues of H. serrata, which provides suitable normalization for analyzing the expression of HupA-biosynthetic gene in transcriptional level in H. serrata.

The infection by a single-stranded DNA virus, Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), causes hypovirulence, a reduced growth rate, and other colony morphological changes in its host Sclerotinia sclerotiorum strain DT-8. However, the mechanisms of the decline are still unclear. Using digital RNA sequencing, a transcriptome analysis was conducted to elucidate the phenotype-related genes with expression changes in response to SsHADV-1 infection. A total of 3110 S. sclerotiorum differentially expressed genes (DEGs) were detected during SsHADV-1 infection, 1741 of which were up-regulated, and 1369 were down-regulated. The identified DEGs were involved in several important pathways. DNA replication, DNA damage response, carbohydrate and lipid metabolism, ribosomal assembly, and translation were the affected categories in S. sclerotiorum upon SsHADV-1 infection. Moreover, the infection of SsHADV-1 also suppressed the expression of antiviral RNA silencing and virulence factor genes. These results provide further detailed insights into the effects of SsHADV-1 infection on the whole genome transcription in S. sclerotiorum.

Rice sheath blight caused by Rhizoctonia solani is the major disease of rice that seriously threatens food security worldwide. Efficient and eco-friendly biological approaches are urgently needed since no resistant cultivars are available. In this study, fallow and paddy soils were initially subjected to microbiome analyses, and the results showed that Talaromyces spp. were significantly more abundant in the paddy soil, while Trichoderma spp. were more abundant in the fallow soil, suggesting that Talaromyces spp. could live and survive better in the paddy soil. Five isolates, namely TF-04, TF-03, TF-02, TF-01, and TA-02, were isolated from the paddy soil using sclerotia of R. solani as baits and were further evaluated for their activity against rice sheath blight. These isolates efficiently parasitized the hyphae and rotted the sclerotia even at higher water contents in sterilized sand and the soil. Isolate TF-04 significantly promoted rice growth, reduced the severity of rice sheath blight, and increased rice yield under outdoor conditions. Defense related genes were upregulated and enzyme activities were enhanced in rice treated with isolate TF-04. Our research supplies a microbiome guided approach to screen biological control agents, provides Talaromyces isolates to biologically control rice sheath blight. This article is protected by copyright. All rights reserved.

Plants in the Oxytropis genus can live with the endophytic fungi Alternaria sect. Undifilum. Swainsonine, the mycotoxin produced by the endophyte render the host plant toxic and this has been detrimental to grazing livestock in both China and U.S.A. Despite previous efforts, many questions remain to be solved, such as the transmission mode and life cycle of host–endophyte symbiont, the biosynthesis pathway of swainsonine, and in particular the ecological role and evolution of such symbiosis. In this review, we compile the literature to synthesize ideas on the diversity of the symbiosis and propagation of the endophyte. We further compare the previous work from both Alternaria sect. Undifilum and other swainsonine producing fungi to orchestrate a more comprehensive biosynthesis pathway of swainsonine. We also connect swainsonine biosynthesis pathway with that of its precursor, lysine, and link this to a potential role in modulating plant stress response. Based on this we hypothesize that this host–endophyte co-evolution originated from the needs for host plant to adapt for stress. Validation of this hypothesis will depend on future research on endophytic symbiosis in Oxytropis and help in better understanding the roles of plant–endophyte symbiosis in non-Poaceae species.

Clubroot, a soil-infective disease caused by Plasmodiophora brassicae, is a serious disease affecting cruciferous plants around the world. There is no effective control measure to completely remove this pathogen from fields after infection. Here, we screened and identified two strains (Hz36, Trichoderma guizhouense; Hk37, Trichoderma koningiopsis) of Trichoderma from the gall of clubroot in rapeseed fields with biocontrol potential for clubroot. The fermentation broth of Hz36 could significantly inhibit the germination of resting spores of P. brassicae, and promote the seed germination and root growth of rapeseed. The biocontrol efficiency of Hz36 strain on clubroot for rapeseed and Arabidopsis thaliana was 44.29% and 52.18%, respectively. The qPCR results revealed that strain Hz36 treatment could significantly reduce the content of P. brassicae in root cells, and paraffin section analysis revealed that it could delay the development of P. brassicae. Strain Hk37 showed similar effects to strain Hz36, whose biocontrol efficiency of clubroot could reach 57.30% in rapeseed and 68.01% in A. thaliana. These results indicate that strains Hz36 and Hk37 have the potential for the biocontrol of clubroot.

Codon usage bias (CUB) could reflect co-evolutionary changes between viruses and hosts in contrast to plant and animal viruses, and the systematic analysis of codon usage among the mycoviruses that infect plant pathogenic fungi is limited. We performed an extensive analysis of codon usage patterns among 98 characterized RNA mycoviruses from eight phytopathogenic fungi. The GC and GC3s contents of mycoviruses have a wide variation from 29.35% to 64.62% and 24.32% to 97.13%, respectively. Mycoviral CUB is weak, and natural selection plays a major role in the formation of mycoviral codon usage pattern. In this study, we demonstrated that the codon usage of mycoviruses is similar to that of some host genes, especially those involved in RNA biosynthetic process and transcription, suggesting that CUB is a potential evolutionary mechanism that mycoviruses adapt to in their hosts.