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In 2012, the symptoms of dwarf plants, yellowed and curled leaves were observed in tomato, pepper, eggplant, datura, poinsettia, florists cyclamen and anthurium in Kashi, Tulufan and Yili regions of Xinjiang autonomous region in China. The results showed that all of the above seven species of plants could be infected by Tomato yellow leaf curl virus (TYLCV). We obtained the full-length DNA-A genome sequences of the virus isolate that KSCTo4, KSCTo16, KZPTo18 and KYCTo20 from tomato, KSCPe6 and KSCPe7 from pepper, KSCEg1 from eggplant and KSCDa from datura. Each isolate had all of the characteristic features of Begomovirus genome. Virus isolate collected from different hosts had little difference in sequence, and shared the similarity of 99.0% - 99.8% with each other. These isolate shared the similarity of 98.6% - 99.5% with TYLCV isolate SH3, ZJ6, SD2A-7, HNSQ and HBBD reported in China. [ABSTRACT FROM AUTHOR]

In fission yeast (Schizosaccharomyces pombe), pad gene was cloned with 99.3% nucleotide sequence similarity with published pad in GenBank. In pET-5a expression system, the expression product of cloned pad in E. coli showed activity to degrade the double-strand RNA. Harboring the binary vector pBI121, which contains pad gene, Agrobacterium tumefaciens strain LBA4404 was used to transform the wheat immature embryos pre-cultured 7-10 d. After preregeneration, regeneration and selection culture stage, totally 41 G418 resistant plants were obtained, in which 25 lines were proved to integrate with transgene and express transgene normally by PCR, Dot blot, RT-PCR and ELISA detection. Antivirus test carried out on 25 positive lines with high dose of Barley yellow dwarf virus-GPV revealed that 12 lines had resistance to BVDV-GPV in low level, another 12 lines had resistance to BVDV- GPV in middle level, and 1 line showed resistance to BVDV-GPV in high level. However, both low and middle level of resistance plants showed no symptoms when infected by viruses at low dose, which suggested the dose-dependent effect of the resistance mediated by pad to BYDV-GPV. [ABSTRACT FROM AUTHOR]

Apple (Malus domestica) fruits exhibiting bright stripe symptoms were identified in Weihai City, Shandong Province, China. To investigate the virome in the apple samples, the method of high throughput sequencing (HTS) was used to identify the viruses. It was found that the sequence of citrus concave gum-associated virus (CCGaV) was involved in the apple transcriptome dataset. The full-length genome of the CCGaV-Weihai isolate contained two segments, the RNA1 was 6674 nt in size containing a conserved RNA-dependent RNA polymerase (RdRp), and the RNA2 was ambisense, 2706 nt in length, encoding a movement protein (MP) and a coat protein (CP). Sequence alignment and phylogenetic analyses indicated that CCGaV-Weihai was more closely related to CCGaV-H2799 isolated from the apple host in the United States and distantly related to CCGaV-CGW2 from Citrus sinensis in Italy, indicating a possibly geographical and host differentiation of CCGaV isolates. This was the first identification and characterization of CCGaV infecting apples in China. Additionally, a rapid and sensitive reverse transcription recombinase polymerase amplification (RT-RPA) assay technique was established for CCGaV detection in apple plants. The RT-RPA of CCGaV was not affected by other common viruses in apple plants and is about 10-fold more sensitive than the conventional reverse transcription polymerase chain reaction method, which can be used in large-scale testing. [ABSTRACT FROM AUTHOR]

Gene-editing technology, specifically the CRISPR-Cas13a system, has shown promise in breeding plants resistant to RNA viruses. This system targets RNA and, theoretically, can also combat RNA-based viroids. To test this, the CRISPR-Cas13a system was introduced into tomato plants via transient expression and into Nicotiana benthamiana through transgenic methods, using CRISPR RNAs (crRNAs) targeting the conserved regions of both sense and antisense genomes of potato spindle tuber viroid (PSTVd). In tomato plants, the expression of CRISPR-Cas13a and crRNAs substantially reduced PSTVd accumulation and alleviated disease symptoms. In transgenic N. benthamiana plants, the PSTVd levels were lower as compared to wild-type plants. Several effective crRNAs targeting the PSTVd genomic RNA were also identified. These results demonstrate that the CRISPR-Cas13a system can effectively target and combat viroid RNAs, despite their compact structures. [ABSTRACT FROM AUTHOR]

Several members of the genus Ilarvirus infect fruit trees and are distributed worldwide. Prunus necrotic ringspot virus (PNRSV) is one of the most prevalent viruses, causing significant losses. Cucumissativus can be infected by several ilarviruses, leading to obvious symptoms, including PNRSV, which suggests that cucumbers could be good hosts for the study of the pathogenesis of ilarviruses. Real-time quantitative PCR is an optimal choice for studying gene expression because of its simplicity and its fast and high sensitivity, while its accuracy is highly dependent on the stability of the reference genes. In this study, we assessed the stability of eleven reference genes with geNorm, NormFinder, ΔCt method, BestKeeper, and the ranking software, RefFinder. The results indicated that the combined use of EF1α and F-BOX was the most accurate normalization method. In addition, the host genes AGO1, AGO4, and RDR6 were selected to test the reliability of the reference genes. This study provides useful information for gene expression analysis during PNRSV infection and will facilitate gene expression studies associated with ilarvirus infection. [ABSTRACT FROM AUTHOR]

Background: The negative effect of abdominal obesity on cognitive function has been widely reported, especially on memory function, however, it is unclear how the effect is mediated. We aim to investigate the mediating role of hypertension and depressive symptoms.Methods: Data were collected from wave 6 (2012-2013) of the English Longitudinal Study of Ageing (ELSA). Abdominal obesity was defined as a waist circumference (WC) ≥88cm for women and ≥102cm for men. Hypertension was determined on the basis of objective blood pressure measurement and previous physician diagnosis. Depressive symptoms were assessed with the 8-item version of the Center for Epidemiologic Studies (CESD) scale. Memory function was measured with the 10-word immediate and delayed recall tests. Baron and Kenny's causal steps and Karlson/Holm/Breen (KHB) method were used to examine the mediating effect.Results: A total of 7,448 participants aged ≥50 years were included in this study. We found a negative effect of abdominal obesity on memory function (β=-0.047, p=0.031). KHB method identified significant mediating effect of hypertension and depressive symptoms on the relationship between abdominal obesity and memory function, they explained 16.92 and 6.32% of the total effect of abdominal obesity on memory function, respectively.Limitations: This study was limited by its cross-sectional design and possibility of residual confounding.Conclusions: Hypertension and depressive symptoms might be possible pathways linking abdominal obesity and poor memory function, suggesting that collaborative interventions of abdominal obesity, hypertension and depressive symptoms are beneficial in maintaining memory function. [ABSTRACT FROM AUTHOR]

RNA interference, or RNA silencing, is an important defence mechanism against viroid infection in plants. Plants encode multiple DICER‐LIKE (DCL) proteins that are key components of the RNA silencing pathway. However, the roles of different DCLs in defence responses against viroid infection remain unclear. Here, we determined the function of tomato DCL2b (SlDCL2b) in defence responses against potato spindle tuber viroid (PSTVd) infection using SlDCL2b loss‐of‐function tomato mutant plants. Compared with wild‐type plants, mutant plants were more susceptible to PSTVd infection, developing more severe symptoms earlier and accumulating higher levels of PSTVd RNAs. Moreover, we verified the feedback mechanism for the regulation of SlDCL2b expression by miR6026. Functional blocking of tomato miR6026, by expressing its target mimics, can enhance resistance to PSTVd infection in tomato plants. These findings deepen the current understanding of RNAi‐based resistance against viroid infection and provide a potentially new strategy for viroid control. [ABSTRACT FROM AUTHOR]

Peach (Prunus persica L.) is one of the most important and oldest stone fruits grown in China. Even though P. persica is one of the most commonly grown stone fruits in China, little is known about the biodiversity of microfungi associated with peach branch diseases. In the present study, samples were collected from a wide range of peach growing areas in China, and fungal pathogens associated with peach branch diseases were isolated. In total, 85 isolates were obtained and further classified into nine genera and 10 species. Most of the isolates belonged to Botryosphaeriaceae (46), including Botryosphaeria, Diplodia, Neofusicoccum, Phaeobotryon, and Lasiodiplodia species; Ascochyta, Didymella, and Nothophoma species representing Didymellaceae were also identified. Herein, we introduce Ascochyta prunus and Lasiodiplodia pruni as novel species. In addition, we report the first records of Nothophoma pruni, Neofusicoccum occulatum, and Phaeobotryon rhois on peach worldwide, and Didymella glomerata, Nothophoma quercina, and Phaeoacremonium scolyti are the first records from China. This research is the first comprehensive investigation to explore the microfungi associated with peach branch disease in China. Future studies are necessary to understand the pathogenicity and disease epidemiology of these identified species. [ABSTRACT FROM AUTHOR]

Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop‐infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus‐transmitting arthropod vectors, and in‐depth interrogation of plant‐encoded resistance and susceptibility determinants. Notably, various plant virus‐based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China. [ABSTRACT FROM AUTHOR]

Aberrant expression of microRNAs hae been shown to be closely associated with glioblastoma cell proliferation, apoptosis and drug resistance. However, mechanisms underlying the role of mcroRNAs in glioblastoma cell growth and apoptosis are not fully understood. In this study, we report that miR-503 is overexpressed in glioblastoma tissue compared with normal human brain tissue. Mechanistically, miR-503 can be induced by TGF-β1 at the transcriptional level by binding the smad2/3 binding elements in the promoter. Ectopic overexpression of miR-503 promotes cell growth and inhibits apoptosis by targeting PDCD4. In contrast, inhibition of miR-503 reduces cell growth. Furthermore, miR-503 inhibitor augments the growth inhibitory effect of temozolomide in glioblastoma cells. These results establish miR-503 as a promising molecular target for glioblastoma therapy. [ABSTRACT FROM AUTHOR]

Apple necrotic mosaic virus (ApNMV) is associated with apple mosaic disease in China. However, the mechanisms of ApNMV infection, as well as host defence against the virus, are still poorly understood. Mitochondrial ATP synthase plays a fundamental role in the regulation of plant growth and development. However, mitochondrial ATP synthase function in response to virus infection remains to be defined. In the present study, a yeast two-hybrid (Y2H) screening revealed that the apple mitochondrial ATP synthase oligomycin sensitivity-conferring protein (OSCP) subunit (MdATPO) interacts with ApNMV coat protein (CP). It was further verified that overexpression of MdATPO in Nicotiana benthamiana inhibited viral accumulation. In contrast, silencing of NbATPO facilitated viral accumulation, indicating that ATPO plays a defensive role during ApNMV infection. Further investigation demonstrated that ApNMV infection accelerated abscisic acid (ABA) accumulation, and ABA negatively regulated ATPO transcription, which was related to the ability of ABA insensitive 5 (ABI5) to bind to the ABA-responsive elements (ABREs) of the ATPO promoter. Taken together, our results indicated that transcription factor ABI5 negatively regulated ATPO transcription by directly binding to its promoter, leading to the susceptibility of apple and N. benthamiana to ApNMV infection. The current study facilitates a comprehensive understanding of the intricate responses of the host to ApNMV infection. [ABSTRACT FROM AUTHOR]

The complete nucleotide sequence of fig fleck-associated virus from Xinjiang Uygur Autonomous Region of China (FFkaV-CN) was determined. The 6,723-nucleotide-long viral genome, excluding a terminal poly(A) tail, contains three open reading frames (ORFs). Pairwise comparisons showed that FFkaV-CN shares 83% and 92% sequence identity with FFkaV-Italy based on the complete genomic sequence and CP aa sequence, respectively, slightly higher than the species demarcation criterion for the genus Maculavirus. Phylogenetic analysis showed that FFkaV-CN and FFkaV-Italy clustered into one group. These results indicate that FFkaV-CN is a novel strain of FFkaV with a genome organization somewhat different from what was reported for FFkaV-Italy. [ABSTRACT FROM AUTHOR]

Intracranial aneurysms (IAs) are common cerebrovascular diseases with high rates of mortality and disability. With the development of endovascular treatment technologies, the treatment of IAs has gradually turned to endovascular methods. However, because of the complex disease characteristics and technical challenges of IA treatment, surgical clipping still plays an important role. However, no summary has been performed of the research status and future trends in IA clipping. Publications related to IA clipping from 2001 to 2021 were retrieved from the Web of Science Core Collection database. We conducted a bibliometric analysis and visualization study with the help of VOSviewer software and R program. We included 4104 articles from 90 countries. The volume of publications on IA clipping, in general, has increased. The United States, Japan, and China were the countries with the most contributions. The University of California, San Francisco, Mayo Clinic, and the Barrow Neurological Institute are the main research institutions. World Neurosurgery and the Journal of Neurosurgery were the most popular journal and most co-cited journal, respectively. These publications came from 12,506 authors, of whom Lawton, Spetzler, and Hernesniemi had reported the most studies. The reports from the past 21 years on IA clipping can generally be divided into 5 parts: (1) characteristics and technical difficulties of IA clipping; (2) perioperative management and imaging evaluation of IA clipping; (3) risk factors for subarachnoid hemorrhage caused by rupture after IA clipping; (4) outcomes, prognosis, and related clinical trials of IA clipping; and (5) endovascular management for IA clipping. "Occlusion," "experience," "internal carotid artery," "intracranial aneurysms," "management," and "subarachnoid hemorrhage" were the major keywords for future research hotspots. The results from our bibliometric study have clarified the global research status of IA clipping between 2001 and 2021. The United States contributed the most publications and citations, and World Neurosurgery and Journal of Neurosurgery can be considered landmark journals in this field. Studies regarding occlusion, experience, management, and subarachnoid hemorrhage will be the research hotspots related to IA clipping in the future. [ABSTRACT FROM AUTHOR]

The small brown planthopper (SBPH, Laodelphax striatellus) is one of the most destructive insect pests in rice (Oryza sativa), which is the world's major grain crop. The dynamic changes in the rice transcriptome and metabolome in response to planthopper female adult feeding and oviposition have been reported. However, the effects of nymph feeding remain unclear. In this study, we found that pre-infestation with SBPH nymphs increased the susceptibility of rice plants to SBPH infestation. We used a combination of broadly targeted metabolomic and transcriptomic studies to investigate the rice metabolites altered by SBPH feeding. We observed that SBPH feeding induced significant changes in 92 metabolites, including 56 defense-related secondary metabolites (34 flavonoids, 17 alkaloids, and 5 phenolic acids). Notably, there were more downregulated metabolites than upregulated metabolites. Additionally, nymph feeding significantly increased the accumulation of seven phenolamines and three phenolic acids but decreased the levels of most flavonoids. In SBPH-infested groups, 29 differentially accumulated flavonoids were downregulated, and this effect was more pronounced with infestation time. The findings of this study indicate that SBPH nymph feeding suppresses flavonoid biosynthesis in rice, resulting in increased susceptibility to SBPH infestation. [ABSTRACT FROM AUTHOR]

To date, viroids have been found to naturally infect only plants, resulting in substantial losses for some crops. Whether viroids or viroid‐like RNAs naturally infect non‐plant hosts remains unknown. Here the existence of a set of exogenous, single‐stranded circular RNAs, ranging in size from 157 to 450 nucleotides, isolated from the fungus Botryosphaeria dothidea and nominated B. dothidea RNAs (BdcRNAs) is reported. BdcRNAs replicate autonomously in the nucleus via a rolling‐circle mechanism following a symmetric pathway. BdcRNA infection induces symptoms, because BdcRNAs can apparently modulate, to different degrees, specific biological traits (e.g., alter morphology, decrease growth rate, attenuate virulence, and increase or decrease tolerance to osmotic and oxidative stress) of the host fungus. Overall, BdcRNAs have genome characteristics similar to those of viroids and exhibit pathogenic effects on fungal hosts. It is proposed that these novel fungus infecting RNAs should be termed mycoviroids. BdcRNA(s) may be considered additional inhabitants at the frontier of life in terms of genomic complexity, and represent a new class of acellular entities endowed with regulatory functions, and novel epigenomic carriers of biological information. [ABSTRACT FROM AUTHOR]

The viromic profile of Polyscias balfouriana cv. Marginata, a perennial woody and ornamental plant, was determined using ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) sequencing. Five viruses (i.e., polyscias mosaic virus, PoMV; one potential novel rhabdovirus; and three novel viruses of Betaflexiviridae and Closteroviridae) were detected and prevalence-surveyed in Hainan province, China. The genomes of polyscias capillovirus 1 (PCaV-1) and polyscias citrivirus 1 (PCiV-1) of family Betaflexiviridae were completed, and the genomes of polyscias crinivirus 1 (PCrV-1) of Closteroviridae were nearly completed lacking the 5′ and 3′ termini. PCaV-1 shares 68% genome nucleotide (nt) identity and 66% replicase (Rep) amino acid (aa) identity with homologues in apple stem grooving virus (ASGV). PCiV-1 shares 65% genome nt identity and 64% Rep aa identity with homologs in citrus leaf blotch virus (CLBV). Meeting the species demarcation criteria, PCaV-1 and PCiV-1 were considered to be new species in genera Capillovirus and Citrivirus, respectively. PCrV-1 shares high genome nt identity (62%), heat shock protein 70-like protein (HSP70h) and RNA-dependent RNA polymerase (RdRp) aa identity (78–80%) with homologues in tomato chlorosis virus (ToCV). We tentatively consider PCrV-1 to be an unclassified member of the Crinivirus genus. PoMV, PCaV-1, PCiV-1, and PCrV-1 are the prevalent viruses with >73% occurrence in the Xinglong Tropical Botanical Garden, Hainan, China. [ABSTRACT FROM AUTHOR]

In the present study, the genome sequence of a potential novel virus, tentatively named "rose virus C" (RVC), was mined from publically available transcriptomic data from a Rosa chinensis plant. The complete genome sequence of RVC consists of 8,386 nt, excluding a 3′ poly(A) tail, and contains five ORFs. Phylogenetic analysis showed that RVC clustered with members of the genus Carlavirus, family Betaflexiviridae. The replicase gene had 48.8-52.1% nt sequence identity to those of other carlaviruses, while the CP gene had 40.4-45.9% nt sequence identity, which is far below the species demarcation cutoff of 72%. The incidence of RVC in rose plants was low (5.4%). Overall, our data suggest that RVC is a novel atypical virus of the genus Carlavirus. [ABSTRACT FROM AUTHOR]

RNA‐dependent RNA polymerase 1 (RDR1) is essential for plant antiviral defence, but its role in plant defence against viroid infection remains unknown. The present study aimed to identify the function and mechanism of RDR1 in plant resistance to viroid infection. Overexpression of Nicotiana tabacum RDR1 (NtRDR1) delayed the accumulation of potato spindle tuber viroid (PSTVd) genomic RNA and PSTVd‐derived small RNA (sRNA) in Nicotiana benthamiana plants at the early invasion stage, but not in the late stage of infection. Conversely, virus‐induced gene silencing of tomato RDR1 (SlRDR1a) increased the susceptibility to PSTVd infection (increased viroid accumulation). Salicylic acid (SA) pretreatment induced SlRDR1a expression and enhanced the defence against PSTVd infection in tomato plants. Our study demonstrated that RDR1 is involved in SA‐mediated defence and restricts the early systemic invasion by PSTVd in plants. The decreased PSTVd accumulation in N. benthamiana was not caused by efficient accumulation of PSTVd sRNAs. These results deepen our understanding of the mechanism of RDR1 in plant defence responses to viroid attack. [ABSTRACT FROM AUTHOR]

China rose (Rosa chinensis Jacq.) is an important ornamental plant grown widely in China. In May 2019, we sampled and analyzed a China rose plant by high-throughput sequencing using small RNAs. A luteovirus, rose spring dwarf-associated virus (RSDaV), was detected in this plant, and its complete nucleotide sequence of 5816 nucleotides was determined. The China rose isolate of RSDaV contains five major open reading frames (ORFs) and three putative small ORFs, typical of members of the genus Luteovirus. It shares 94.4% nt sequence identity with the Californian (USA) isolate of the virus. Genomic analysis revealed a deletion of a single U at nt position 5295, which introduced a frameshift mutation, and an insertion of nine nucleotides (AUAAAUGAU) at position 5706-5714, which did not change the reading frame. The aa sequence in that portion of the protein was 90.5% identical to that of the Californian isolate. This is the first report on the occurrence of RSDaV infecting rose plants in China. [ABSTRACT FROM AUTHOR]

Prunus necrotic ringspot virus (PNRSV) is a viral pathogen with worldwide distribution, infecting many commercial fruit trees and ornamental plants. So far, the correlation between PNRSV infection and China rose mosaic disease has not been studied. Rose mosaic disease is characterized by severe symptoms, including mosaic, line pattern, and ringspot. Six viruses that were potentially associated with mosaic disease, including PNRSV, were tested in China roses. Only PNRSV was detected in China roses showing mosaic disease, and asymptomatic samples tested negative for this virus. This result was confirmed by small RNA sequencing, but rose leaf rosette-associated virus and rose spring dwarf-associated virus were also identified in both samples with mosaic disease and asymptomatic samples. This implied that PNRSV might be associated with China rose mosaic disease. Full genome sequences of two PNRSV isolates were determined, and the RNA1, 2 and 3 segments were found to be 3,332, 2,594 and 1,951 nucleotides (nt) in length, respectively. The three RNA segments shared 88.7–89.1% nt sequence identity in the 3′UTR, while RNA2 and RNA3 shared 98.2–99.4% identity. The higher variability in RNA1 suggests that it might have been under greater selection pressure. Phylogenetic analysis showed that the two PNRSV isolates clustered in group PV-32. Full-length infectious cDNA clones of PNRSV from China rose were constructed and used to agroinfiltrate cucumber seedlings. The inoculated cucumber leaves showed yellowing, chlorotic spots, necrosis, dwarfing, and decline at 23 to 39 days post-inoculation, demonstrating the virulence of the PNRSV isolate from China rose. These data lay a foundation for determining the molecular mechanism of rose mosaic disease caused by PNRSV. [ABSTRACT FROM AUTHOR]

[Display omitted] • The expression of cytoplasmic PGK1 is decreased but mitochondrial PGK1 level is increased in neurons after oxygen-glucose deprivation (OGD) • Inhibiting the activity of mitochondrial PGK1 alleviates neuronal injury after OGD. • Upregulation of mitochondrial PGK1 by ROS-TBC1D15 signaling promotes neuronal death after OGD. Phosphoglycerate kinase 1 (PGK1) is extensively located in the cytosol and mitochondria. The role of PGK1 in ischemic neuronal injury remains elusive. In the in vitro model of oxygen-glucose deprivation/reoxygenation (OGD/R), we showed that PGK1 expression was increased in cortical neurons. Knockdown of PGK1 led to a reduction of OGD/R-induced neuronal death. The expression of cytosolic PGK1 was reduced, but the levels of mitochondrial PGK1 were increased in OGD/R-insulted neurons. Inhibiting the activity of mitochondrial PGK1 alleviated the neuronal injury after OGD/R insult. We further showed that the protein levels of TBC domain family member 15 (TBC1D15) were decreased in OGD/R-insulted neurons. Knockdown of TBC1D15 led to increased levels of mitochondrial PGK1 after OGD/R insult in cortical neurons. Moreover, increased reactive oxygen species (ROS) resulted in a reduction of TBC1D15 in OGD/R-insulted neurons. These results suggest that the upregulation of mitochondrial PGK1 by ROS-TBC1D15 signaling pathway promotes neuronal death after OGD/R injury. Mitochondrial PGK1 may act as a regulator of neuronal survival and interventions in the PGK1-dependent pathway may be a potential therapeutic strategy. [ABSTRACT FROM AUTHOR]

In the course of a systematic screen of plant transcriptomic data, the sequence of a novel viroid-like RNA was identified in four contigs in a recent Transcriptome Shotgun Assembly (TSA) from lychee in China. Portions of this sequence are closely related to the central conserved region (CCR) and terminal conserved region (TCR) present in members of the genus Apscaviroid , sequences that are important criteria for viroid classification. RT-PCR with two divergent adjacent primers amplified the full 304 nucleotide sequence of this viroid-like RNA which can be folded into the rod-like secondary structure that is a typical feature of viroids in the family Pospiviroidae . Northern-blot hybridization following denaturing PAGE and sequential polyacrylamide gel electrophoresis (sPAGE) revealed the presence of both circular and linear forms of the viroid-like RNA in lychee leaf tissue. Phylogenetic analysis indicates that this RNA groups with known members of the genus Apscaviroid with a maximum pairwise sequence identity of <62%. Field surveys revealed the presence of this viroid-like RNA in most lychee samples collected in China; however, it was not found in the accessions in a germplasm collection of lychees that originated from a wide range of other countries. None of the four herbaceous hosts and one woody host tested were susceptible to infection with the lychee viroid-like RNA via agroinoculation and RNA inoculation. The provisional name lychee viroid-like RNA (LVd-like RNA) is proposed for this tentative new species in the genus Apscaviroid . [ABSTRACT FROM AUTHOR]

The causal agent of apple mosaic disease has been previously thought to be solely caused by apple mosaic virus (ApMV). In this study, we report that a novel ilarvirus is also associated with apple mosaic disease. Next-generation sequencing analysis of an apple tree showing mosaic symptoms revealed that the tree was infected with three apple latent viruses (apple stem pitting virus, apple stem grooving virus, and apple chlorotic leaf spot virus) and a novel ilarvirus (given the name apple necrotic mosaic virus (ApNMV)) that is closely related to Prunus necrotic ringspot virus (PNRSV) and ApMV. The genome of ApNMV consists of RNA1 (3378 nt), RNA2 (2767 nt), and RNA3 (1956 nt). A phylogenetic analysis based on the coat protein amino acid sequences indicated that the novel virus belongs to the same subgroup 3 of the genus Ilarvirus as PNRSV and ApMV. The presence of mosaic leaves, which tend to be unevenly distributed in diseased apple trees, was correlated with the internal distribution of ApNMV. RT-PCR detection of mosaic-diseased apple trees in Japan indicated that ApNMV was detected in apple trees introduced from China, whereas ApMV was detected from cultivated apple trees in domestic orchards. Consistent with these findings, a survey of mosaic-diseased apple trees in major apple-producing provinces in China revealed that the majority of apple trees showing mosaic symptoms in China are infected with ApNMV. [ABSTRACT FROM AUTHOR]

Contigs with sequence homologies to apple chlorotic leaf spot virus (ACLSV) were identified by high-throughput sequencing analysis in three peach samples. Complete genomic sequences of RP19-1 and RP19-2 of the virus consisted of 7,466 and 7,465 nucleotides (nts), respectively, excluding the poly (A) tails. They shared the highest identity with Ta Tao 5, but lower than 70% of sequence similarity with other ACLSV isolates. Furthermore, phylogenetic analysis revealed that these two isolates clustered with Ta Tao 5, which is distinct from other ACLSV isolates. According to the criteria for species demarcation within the genus Trichovirus, these two isolates as well as Ta Tao 5 should be recognized as a new virus species, tentatively named “Peach chlorotic leaf spot virus”. [ABSTRACT FROM AUTHOR]

Sugarcane streak mosaic virus (SCSMV) causes mosaic and streak symptoms on sugarcane and sorghum crops, and has a broad host range. SCSMV is a member of the genus Poacevirus in the family Potyviridae. Ten SCSMV isolates were collected from sugarcane plants showing mosaic and streaking in Southern China from 2009–2011. Sequence-based phylogenetic and population genetic analyses were conducted using four partial genomic sequences covering the full genomes. These analyses were used to estimate the subpopulation differentiation and divergence within the Chinese virus population, and were compared with isolates from India. SCSMV-infected sugarcane plants in the field commonly harbor virus quasispecies (mutant cloud), and often have mixed infections with the same virus isolates. Inter- and intra-lineage recombination sites were identified in the protein 1, helper-component proteinase, coat protein and 3′ non-coding regions of the Chinese isolates. All the Chinese non-recombinant isolates fell into at least nine lineages, and many clustered with Indian isolates. However, estimates of genetic differentiation and gene flow indicated that the SCSMV populations in China and India are genetically independent. Our genetic study of a poacevirus population in South Asia regions indicates the importance of the evolutionary-based design to control viruses. [ABSTRACT FROM AUTHOR]

Replicating circular RNAs are independent plant pathogens known as viroids, or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs. The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consuming. We previously described an approach for homology-independent discovery of replicating circular RNAs by analysing the total small RNA populations from samples of diseased tissues with a computational program known as progressive filtering of overlapping small RNAs (PFOR). However, PFOR written in PERL language is extremely slow and is unable to discover those subviral pathogens that do not trigger in vivo accumulation of extensively overlapping small RNAs. Moreover, PFOR is yet to identify a new viroid capable of initiating independent infection. Here we report the development of PFOR2 that adopted parallel programming in the C++ language and was 3 to 8 times faster than PFOR. A new computational program was further developed and incorporated into PFOR2 to allow the identification of circular RNAs by deep sequencing of long RNAs instead of small RNAs. PFOR2 analysis of the small RNA libraries from grapevine and apple plants led to the discovery of Grapevine latent viroid (GLVd) and Apple hammerhead viroid-like RNA (AHVd-like RNA), respectively. GLVd was proposed as a new species in the genus Apscaviroid, because it contained the typical structural elements found in this group of viroids and initiated independent infection in grapevine seedlings. AHVd-like RNA encoded a biologically active hammerhead ribozyme in both polarities, and was not specifically associated with any of the viruses found in apple plants. We propose that these computational algorithms have the potential to discover novel circular RNAs in plants, invertebrates and vertebrates regardless of whether they replicate and/or induce the in vivo accumulation of small RNAs. [ABSTRACT FROM AUTHOR]

Potato virus M (PVM, genus Carlavirus, family Betaflexviridae) is considered to be one of most economically important pathogens of pepino in China. However, the details and the mechanisms underlying PVM evolution are unknown. In this study, we determined and analyzed 40 TGB 1 gene sequences, 67 TGB 2 and TGB 3 gene sequences, and 88 CP and NABP gene sequences from viruses isolated from 19 samples of pepino ( Solanum muricatum) and one sample of tomato ( S. lycopersicum) collected from different areas of China. Recombination analysis identified only one clear recombinant in the TGB2-TGB3-CP region, but no recombinants were detected for each of the five individual genes. Phylogenetic analysis showed that all PVM isolates could be divided into at least two lineages in trees derived from the TGB 2, CP, and NABP gene sequences, and the lineages seemed to reflect geographical origin. The five PVM genes in this study were found to be under strong negative selection pressure. The PVM isolates examined showed frequent gene flow between the Chinese and European populations, and also within the Chinese population. Clear star phylogenies and the neutral equilibrium model test showed that pepino isolates of PVM appear to be experiencing a new expansion after a recent introduction into China, and these isolates display low levels of genetic diversity. To our knowledge, this study is the first report describing genetic structure, recombination, and gene flow in PVM populations, and it provides strong evolutionary evidence for the virus populations from different geographic regions of China. [ABSTRACT FROM AUTHOR]

In this study, we generated sequences of the apple chlorotic leaf spot virus (ACLSV) coat protein (CP) gene. Genetic variation and phylogenetic analyses were carried out on these sequences along with others reported previously. ACLSV populations clustered into four types: in three of the four types, combinations of three amino acids at positions of 40, 75 and 79 were conserved. The fourth phylogenetic type, newly identified here, was characterized by co-variation of Ser-Tyr-Ser. Statistically significant genetic differentiation and infrequent gene flow were detected among the four types. Two natural recombinants were detected for the first time among ACLSV isolates/genotypes from China. [ABSTRACT FROM AUTHOR]