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Tomato mosaic virus (ToMV) is a tobamovirus affecting solanaceous crops worldwide. The process of its emergence, however, is poorly understood. Here, Bayesian phylogenetic framework was employed to reconstruct the phylogeography of ToMV in Eurasia. The results showed that the ToMV in Europe, Middle East and East Asia has been evolving at a rate of 4.05 × 10−4 substitutions/site/year (95% credibility interval 2.43 × 10−4 – 5.62 × 10−4). Their most recent common ancestor (MRCA), most probably first appeared in Europe, was dated to around 1757 Common Era. The first introduction of ToMV into Middle East occurred in 1920s, with Europe as the source, while the first introduction of ToMV into East Asia occurred shortly afterwards, with Middle East as the source. From about 1950 onwards, inter-regional migrations of ToMV between Europe, Middle East and East Asia have been common. Overall, these data provide a glimpse into the phylogeographic history of ToMV in Eurasia.

The complete sequence of ZZ-2, a narcissus yellow stripe virus (NYSV) isolate identified from Chinese narcissus sample in China, was determined. Its entire RNA genomes comprised 9654 nucleotides (nt) in length, excluding the 3′-terminal poly(A) tail and encoded a polyprotein of 3105 amino acids (aa), flanked by 5′ and 3′ untranslated regions (UTR) of 130 and 206 nts, respectively. Sequence analyses indicated that ZZ-2 shared highest 94% nt and 97% aa sequence identities with NYSV NY-CB5 and NY-EH173 isolates at the polyprotein level, whereas only 75% nt and 79% aa identities respectively with the representative of NYSV isolate (NYSV-Zhangzhou), which are less than the threshold values of the proposed species demarcation for the genus Potyvirus. However, ZZ-2 shared more than 81%–97% nt and 83%–99% aa sequence identities with all NYSV isolates in the coat protein, respectively, but less than 80% aa sequences with NLSYV isolates. Phylogenetic analysis revealed that ZZ-2 clustered together with NY-CB5 and NY-EH173. This suggests that ZZ-2, NY-CB5 and NY-EH173 represent a divergent group of NYSV isolates but share specific motifs in the cleavage sites at the junction of P1/HC-Pro and P3/6K1, which are differed from those of NLSYV isolates.

Tobacco ringspot virus (TRSV) is an important plant pathogen that causes severe diseases in tobacco plants. In recent years, this virus has been reported in a number of ornamental plants. However, it has never been reported from Japanese iris, a famous traditional ornamental plant distributed in Asian countries. In this study, the near-complete bipartite genome of a nepovirus (TRSV-Iris) infecting Japanese iris from Taiwan of China was determined. The RNA1 and RNA2 are 7512 and 3899 nucleotides in length, and encodes a polyprotein of 2303 and 1078 amino acids, respectively. Sequence analysis indicates that TRSV-Iris shares more than 80% amino acid sequence identity, the threshold values of the species demarcation for the genus Nepovirus, with known TRSV isolates either in the conserved Pro-Pol or CP regions, respectively. Phylogenetic analysis indicates that TRSV-Iris is a TRSV isolate.

Passionfruit (Passiflora edulis) is widely cultivated in tropical and subtropical regions around the world. Several viruses of the genus Potyvirus pose serious threat to passion fruit production. The origin, dispersal and evolution of these potyviruses, however, are poorly understood. Here, we investigated the genetic structure of telosma mosaic virus (TelMV), a potyvirus that infects passionfruit in East and Southeast Asia, after a survey of its incidence in passionfruit plants of China. The phylogeny inferred from 140 nucleotide sequences of the coat protein (CP) gene of TelMV, including 96 determined in this study, separated this virus into 4 clades. TelMV isolates from passionfruit were placed into Clade 1–3, while those from other plant species into Clade 4. Interestingly, TelMV isolates of passionfruit from Thailand were found in all the three clades of Clade 1–3, but those from China and Vietnam were found exclusively in Clade 1. Nevertheless, TelMV isolates within Clade 1 tended to cluster according to their geographical origin. Geographical populations from Thailand, Taiwan and Hainan islands of China showed significant genetic differences with one another and with those from Guangxi, Fujian, Guangdong, Yunnan and Jiangsu provinces of China. Altogether, these data suggest that several distinct TelMV clades had arisen from the passionfruit of Thailand, but only one of which was dispersed. In expanding its distribution, this clade of TelMV has undergone geography-associated evolution. Further studies on this hypothesis may shed new insights into mechanisms underlying the emergence of potyviral diseases in passionfruit plants.

A potyvirus (isolate PFV-FJ) infecting passion fruit in China was identified by small-RNA sequencing. The complete genome sequence of PFV-FJ was determined to be 9974 nucleotides, excluding the poly(A) tail. PFV-FJ shares 70-72% nucleotide and 69-74% amino acid sequence identity at the polyprotein level with seven reported potyviruses, but 89% nucleotide and 91% amino acid sequence identity with an unreported potyvirus, tentatively named "passionfruit Vietnam potyvirus" (PVNV-DakNong). This suggests that PFV-FJ and PVNV-DakNong should belong to the same potyvirus species and that PFV-FJ is a new member of the genus Potyvirus. This new potyvirus was tentatively named "passion fruit severe mottle-associated virus".

Significance Our article presents the most comprehensive reconstruction of the evolutionary and phylogeographic history of a major plant pathogen of brassica vegetables in Eurasia. Sampling across such a large landmass poses considerable challenges, and our study attempts to describe the spatial and temporal patterns of migration for a plant pathogen on a large scale. Our phylogeographic and molecular clock analyses show that the migration pathways of turnip mosaic potyvirus retrace some of the historical trade arteries of the Silk Road. This study demonstrates how a comprehensive genetic analysis can provide a large-scale view of the epidemiology and human-mediated spread of a plant pathogen across centuries of evolutionary history., Plant pathogens have agricultural impacts on a global scale and resolving the timing and route of their spread can aid crop protection and inform control strategies. However, the evolutionary and phylogeographic history of plant pathogens in Eurasia remains largely unknown because of the difficulties in sampling across such a large landmass. Here, we show that turnip mosaic potyvirus (TuMV), a significant pathogen of brassica crops, spread from west to east across Eurasia from about the 17th century CE. We used a Bayesian phylogenetic approach to analyze 579 whole genome sequences and up to 713 partial sequences of TuMV, including 122 previously unknown genome sequences from isolates that we collected over the past five decades. Our phylogeographic and molecular clock analyses showed that TuMV isolates of the Asian-Brassica/Raphanus (BR) and basal-BR groups and world-Brassica3 (B3) subgroup spread from the center of emergence to the rest of Eurasia in relation to the host plants grown in each country. The migration pathways of TuMV have retraced some of the major historical trade arteries in Eurasia, a network that formed the Silk Road, and the regional variation of the virus is partly characterized by different type patterns of recombinants. Our study presents a complex and detailed picture of the timescale and major transmission routes of an important plant pathogen.

Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the phylodynamics of the virus by analysing 253 nucleotide sequences of the genes encoding the third protein (P3), cylindrical inclusion protein (CI), and the nuclear inclusion protein (NIb). Our Bayesian phylogenetic analyses showed that the mean substitution rates of different regions of the genome ranged from 8.50 × 10−5 to 1.34 × 10−4 substitutions/site/year, whereas the time to the most recent common ancestor of PVY varied with the length of the genomic regions and with the number of viral isolates being analysed. Our phylogeographic analysis showed that the PVY population originated in South America and was introduced into Europe in the 19th century, from where it spread around the globe. The migration pathways of PVY correlate well with the trade routes of potato tubers, suggesting that the global spread of PVY is associated with human activities.

Phytophthora infestans is a widespread destructive plant pathogen that causes economic losses worldwide to potato production. In this study, we sequenced four mitochondrial DNA gene sequences of 101 P. infestans isolates from five potato-growing regions in China to investigate the population structure and dispersal pattern of this pathogen. The concatenated mtDNA sequences in the populations showed high haplotype diversity, but low nucleotide diversity. Although there was a degree of spatial structure, our phylogeographic analyses support frequent gene flow between populations and the direction of gene flow, primarily from north to south, corresponds to the route of seed potato transportation, suggesting a role of human activities in the dispersal of P. infestans in China.

Narcissus (Narcissus spp.) is an important commercial crop and millions of narcissus bulbs are traded across the world annually. Three major viruses, namely, Narcissus yellow stripe virus (NYSV), N...

Potato virus S (PVS) is a major plant pathogen that causes considerable losses in global potato production. Knowledge of the evolutionary history and spatio-temporal dynamics of PVS is vital for developing sustainable management schemes. In this study, we investigated the phylodynamics of the virus by analysing 103 nucleotide sequences of the coat protein gene, sampled between 1985 and 2014. Our Bayesian phylogenetic analyses showed that PVS has been evolving at a rate of 3.32 × 10−4 substitutions/site/year (95% credibility interval 1.33 × 10−4–5.58 × 10−4). We dated the crown group to the year 1325 CE (95% credibility interval 762–1743 CE). Our phylogeographic analyses pointed to viral origins in South America and identified multiple migration pathways between Europe and other regions, suggesting that Europe has been a major hub for PVS transmission. The results of our study have potential implications for developing effective strategies for the control of this pathogen.

Pepper mild mottle virus (PMMoV) is one of the most destructive pathogens of pepper crops and has major impacts on global crop yields. Some aspects of the molecular biology of PMMoV have been studied intensively, but estimates of its evolutionary rate have shown considerable variation. We investigated the phylodynamics of PMMoV by analysing 171 nucleotide sequences of the coat protein gene, sampled between 1980 and 2016. Our Bayesian phylogenetic analyses, using the structured coalescent, dated the crown group to 1949 (95% credibility interval 1935–1962). We reveal that PMMoV has been evolving at a rate of 9.363 × 10−4 substitutions/site/year (95% credibility interval 7.362 × 10−4–1.138 × 10−3). This is similar to evolutionary rates estimated for animal RNA viruses, indicating that PMMoV has been undergoing rapid evolutionary dynamics.

Aims Development of a multiplex TaqMan RT-qPCR assay to simultaneously detect Narcissus yellow stripe virus (NYSV) and Narcissus mosaic virus (NMV), frequently causing mixed narcissus infection. Feasibility verification was confirmed in natural samples. Methods and Results Primers and probes were designed based on the conserved CP gene regions of NYSV or NMV and their suitability for singleplex and multiplex TaqMan RT-qPCR assays as well as for conventional RT-PCR. Conventional RT-PCR, singleplex and multiplex TaqMan RT-qPCR assays proved to be NYSV and NMV specific. P-values and coefficients of variation of TaqMan RT-qPCR assays indicated high reproducibility. Significantly increased sensitivity was achieved compared to conventional RT-PCR. The detection limit of both viruses was 103 copies with superior correlation coefficients and linear standard curve responses between plasmid concentrations and Ct values. NYSV and NMV infection of narcissus leaves, petals and bulbs could successfully be detected via our multiplex RT-qPCR method at 1·25 mg. Conclusion Our multiplex TaqMan RT-qPCR assay provides rapid, specific, sensitive and reliable testing to simultaneously detect NYSV and NMV, supplying useful routine monitoring for different narcissus samples. Significance and Impact of the Study Efficient identification and discrimination of the narcissus viruses provides reliable information for scientists and conventional growers. Furthermore, it enriches the information of NYSV, NMV and other narcissus viruses.

Telosma mosaic virus (TeMV) is an important plant virus causing considerable economic losses to passion fruit (Passiflora edulis) production worldwide, including China. In this study, the complete genome sequence (excluding the poly (A) tail) of two TeMV isolates, Fuzhou and Wuyishan, were determined to be 10,050 and 10,057 nucleotides, respectively. Sequence analysis indicated that Fuzhou and Wuyishan isolates share 78–98% nucleotide and 83–99% amino acid sequence identities with two TeMV isolates of Hanoi and GX, and a proposed new potyvirus, tentatively named PasFru. Phylogenetic analysis indicated that these TeMV isolates and PasFru were clustered into a monophyletic clade with high confidences. This indicated that PasFru and the four TeMV isolates should be considered as one potyvirus species. Two recombination breakpoints were identified within the CI and NIb genes of the Fuzhou isolate, and also within the P1 gene of the Wuyishan isolate. To the best of our knowledge, this is the first report of TeMV recombinants worldwide.

Potato Alternaria leaf blight is one of the economically most important disease in potato production worldwide. A recent study reported a quick method to distinguish main Alternaria pathogens A. tenuissima, A. alternata, and A. solani using partial histone H3 gene sequences. Using this method, our collection of 79 isolates from 8 provinces in China were presumably separated into A. tenussima and A. alternata. But in depth morphological and genetic analysis casted doubt on this identification. Culture morphologies of six presumed A. alternata isolates (PresA_alt) and six presumed A. tenuissima isolates (PresA_ten) were not significantly different. PresA_ten isolates also produced conidia in branched chains which supposed to be A. aternata. Phylogenetic analyses were conducted using internal transcribed spacer region (ITS) and five genes commonly used for species identification including glyceraldehyde-3-phosphate dehydrogenase (GPDH), translation elongation factor 1-alpha (TEF1), β-tubulin, plasma membrane ATPase (ATPase), and calmodulin genes. The results showed that GPDH and TEF1 sequences of PresA_alt and PresA_ten isolates were identical. The 12 isolates did not cluster by presumed species neither by individual or concatenated sequence comparisons. The phylogeny–trait association analysis confirmed that the two group isolates were undistinguishable by those molecular markers. Analysis of histone H3 gene sequences revealed variable intron sequences between PresA_ten and PresA_alt isolates, but the amino acid sequences were identical. Our results indicate that the previously published method to distinguish Alternaria species based on histone H3 gene sequence variation is inaccurate and that the prevalence of A. tenuissima isolates in China was likely overestimated.

Tobacco mosaic virus (TMV) is widespread in China and causes considerable economic losses to tobacco production. The molecular epidemiology of this virus is, however, poorly understood. In this study, we sequenced the genomes of 51 TMV isolates from five tobacco-producing regions in China and investigated the dispersal patterns of this virus. Our phylogenetic analysis showed that TMV might have been introduced to China in the early 1900s, probably first to southwest China. However, TMV then moved to the north of the country, where it expanded. The north became the main seeding region for the subsequent movements of the virus within China. The north-to-south movement of TMV coincides with a shift of major tobacco-producing areas from north to south in this century, suggesting a link between human activities and the dispersal of TMV in China.

The complete genome sequences of three isolates of bamboo mosaic virus (BaMV) from mainland China were determined and compared to those of BaMV isolates from Taiwan. Sequence analysis showed that isolate BaMV-JXYBZ1 from Fuzhou shares 98 % nucleotide sequence identity with BaMV-YTHSL14 from nucleotides 2586 to 6306, and more than 94 % nucleotide sequence identity with BaMV-MUZHUBZ2 in other regions. Recombination and phylogenetic analyses indicate that BaMV-JXYBZ1 is a recombinant with one recombination breakpoint. To our knowledge, this is the first report of a BaMV recombinant worldwide.

Chilli veinal mottle virus (ChiVMV) is an important plant pathogen with a wide host range. The genetic structure of ChiVMV was investigated by analyzing the coat protein (CP) genes of 87 ChiVMV isolates from seven Asian regions. Pairwise F ST values between ChiVMV populations ranged from 0.108 to 0.681, indicating a significant spatial structure for this pathogen. In phylogeny-trait association analysis, the viral isolates from the same region tended to group together, showing a distinct geographic feature. These results suggest that geographic driven adaptation may be an important determinant of the genetic diversity of ChiVMV.

The complete sequence of CF_YL21, a Potato virus Y (PVY) isolate from Solanum tuberosum in China, was determined to be 9718 nucleotides in length, excluding the 3′-terminal poly(A) tail. The viral genome had a single open reading frame of 9186 nucleotides encoding a polyprotein of 3061 amino acids. The polyprotein was predicted to be cleaved into ten functional proteins by three viral proteases. Sequence analyses indicated that CF_YL21 shared 97% nucleotide identity with Wilga5 (PVYN-Wi), and two putative recombination signals were detected in the P1 and HC-Pro/P3 regions. Phylogenetic analyses, Bayesian Tip-association Significance (BaTS) test, and multiplex RT-PCR assay confirmed that the isolate had the similar molecular and genomic structure with PVYN-Wi, a PVY strain formed by recombination between PVYN and PVYO. To our knowledge, this is the first report of the complete sequence structure of PVYN-Wi strain from potato in China.

Ornithogalum mosaic virus(OrMV) has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP) gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have significant subpopulation differentiation with anFSTvalue of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints withdN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the generaOrnithogalum, LachenaliaandDiuritended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation.

Most segmented negative-sense RNA viruses employ a process termed cap snatching, during which they snatch capped RNA leaders from host cellular mRNAs and use the snatched leaders as primers for transcription, leading to the synthesis of viral mRNAs with 5′ heterogeneous sequences (HSs). With traditional methods, only a few HSs can be determined, and identification of their donors is difficult. Here, the mRNA 5′ ends of Rice stripe tenuivirus (RSV) and Rice grassy stunt tenuivirus (RGSV) and those of their host rice were determined by high-throughput sequencing. Millions of tenuiviral HSs were obtained, and a large number of them mapped to the 5′ ends of corresponding host cellular mRNAs. Repeats of the dinucleotide AC, which are complementary to the U 1 G 2 of the tenuiviral template 3′-U 1 G 2 U 3 G 4 UUUCG, were found to be prevalent at the 3′ termini of tenuiviral HSs. Most of these ACs did not match host cellular mRNAs, supporting the idea that tenuiviruses use the prime-and-realign mechanism during cap snatching. We previously reported a greater tendency of RSV than RGSV to use the prime-and-realign mechanism in transcription with leaders cap snatched from a coinfecting reovirus. Besides confirming this observation in natural tenuiviral infections, the data here additionally reveal that RSV has a greater tendency to use this mechanism in transcribing genomic than in transcribing antigenomic templates. The data also suggest that tenuiviruses cap snatch host cellular mRNAs from translation- and photosynthesis-related genes, and capped RNA leaders snatched by tenuiviruses base pair with U 1 /U 3 or G 2 /G 4 of viral templates. These results provide unprecedented insights into the cap-snatching process of tenuiviruses. IMPORTANCE Many segmented negative-sense RNA viruses (segmented NSVs) are medically or agriculturally important pathogens. The cap-snatching process is a promising target for the development of antiviral strategies against this group of viruses. However, many details of this process remain poorly characterized. Tenuiviruses constitute a genus of agriculturally important segmented NSVs, several members of which are major viral pathogens of rice. Here, we for the first time adopted a high-throughput sequencing strategy to determine the 5′ heterogeneous sequences (HSs) of tenuiviruses and mapped them to host cellular mRNAs. Besides providing deep insights into the cap snatching of tenuiviruses, the data obtained provide clear evidence to support several previously proposed models regarding cap snatching. Curiously and importantly, the data here reveal that not only different tenuiviruses but also the same tenuivirus synthesizing different mRNAs use the prime-and-realign mechanism with different tendencies during their cap snatching.

Ornithogalum mosaic virus (OrMV) has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP) gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have a significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with ω-values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from molecular variance of analysis (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. In BaTS analysis, OrMV isolates from the genera Ornithogalum, Lachenalia, Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation. Furthermore, age calculations suggested that the first divergence event of the OrMV isolates analyzed might take place around 1068 BC.

The complete sequence of a narcissus virus isolated from the Netherlands (Narv-NL) was determined to be 8172 nucleotides in length with an open reading frame encoding for 2624 amino acids. Phylogenetic analysis indicates that Narv-NL is clustered with high confidence among representative members from the genus Macluravirus, including artichoke latent virus (ArLV) and Chinese yam necrotic mosaic virus (CYNMV). Sequence analyses indicated Narv-NL shares 67%-69% nucleotide and 51%-68% amino acid sequence identity with ArLV and CYNMV either in the complete ORF or the coat protein (CP) gene, whereas it had 81%-99 % nucleotide and 80%-99 % amino acid sequence identity with the corresponding CP sequences of narcissus latent virus (NLV) isolates, suggesting that Narv-NL is a member of NLV. To our knowledge, this is the first report of the complete sequence of a NLV isolate.

The fermentation and isolation of metabolites produced by an endophytic fungus, which was identified as Phomopsis sp. FJBR-11, based on phylogenetic analysis, led to the identification of six compounds, including dothiorelones A–C, and H, and cytosporones C and U. Among these compounds, cytosporone U exhibited potent inhibitory activity against Tobacco mosaic virus (TMV). Moreover, the crude and a purified exopolysaccharide were proved to possess strong inhibitory effects against the virus infection.

The complete sequence of GF_YL20, a potato virus Y (PVY) isolate from China, encodes a polyprotein of 3,061 amino acids. Sequence analysis indicates that GF_YL20 has a genomic structure different from previously reported PVY strains. It shares 99 % nucleotide sequence identity with PB209 (PVY(N:O)) except in VPg, but more than 97 % nucleotide sequence identity with the VPg of Mont (PVY(N)), PB312 (PVY(NTN)) and HN2 (SYR-I). Phylogenetic analysis indicates that GF_YL20 is a novel N:O recombinant with three recombination breakpoints.

The complete genome sequence of a Laixi isolate of Peanut stripe virus (PStV-Laixi) from China was determined to be 10, 056 nucleotides in length, excluding the 3′-terminal poly (A) tail. The viral genome contains a single long open reading frame of 9669 nucleotides encoding a polyprotein of 3222 amino acids. The polyprotein was predicted to be cleaved into ten functional proteins by three viral proteases. An additional protein, termed ‘PIPO’, is also found in the P3 cistron. The complete genome sequence comparison and phylogenetic analysis indicated that PStV-Laixi was most closely related to three other isolates of PStV (two from USA and one from Taiwan). To our knowledge, this is the first report of the complete sequence of a PStV isolate from China.

The objectives of this study were to understand the sequence variation and the putative protein structure of pipo gene in the Potato virus Y (PVY) collected from Solanum tuberosum. The pipo gene in PVY was cloned using a pair of degenerate primers designed from its conserved region and its sequences were used to re-construct phylogenetic tree in Potyvirus genera by a Bayesian inference method. An expected fragment of 235 bp was amplified in all 20 samples by RT-PCR and the pipo genes in the 20 samples assayed shared more than 92% nucleotide sequence similarity with the published sequences of PVY strains. Among the 20 pipo gene sequences, 13 polymorphic sites were detected, including 4 parsimony informative sites and 9 singleton variable sites. These results indicate that PVY pipo gene is highly conserved but some sequence variations exist. Further analyses suggest that the pipo gene encodes a hydrophilic protein without signal peptide and transmembrane region. The protein has theoretical isoelectric points (pI) ranging from 11.26 to 11.62 and contains three highly conserved regions, especially between aa 10 and 59. The protein is likely located in the mitochondria and has a-helix secondary structure. Bayesian inference of phylogenetic trees reveals that PVY isolates are clustered in the same branch with high posterior probability, while Sunflower chlorotic mottle virus (SoCMoV) and Pepper severe mosaic virus (PepSMV) are closely related, consisting with the classification of Potyvirus genera using other approaches. Our analyses suggest that the pipo gene can be a new marker for phylogenetic analysis of the genera. The results reported in this paper provide useful insights in the genetic variation and the evolution of PVY and can stimulate further research on structure and function of the PIPO protein.

Nucleolar proteins play important roles in plant cytology, growth, and development. Fibrillarin2 is a nucleolar protein ofNicotiana benthamiana(N. benthamiana). Its cDNA was amplified by RT-PCR and inserted into expression vector pEarley101 labeled with yellow fluorescent protein (YFP). The fusion protein was localized in the nucleolus and Cajal body of leaf epidermal cells ofN. benthamiana. TheN. benthamianafibrillarin2 (NbFib2) protein has three functional domains (i.e., glycine and arginine rich domain, RNA-binding domain, andα-helical domain) and a nuclear localization signal (NLS) in C-terminal. The protein 3D structure analysis predicted that NbFib2 is anα/βprotein. In addition, the virus induced gene silencing (VIGS) approach was used to determine the function of NbFib2. Our results showed that symptoms including growth retardation, organ deformation, chlorosis, and necrosis appeared in NbFib2-silencedN. benthamiana.

The genome of a potyvirus (isolate JaVT_FZ) recovered from jasmine (Jasminum sambac L.) showing yellow ringspot symptoms in Fuzhou, China, was sequenced. JaVT_FZ is closely related to seven other potyviruses with completely sequenced genomes, with which it shares 66-70 % nucleotide and 52-56 % amino acid sequence identity. However, the coat protein (CP) gene shares 82-92 % nucleotide and 90-97 % amino acid sequence identity with those of two partially sequenced potyviruses, named jasmine potyvirus T (JaVT-jasmine) and jasmine yellow mosaic potyvirus (JaYMV-India), respectively. This suggests that JaVT_FZ, JaVT-jasmine and JaYMV-India should be regarded as members of a single potyvirus species, for which the name "Jasmine virus T" has priority.

Arabis mosaic virus (ArMV) is a virus with a wide host range. In this study, the genetic diversity of ArMV and the molecular mechanisms underlying its evolution were investigated using the coat protein (CP) sequence. Of the 33 ArMV isolates studied, three were found to be recombinants. The other 30 recombination-free ArMV isolates could be separated into two major lineages with a significant F ST value (0.384) and tended to cluster according to their geographical origin. Different evolutionary constraints were detected for the two linages, pointing to a role of natural selection in the differentiation of ArMV.

Host resistance and synthetic antimicrobials such as fungicides are two of the main approaches used to control plant diseases in conventional agriculture. Although pathogens often evolve to overcome host resistance and antimicrobials, the majority of reports have involved qualitative host – pathogen interactions or antimicrobials targeting a single pathogen protein or metabolic pathway. Studies that consider jointly the evolution of virulence, defined as the degree of damage caused to a host by parasite infection, and antimicrobial resistance are rare. Here we compared virulence and fungicide tolerance in the fungal pathogen Mycosphaerella graminicola sampled from wheat fields across three continents and found a positive correlation between virulence and tolerance to a triazole fungicide. We also found that quantitative host resistance selected for higher pathogen virulence. The possible mechanisms responsible for these observations and their consequences for sustainable disease management are discussed., PLoS ONE, 8 (3), ISSN:1932-6203

The complete genome sequence of a Chinese narcissus isolate of narcissus late season yellows virus from Zhangzhou, China (NLSYV-ZZ), was determined to be 9,651 nucleotides in length, excluding the 3′-terminal poly (A) tail, by amplification and sequencing of virus RNA. The viral genome contains a single long open reading frame of 9,315 nucleotides encoding a polyprotein of 3,105 amino acids. The polyprotein was predicted to be cleaved into ten mature proteins by three viral proteases. Complete genome sequence comparison and phylogenetic analysis indicated that NLSYV-ZZ was most closely related to narcissus yellow stripe virus (NYSV), which was also isolated from narcissus. These viruses shared 69.9 % identity in their complete nucleotide sequences and 77.0 % identity in their polyprotein amino acid sequences.

To obtain the P8 protein of Rice gall dwarf virus (RGDV) with biological activity, its outer coat protein gene S8 was expressed in Spodoptera frugiperda (Sf9) insect cells using the baculovirus expression system. The S8 gene was subcloned into the pFastBac™1 vector, to produce the recombinant baculovirus transfer vector pFB-S8. After transformation, pFB-S8 was introduced into the competent cells (E. coli DH10Bac) containing a shuttle vector, Bacmid, generating the recombinant bacmid rbpFB-S8. After being infected by recombinant baculovirus rvpFB-S8 at different multiplicities of infection, Sf9 cells were collected at different times and analyzed by SDS-PAGE, Western blotting and immunofluorescence microscopy. The expression level of the P8 protein was highest between 48–72 h after transfection of Sf9 cells. Immunofluorescence microscopy showed that P8 protein of RGDV formed punctate structures in the cytoplasm of Sf9 cells.

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.