Size Restriction Is Required for Proper Functioning of a Bipartite Begomovirus AC4 Protein.

Many geminiviruses, including members of the genus , produce a protein known as C4 or AC4. Whereas C4/AC4 typically consists of more than 80 amino acid residues, a few are much shorter. The significance of these shorter C4/AC4 proteins in viral infection and why the virus maintains their abbreviated length is not yet understood.

Transcription start site mapping of geminiviruses using the in vitro cap-snatching of a tenuivirus.

Geminiviruses are a family of single-stranded DNA viruses that cause significant yield losses in crop production worldwide. Transcription start site (TSS) mapping is crucial in understanding the gene expression mechanisms of geminiviruses. However, this often requires costly and laborious experiments.

Bayesian Phylogeographic Inference Suggests Japan as the Center for the Origin and Dissemination of Rice Stripe Virus.

Rice stripe virus (RSV) is one of the most important viral pathogens of rice in East Asia. The origin and dispersal of RSV remain poorly understood, but an emerging hypothesis suggests that: (i) RSV originates from Yunnan, a southwest province of China; and (ii) some places of eastern China have acted as a center for the international dissemination of RSV. This hypothesis, however, has never been tested rigorously.

The Spatial Diffusion of Cherry Leaf Roll Virus Revealed by a Bayesian Phylodynamic Analysis.

Cherry leaf roll virus (CLRV) is an important plant pathogen that causes severe and detrimental effects on cherry and other fruit plants. Despite recent progress in plant pathology, molecular biology, and population genetics of CLRV, the spatiotemporal spread of this virus remains poorly studied. In this study, we employed a Bayesian phylodynamics framework to investigate the spatial diffusion patterns of CLRV by analyzing the coat protein gene sequences of 81 viral isolates collected from five different countries.

The cap-snatching frequency of a plant bunyavirus from nonsense mRNAs is low but is increased by silencing of UPF1 or SMG7.

Bunyaviruses cleave host cellular mRNAs to acquire cap structures for their own mRNAs in a process called cap-snatching. How bunyaviruses interact with cellular mRNA surveillance pathways such as nonsense-mediated decay (NMD) during cap-snatching remains poorly understood, especially in plants. Rice stripe virus (RSV) is a plant bunyavirus threatening rice production in East Asia.

The phylogeographic history of tomato mosaic virus in Eurasia.

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.

C4, the Pathogenic Determinant of , May Suppress Post-transcriptional Gene Silencing by Interacting With BAM1 Protein.

(ToLCGdV) is a begomovirus associated with a Tomato yellow leaf curl disease (TYLCD) epidemic in Guangdong province, China. Being the least conserved protein among geminivirus proteins, the function of C4 during ToLCGdV infection has not been elucidated. In this study, the infectious clones of ToLCGdV and a ToLCGdV mutant (ToLCGdV) with disrupted C4 ORF were constructed.

Four distinct isolates of Helminthosporium victoriae virus 190S identified from Bipolaris maydis.

Helminthosporium victoriae virus 190S (HvV190S) is the type species of the genus Victorivirus under the family Totiviridae. To date, HvV190S has never been found in places outside of the USA and has Helminthosporium victoriae as its only know natural host fungus in the field. Here, we report the identification of 4 double-stranded RNA (dsRNA) viruses from Bipolaris maydis in Hubei province of China.

A convenient in vivo cap donor delivery system to investigate the cap snatching of plant bunyaviruses.

Like their animal-infecting counterparts, plant bunyaviruses use capped RNA leaders cleaved from host cellular mRNAs to prime viral genome transcription in a process called cap-snatching, but in vivo systems to investigate the details of this process are lacking for them. Here, we report that Rice stripe tenuivirus (RSV) and Tomato spotted wilt tospovirus (TSWV) cleave capped RNA leaders from mRNAs transiently expressed by agroinfiltration, which makes it possible to artificially deliver defined cap donors to the two plant bunyaviruses with unprecedented convenience. With this system, some ideas regarding how plant bunyaviruses select and use capped RNA leaders can be tested easily.

The complete genome sequence of a novel cytorhabdovirus identified in strawberry (Fragaria ananassa Duch.).

A cytorhabdovirus, tentatively named "strawberry-associated virus 1" (SaV1), was identified in strawberry (Fragaria ananassa Duch.), and its complete genome sequence was determined. Its negative-sense single-stranded RNA genome is composed of 14,159 nucleotides and contains eight open reading frames (ORFs) in the canonical order 3'-N-P-P3-M-G-P6-P7-L-5.

EasyCodeML: A visual tool for analysis of selection using CodeML.

The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations.

Bayesian phylodynamic analysis reveals the dispersal patterns of tobacco mosaic virus in China.

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.

Europe was a hub for the global spread of potato virus S in the 19th century.

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.

Rapid evolutionary dynamics of pepper mild mottle virus.

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.

Genetic diversity of the families Aeshnidae, Gomphidae and Libellulidae through COI gene from South China.

Adult dragonflies (Anisoptera) were collected from different localities of South China covering eight provinces. Representative sequences were sixty-one, including 16 species, 11 genera and three families (Aeshnidae, Gomphidae and Libellulidae), under cytochrome oxidase subunit I (COI) gene. After alignment of sequences by BioEdit v6, genetic interaction and divergence were computed by MEGA 7 whereas all the indices of genetic diversity were calculated by DnaSP v5 software.

Complete genome sequences of three novel cycloviruses identified in a dragonfly (Odonata: Anisoptera) from China.

Three cycloviruses (genus Cyclovirus, family Circoviridae) were recovered from a dragonfly (Odonata: Anisoptera) captured in Fuzhou, China. The three cycloviruses, named dragonfly associated cyclovirus 9, 10 and 11 (DfCyV-9, -10, -11), respectively, show 56.1-79.

A nation-wide genetic survey revealed a complex population structure of Bemisia tabaci in Pakistan.

The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex distributed worldwide. In Pakistan, B. tabaci poses a serious threat to agriculture production.

Genetic diversity and molecular evolution of based on the coat protein gene sequence.

(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 an value of 0.

Genetic diversity of begomoviruses in Pakistan captured through a vector based survey.

Begomoviruses (Geminiviridea), transmitted by whiteflies, constitute one of the most dangerous groups of plant viruses posing a severe threat to economically important crops in tropical and sub-tropical areas. In this study, whiteflies were collected from various locations all over Pakistan. The begomoviruses carried by these whiteflies were detected by PCR with the degenerative primers pair AV94/Dep3.

Genetic interaction and diversity of the families Libellulidae and Gomphidae through COI gene from China and Pakistan.

A total of 300 dragonflies (Odonata) were collected from six different localities of China and Pakistan. Sixty seven representative samples were selected to sequence their mitochondrial cytochrome oxidase subunit I (COI). An examination of the resultant sequences identified 21 different dragonfly species, belonging to 15 distinct genera, two families, Libellulidae and Gomphidae.

The Cap Snatching of Segmented Negative Sense RNA Viruses as a Tool to Map the Transcription Start Sites of Heterologous Co-infecting Viruses.

Identification of the transcription start sites (TSSs) of a virus is of great importance to understand and dissect the mechanism of viral genome transcription but this often requires costly and laborious experiments. Many segmented negative-sense RNA viruses (sNSVs) cleave capped leader sequences from a large variety of mRNAs and use these cleaved leaders as primers for transcription in a conserved process called cap snatching. The recent developments in high-throughput sequencing have made it possible to determine most, if not all, of the capped RNAs snatched by a sNSV.

Rice Stripe Tenuivirus Has a Greater Tendency To Use the Prime-and-Realign Mechanism in Transcription of Genomic than in Transcription of Antigenomic Template RNAs.

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 (RSV) and (RGSV) and those of their host rice were determined by high-throughput sequencing.

A new putative alphapartitivirus recovered from the powdery mildew fungus Erysiphe palczewskii.

Two double-stranded RNAs (dsRNA) likely representing the genome of a novel alphapartitivirus which we provisionally named Erysiphe palczewskii alphapartitivirus 1 (EpV1) were recovered from the powdery mildew fungus E. palczewskii infecting Sophora japonica in Jingzhou, Hubei province of China. The two dsRNAs, 1955 (dsRNA1) and 1917 (dsRNA2) bp in size, respectively, each contains a single open reading frame (ORF) encoding a 585- and 528-aa protein, respectively.

Rice grassy stunt virus p5 interacts with two protein components of the plant-specific CBL-CIPK Ca signaling network of rice.

Rice grassy stunt virus (RGSV) is a tenuivirus posing a threat to rice production in many South, Southeast, and East Asian countries. To date, no host factor interacting with RGSV has been reported. In this study, we screened a rice cDNA library with the GAL4-based yeast two-hybrid system using RGSV p5 as the bait.