Coinfection of Cotton Plants with Watermelon Mosaic Virus and a Novel Polerovirus in China.
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ABSTRACT:
SUBMITTER: Yang X
PROVIDER: S-EPMC8618073 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some groups of viruses. However, nothing is known about the vsRNAs produced during infections of members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, we report the characterization of a population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae. RESULTS: Deep sequencing of small RNAs (sRNAs) from leaves of CLRDV-infected cotton plants revealed that the vsRNAs were 21- to 24-nucleotides (nt) long and that their sequences matched the viral genome, with higher frequencies of matches in the 3- region. There were equivalent amounts of sense and antisense vsRNAs, and the 22-nt class of small RNAs was predominant. During infection, cotton Dcl transcripts appeared to be up-regulated, while Dcl2 appeared to be down-regulated. CONCLUSIONS: This is the first report on the profile of sRNAs in a plant infected with a virus from the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAs. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpectedly high accumulation of 22-nt vsRNAs are discussed. CLRDV is the causal agent of Cotton blue disease, which occurs worldwide. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases.
| S-EPMC3189115 | biostudies-literature
Project description:In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some group of viruses. However, nothing is known for members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, the population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae, is characterized.Deep sequencing of small RNAs (sRNAs) from CLRDV-infected cotton leaves was performed. Results showed 21-nt to 24-nt long vsRNAs matching all the viral genome, with a higher frequency of matches in the 3â region. Equivalent amounts of sense and antisense vsRNAs were found, and the 22-nt long small RNA class was the most prominent one. Looking for cotton Dcl transcripts levels during infection, we could observe that Dcl4 seems to be up-regulated, while Dcl2 seems to be down-regulated.This is the first report on the profile of sRNAs coming from a plant infected with a member of the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAsOur results indicate that secondary structures of the viral RNAs are not the main source of the viRNAs observed, as suggested for other viruses. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpected high accumulation of 22-nt viRNAvsRNAs are discussed. CLRDV is the causal agent of worldwide cotton pathology named Cotton blue disease. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases.
2012-07-16 | GSE31062 | GEO
Project description:In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some group of viruses. However, nothing is known for members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, the population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae, is characterized.Deep sequencing of small RNAs (sRNAs) from CLRDV-infected cotton leaves was performed. Results showed 21-nt to 24-nt long vsRNAs matching all the viral genome, with a higher frequency of matches in the 3M-CM-"M-BM-^@M-BM-^Y region. Equivalent amounts of sense and antisense vsRNAs were found, and the 22-nt long small RNA class was the most prominent one. Looking for cotton Dcl transcripts levels during infection, we could observe that Dcl4 seems to be up-regulated, while Dcl2 seems to be down-regulated.This is the first report on the profile of sRNAs coming from a plant infected with a member of the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAsOur results indicate that secondary structures of the viral RNAs are not the main source of the viRNAs observed, as suggested for other viruses. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpected high accumulation of 22-nt viRNAvsRNAs are discussed. CLRDV is the causal agent of worldwide cotton pathology named Cotton blue disease. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases. Total RNA obtained from leaves of the cotton plant 5 days post-infection with Cotton leafrol dawrf virus (CLRDV) compared to not-infected control.
2012-07-16 | E-GEOD-31062 | biostudies-arrayexpress
Project description:With continued expansion of Cucurbita pepo L. cultivation, viral diseases affecting the crop have become more serious in recent years, causing enormous losses in yield and quality. A virus sample was obtained from Wenshui in Shanxi province, China. Double-stranded RNA technology and sequence-independent amplification (SIA) were used to identify the virus that induced C. pepo L. mosaic disease. SIA and sequencing results showed the presence of watermelon mosaic virus (WMV) in diseased C. pepo L. leaves. The complete sequence of WMV from the Shanxi isolate (i.e., WMV-WS) was cloned and analyzed for further characterization. The genomic RNA of WMV-WS is 10,040 nucleotides in length and encodes a putative polyprotein of 3218 amino acids. Phylogenetic analysis indicate that all WMV isolates were divided into four groups and WMV-WS isolate belong to Group 4. Further analysis showed that these WMV isolates were not only to a certain degree related to the host, but also related to geographical origin of isolates. Our results provide information for a better understanding of the genetic diversity of WMV isolates infecting C. pepo L. in Shanxi, China.
| S-EPMC5684996 | biostudies-literature
Project description:The genus Cucurbita comprises many popular vegetable and ornamental plants, including pumpkins, squashes, and gourds, that are highly valued in China as well as in many other countries. During a survey conducted in Zhejiang province, Southeast China in 2016, severe symptoms of viral infection were observed on Cucurbita maxima Duch. ex Lam. Diseased plants showed symptoms such as stunting, mosaicking, Shoe string, blistering, yellowing, leaf deformation, and fruit distortion. Approximately, 50% of Cucurbita crops produced in Jinhua were diseased, causing an estimated yield loss of 35%. In this study, we developed a method using all known virus genomes from the NCBI database as a reference to map small RNAs to develop a diagnostic tool that could be used to diagnose virus diseases of C. maxima. 25 leaf samples from different symptomatic plants and 25 leaf samples from non-symptomatic plants were collected from the experimental field of Jihua National Agricultural Technology Garden for pathogen identification. Small RNAs from each set of three symptomatic and non-symptomatic samples were extracted and sequenced by Illumina sequencing. Twenty-four different viruses were detected in total. However, the majority of the small RNAs were from Zucchini yellow mosaic virus (ZYMV), Watermelon mosaic virus (WMV), and Cucumber mosaic virus (CMV). Mixed infections of these three viruses were diagnosed in leaf samples from diseased plants and confirmed by reverse transcription PCR (RT-PCR) using primers specific to these three viruses. Crude sap extract from symptomatic leaf samples was mechanically inoculated back into healthy C. maxima plants growing under greenhouse conditions. Inoculated plants developed the same disease symptoms as those observed in the diseased plants and a mixed infection of ZYMV, WMV, and CMV was detected again by RT-PCR, thus fulfilling Koch's postulates. The diagnostic method developed in this study involves fewer bioinformatics processes than other diagnostic methods, does not require complex settings for bioinformatics parameters, provides a high level of sensitivity to rapidly diagnose plant samples with symptoms of virus diseases and can be performed cheaply. This method therefore has the potential to be widely applied as a diagnostic tool for viruses that have genome information in the NCBI database.
| S-EPMC6815192 | biostudies-literature
Project description:The occurrence of Watermelon mosaic virus (WMV) in sweet pepper (Capsicum annuum L.) in Kurdistan province, Iran was confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR) and partial characterization of coat protein. To the best of our knowledge, this is the first report of WMV infecting C. annuum, adding a new host to list of more than 170 species infected by this virus.
| S-EPMC4758315 | biostudies-literature
Project description:A novel virus, tentatively named Maize Yellow Mosaic Virus (MaYMV), was identified from the field-grown maize plants showing yellow mosaic symptoms on the leaves collected from the Yunnan Province of China by the deep sequencing of small RNAs. The complete 5642 nucleotide (nt)-long genome of the MaYMV shared the highest nucleotide sequence identity (73%) to Maize Yellow Dwarf Virus-RMV. Sequence comparisons and phylogenetic analyses suggested that MaYMV represents a new member of the genus Polerovirus in the family Luteoviridae. Furthermore, the P0 protein encoded by MaYMV was demonstrated to inhibit both local and systemic RNA silencing by co-infiltration assays using transgenic Nicotiana benthamiana line 16c carrying the GFP reporter gene, which further supported the identification of a new polerovirus. The biologically-active cDNA clone of MaYMV was generated by inserting the full-length cDNA of MaYMV into the binary vector pCB301. RT-PCR and Northern blot analyses showed that this clone was systemically infectious upon agro-inoculation into N. benthamiana. Subsequently, 13 different isolates of MaYMV from field-grown maize plants in different geographical locations of Yunnan and Guizhou provinces of China were sequenced. Analyses of their molecular variation indicate that the 3' half of P3-P5 read-through protein coding region was the most variable, whereas the coat protein- (CP-) and movement protein- (MP-)coding regions were the most conserved.
| S-EPMC4885075 | biostudies-literature
Project description:Watermelon mosaic virus was first reported in 1965 from the Rio Grande Valley, TX. We report here the first complete genome sequence of a watermelon mosaic virus isolate from watermelon collected from the Rio Grande Valley of Texas.
| S-EPMC4841139 | biostudies-literature
Project description:Poleroviruses are positive-sense, single-stranded viruses. In this study, we describe the identification of a novel polerovirus isolated from soybean displaying curled leaves. The complete viral genome sequence was identified using high-throughput sequencing and confirmed using rapid amplification of cDNA ends (RACE), RT-PCR and Sanger sequencing. Its genome organization is typical of the members of genus Polerovirus, containing seven putative open reading frames (ORFs). The full genome is composed of single-stranded RNA of 5822 nucleotides in length, with the highest nucleotide sequence identity (79.07% with 63% coverage) for cowpea polerovirus 2 (CPPV2). Amino acid sequence identities of the protein products between the virus and its relatives are below the threshold determined by the International Committee of Taxonomy of Viruses (ICTV) for species demarcation, and this strongly supports this virus’ status as a novel species, for which the name soybean chlorotic leafroll virus (SbCLRV) is proposed. Recombination analysis identified a recombination event in the ORF5 of the 3’ portion in the genome. Phylogenetic analyses of the genome and encoded protein sequences revealed that the new virus is closely related to phasey bean mild yellows virus, CPPV2 and siratro latent polerovirus. Subsequently, we demonstrated the infectivity of SbCLRV in Nicotiana benthamiana via infectious cDNA clone generation and agroinoculation.
| S-EPMC9322011 | biostudies-literature
Project description:Tobacco mosaic virus (TMV) infects several crops of economic importance (e.g., tomato) and remains as one of the major concerns to the farmers. TMV enters the host cell and produces the capping enzyme RNA polymerase. The viral genome replicates further to produce multiple mRNAs which encodes several proteins, including the coat protein and an RNA-dependent RNA polymerase (RdRp), as well as the movement protein. TMV replicase domain was chosen for the virtual screening studies against small molecules derived from ligand databases such as PubChem and ChemBank. Catalytic sites of the RdRp domain were identified and subjected to docking analysis with screened ligands derived from virtual screening LigandFit. Small molecules that interact with the target molecule at the catalytic domain region amino acids, GDD, were chosen as the best inhibitors for controlling the TMV replicase activity.
| S-EPMC4628775 | biostudies-literature