Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations
Ontology highlight
ABSTRACT:
ORGANISM(S): Cucumis melo
PROVIDER: GSE74840 | GEO | 2016/06/07
SECONDARY ACCESSION(S): PRJNA301626
REPOSITORIES: GEO
Similar Datasets
Project description:BackgroundViruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumis melo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon have been extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes for breeding new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3'-untranslated regions.ResultsMelon plant tissues from the cultivars Tendral or Planters Jumbo were locally infected with either MNSV-Mα5 or MNSV-Mα5/3'264 and analysed in a time-course experiment. Principal component and hierarchical clustering analyses identified treatment (healthy vs. infected) and sampling date (3 vs. 5 dpi) as the primary and secondary variables, respectively. Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3'264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3'264 specifically deregulated 2925 and 1618 genes in Tendral and Planters Jumbo, respectively. The GO categories that were significantly affected were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed for the identification of two groups that were specifically deregulated by MNSV-Mα5/3'264 with respect to MNSV-Mα5 in Tendral, and one group that was antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3'264 infection. Genes in these three groups belonged to diverse functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene that was deregulated by all three viruses, with infection dynamics correlating with the amplitude of transcriptome remodeling.ConclusionsStrain-specific changes, as well as cultivar-specific changes, were identified by profiling the transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional pathways.
| S-EPMC4897865 | biostudies-literature
Project description:Viruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumismelo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon are being extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes to breed new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3´-untranslated regions. Tissues of melon plants from cultivars Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3’264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3’264 specifically deregulated 2925 and 1618 genes in Planters Jumbo and Tendral, respectively. Thus, significantly affected GO categories were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed the identification of two groups specifically deregulated by MNSV-Mα5/3’264 with respect to MNSV-Mα5 in Tendral, and one group antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3’264 infection. Genes in these three groups belong to a diversity of functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene deregulated by the three viruses, with infections dynamics correlating with the amplitude of transcriptome remodeling. Both common and strain-specific changes, as well as common but also cultivar-specific changes, have been identified by profiling transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional implications. Viruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumismelo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon are being extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes to breed new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3´-untranslated regions. Tissues of melon plants from cultivars Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3’264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3’264 specifically deregulated 2925 and 1618 genes in Planters Jumbo and Tendral, respectively. Thus, significantly affected GO categories were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed the identification of two groups specifically deregulated by MNSV-Mα5/3’264 with respect to MNSV-Mα5 in Tendral, and one group antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3’264 infection. Genes in these three groups belong to a diversity of functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene deregulated by the three viruses, with infections dynamics correlating with the amplitude of transcriptome remodeling. Both common and strain-specific changes, as well as common but also cultivar-specific changes, have been identified by profiling transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional implications.
2016-06-07 | GSE74838 | GEO
Project description:Viruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumismelo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon are being extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes to breed new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3´-untranslated regions. Tissues of melon plants from cultivars Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3’264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3’264 specifically deregulated 2925 and 1618 genes in Planters Jumbo and Tendral, respectively. Thus, significantly affected GO categories were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed the identification of two groups specifically deregulated by MNSV-Mα5/3’264 with respect to MNSV-Mα5 in Tendral, and one group antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3’264 infection. Genes in these three groups belong to a diversity of functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene deregulated by the three viruses, with infections dynamics correlating with the amplitude of transcriptome remodeling. Both common and strain-specific changes, as well as common but also cultivar-specific changes, have been identified by profiling transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional implications. Viruses are among the most destructive and difficult to control plant pathogens. Melon (Cucumismelo L.) has become the model species for the agriculturally important Cucurbitaceae family. Approaches that take advantage of recently developed genomic tools in melon are being extremely useful for understanding viral pathogenesis and can contribute to the identification of target genes to breed new resistant cultivars. In this work, we have used a recently described melon microarray for transcriptome profiling of two melon cultivars infected with two strains of Melon necrotic spot virus (MNSV) that only differ on their 3´-untranslated regions. Tissues of melon plants from cultivars Out of 7566 and 7074 genes deregulated by MNSV-Mα5 and MNSV-Mα5/3’264, 1851 and 1356, respectively, were strain-specific. Likewise, MNSV-Mα5/3’264 specifically deregulated 2925 and 1618 genes in Planters Jumbo and Tendral, respectively. Thus, significantly affected GO categories were clearly different for the different virus/host combinations. Grouping genes according to their patterns of expression allowed the identification of two groups specifically deregulated by MNSV-Mα5/3’264 with respect to MNSV-Mα5 in Tendral, and one group antagonistically regulated in Planters Jumbo vs. Tendral after MNSV-Mα5/3’264 infection. Genes in these three groups belong to a diversity of functional classes, and no obvious regulatory commonalities were identified. When data on MNSV-Mα5/Tendral infections were compared to equivalent data on cucumber mosaic virus or watermelon mosaic virus infections, cytokinin-O-glucosyltransferase2 was identified as the only gene deregulated by the three viruses, with infections dynamics correlating with the amplitude of transcriptome remodeling. Both common and strain-specific changes, as well as common but also cultivar-specific changes, have been identified by profiling transcriptomes of plants from two melon cultivars infected with two MNSV strains. No obvious regulatory features shared among deregulated genes have been identified, pointing toward regulation through differential functional implications.
2016-06-07 | GSE74835 | GEO
Project description:Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations
| PRJNA301626 | ENA
Project description:The structure of melon necrotic spot virus (MNSV) was determined at 2.8 A resolution. Although MNSV is classified into the genus Carmovirus of the family Tombusviridae, the three-dimensional structure of MNSV showed a higher degree of similarity to tomato bushy stunt virus (TBSV), which belongs to the genus Tombusvirus, than to carnation mottle virus (CMtV), turnip crinkle virus (TCV) or cowpea mottle virus (CPMtV) from the genus Carmovirus. Thus, the classification of the family Tombusviridae at the genus level conflicts with the patterns of similarity among coat-protein structures. MNSV is one of the viruses belonging to the genera Tombusvirus or Carmovirus that are naturally transmitted in the soil by zoospores of fungal vectors. The X-ray structure of MNSV provides us with a representative structure of viruses transmitted by fungi.
| S-EPMC2374003 | biostudies-literature
Project description:Melon necrotic spot virus (MNSV) can cause significant economic losses due to decreased quality in cucurbit crops. The current study is the first to use reverse transcription loop-mediated isothermal amplification (RT-LAMP) for detection of MNSV. A set of four LAMP primers was designed based on the coat protein gene sequence of MNSV, and a RT-LAMP reaction was successfully performed for 1 h at 62°C. The results of RT-LAMP showed high specificity for MNSV and no cross-reaction with other viruses. Compared to traditional reverse transcription-PCR (RT-PCR), the RT-LAMP assay was 103-fold more sensitive in detecting MNSV. Due to its sensitivity, speed and visual assessment, RT-LAMP is appropriate for detecting MNSV in the laboratory.
| S-EPMC7058275 | biostudies-literature
Project description:The complete genome sequence (4,267 nt) of a Melon necrotic spot virus (MNSV) isolate (ABCA13-01) infecting greenhouse cucumber in Canada was determined through deep sequencing of small RNAs. Its genome sequence was most closely related to MNSV-N (97%) but lacked a 55-nucleotide insertion at the 3' untranslated region for resistance breaking.
| S-EPMC4505125 | biostudies-literature
Project description:We have shown previously that the translation of Melon necrotic spot virus (MNSV, family Tombusviridae, genus Carmovirus) RNAs is controlled by a 3'-cap-independent translation enhancer (CITE), which is genetically and functionally dependent on the eukaryotic translation initiation factor (eIF) 4E. Here, we describe structural and functional analyses of the MNSV-Mα5 3'-CITE and its translation initiation factor partner. We first mapped the minimal 3'-CITE (Ma5TE) to a 45-nucleotide sequence, which consists of a stem-loop structure with two internal loops, similar to other I-shaped 3'-CITEs. UV crosslinking, followed by gel retardation assays, indicated that Ma5TE interacts in vitro with the complex formed by eIF4E + eIF4G980-1159 (eIF4Fp20 ), but not with each subunit alone or with eIF4E + eIF4G1003-1092 , suggesting binding either through interaction with eIF4E following a conformational change induced by its binding to eIF4G980-1159 , or through a double interaction with eIF4E and eIF4G980-1159 . Critical residues for this interaction reside in an internal bulge of Ma5TE, so that their mutation abolished binding to eIF4E + eIF4G1003-1092 and cap-independent translation. We also developed an in vivo system to test the effect of mutations in eIF4E in Ma5TE-driven cap-independent translation, showing that conserved amino acids in a positively charged RNA-binding motif around amino acid position 228, implicated in eIF4E-eIF4G binding or belonging to the cap-recognition pocket, are essential for cap-independent translation controlled by Ma5TE, and thus for the multiplication of MNSV.
| S-EPMC6638222 | biostudies-literature
Project description:The complete coding sequences of three melon necrotic spot viruses (MNSVs) were obtained from viral metagenomics of stool samples from patients with acute gastroenteritis. These genomes were most similar to Spanish strains sequenced in 2003 and a novel MNSV watermelon strain in 2014.
| S-EPMC5356068 | biostudies-literature
Project description:The coat protein (CP) of Melon necrotic spot virus (MNSV) is structurally composed of three major domains. The middle S-domain builds a robust protein shell around the viral genome, whereas the C-terminal protruding domain, or P-domain, is involved in the attachment of virions to the transmission vector. Here, we have shown that the N-terminal domain, or R-domain, and the arm region, which connects the R-domain and S-domain, are involved in different key steps of the viral cycle, such as cell-to-cell movement and the suppression of RNA silencing and pathogenesis through their RNA-binding capabilities. Deletion mutants revealed that the CP RNA-binding ability was abolished only after complete, but not partial, deletion of the R-domain and the arm region. However, a comparison of the apparent dissociation constants for the CP RNA-binding reaction of several partial deletion mutants showed that the arm region played a more relevant role than the R-domain in in vitro RNA binding. Similar results were obtained in in vivo assays, although, in this case, full-length CPs were required to encapsidate full-length genomes. We also found that the R-domain carboxyl portion and the arm region were essential for efficient cell-to-cell movement, for enhancement of Potato virus X pathogenicity, for suppression of systemic RNA silencing and for binding of small RNAs. Therefore, unlike other carmovirus CPs, the R-domain and the arm region of MNSV CP have acquired, in addition to other essential functions such as genome binding and encapsidation functions, the ability to suppress RNA silencing by preventing systemic small RNA transport.
| S-EPMC6638237 | biostudies-literature