Comparative transcriptome analysis provides molecular insights into the interaction of Beet necrotic yellow vein virus and Beet soil-borne mosaic virus with their host sugar beet
ABSTRACT: Beet necrotic yellow vein virus (BNYVV) and Beet soil-borne mosaic virus (BSBMV) belong to the genus Benyvirus. Both viruses share a similar genome organization, but disease development induced in their major host plant sugar beet displays striking differences. BNYVV induces excessive lateral root (LR) formation by hijacking auxin-regulated pathways; whereas BSBMV infected roots appear asymptomatic. To elucidate transcriptomic changes associated with the virus-specific disease development of BNYVV and BSBMV, we performed a comparative transcriptome analysis of a virus infected susceptible sugar beet genotype.
Project description:In this work, the high taproot yield cultivar SD13829 (E-type; E) and high sucrose content cultivar BS02 (Z-type; Z) of sugar beet at five different developmental stages were used to perform transcriptomic analyses. We demonstrate that the weight and sucrose content of taproot rely on its growth strategy, which is controlled by brassinosteroid, auxin, cytokinin, and gibberellin signaling. Among them, an antagonistic expression pattern of brassinosteroid- and auxin-related genes in taproot might play a crucial role for its rapid growth at 82 DAE.
Project description:Title : Characterization of genes differentially expressed in roots of transgenic arabidopsis lines expressing the p25 protein of beet necrotic yellow vein virus.<br> <br> Biological question : <br> Rhizomania ("crazy root") is a severe disease of sugar beet caused by beet necrotic yellow vein virus (BNYVV), which is transmitted by the soil-inhabiting fungus Polymyxa betae. Symptoms of virus infection are characterized by a constricted tap root and a massive proliferation of fine rootlets that often undergo necrosis. BNYVV RNA-3 encodes a 25 kDa (p25) which is an important determinant of leaf symptom phenotype. It also governs BNYVV invasion of the plant root system and induction of rootlet proliferation in sugar beet.<br> In order to obtain a better understanding of molecular aspects of disease development in roots and to characterize specific host genes involved in response to viral infection, transgenic Arabidopsis overexpressors of p25 viral protein was obtained and better characterized. It was shown that transgenic plants that efficiently expressed p25 protein produced more lateral roots. <br> Comparative analysis (microarray) was performed between wild type Arabidopsis roots and transgenic Arabidopsis roots expressing p25 protein, in order to identify Arabidopsis genes differentially expressed in response to p25 viral protein.<br> <br> Experiment description: <br> Seeds were surface sterilized, chilled at 4C for 4 days, and then germinated and grown on square Petri plates containing sterilized Murashige and Skoog (MS) medium with 1% sucrose. Such stock plates were arranged vertically in plastic racks and placed into growth chamber. After 5 days, plants were transferred carefully onto fresh MS medium big round plates. On each plate, 60 Wild Type (WT) plantlets were transferred on the half right of the plate, and 60 transgenic plantlets (B, E or T lines) were transferred on the half left of the plate. Plates were arranged horizontally and placed into growth chamber. <br> <br>Experiment 1 : 5 plates containing WT0A control plants and B0A transgenic plants. <br> <br>Experiment 2 : 5 plates containing WT1 control plants and B transgenic plants. <br>5 plates containing WT2 control plants and E transgenic plants. <br>5 plates containing WT3 control plants and T transgenic plants. <br> <br>Plants were harvested after 7 days (experiment 1) or 12 days (experiment 2), and WT roots or transgenic roots were pooled and conserved at -80C.
Project description:Micrarray analysis was used to identify gene expression changes associated with disease development and virus movement in N.benthamina plants induced by infection with the SACMV 1-Plex , 385K array Nicotiana benthamiana (NimbleGen design name: 110121_N_benthamiana_60mer_exp) was used in this study to monitor changes in gene expression levels in SACMV- infected leaf tissue. Three biological replicates were used for infected leaf tissue and one pooled mock-inoculated sample was used as a control/reference.
Project description:Background: Sugar beet is an important root crop, accounting for 30 % of the sugar production worldwide. The long growing season make sugar beets exposed to a range of plant pathogens for longer periods than most other crops. Here, contrasting sugar beet genotypes were used for transcriptome analysis to reveal differential responses and new defense genes to Rhizoctonia solani, a soilborn fungal pathogen. Results: After curation of primary RNA-sequencing reads, 16,768 genes deriving from 36 samples composed of two susceptible and two resistant sugar beet genotypes, three time-points (0, two and five days post inoculation), each in three replicates were subjected for analysis. Among the elevated 217 transcripts at 2 dpi, three resistance-like genes (Bv4_088600_cumk, Bv8u_204980_frqg, and Bv_44840_iifo) were activated. By employing edgeR package statistics, 660 genes were significantly different (false discovery rate < 0.05) between resistant and susceptible genotypes in their response to R. solani inoculation. A combination of eukaryotic orthologous group assignments and gene ontology enrichment analyses, revealed three Bet v I/Major latex protein homologous genes (Bv7_162510_pymu, Bv7_162520_etow, Bv_27270_xeas) in the resistant genotypes after five days of fungal challenge. Co-expression network analysis of differentially expressed sugar beet genes further identified a MYB46 transcription factor, a plant disease resistance response protein (DRR206) and a flavonoid o-methyltransferase protein. MYB46 has a key function in secondary cell wall formation and exist as a singleton in the sugar beet genome. The genome of R. solani is enriched in cell wall degrading enzyme encoding genes and it is anticipated that they represent important virulence factors. Compared to Arabidopsis thaliana, sugar beet has 2.4-fold more carbohydrate esterases and particularly large numbers (26-fold) of auxiliary activity encoding genes whose function in cell wall biosynthesis is largely unknown. Conclusions: Based on components identified in this sugar beet transcript data set we conclude that defense responses to R. solani are attributed to a wide range of gene categories but functional information is missing to a large extent. This calls for careful integration to avoid negative side effects to obtain optimal combinations of these traits in order to reach the long-term goal of improved resistance in sugar beet. Overall design: Four sugar beet genotypes, three time-points and three biological replicates were sequenced.
Project description:The project compares the genomes of multiple Aspergillus species. In particular, the genes involved in the degradation of plant-derived biomass have been analyzed. As well, the extracellular proteins produced by the fungi during the utilization of sugar beet pulp and wheat bran were examined by LC-MS/MS. Results show that closely related species can deploy different enzyme mixtures in the hydrolysis of plant-derived biomass. These results imply that efficient hydrolysis of biomass can be achieved by combining enzyme mixtures from two or more fungi.
Project description:Experimental infection of (2 days old) adult honey bee workers (30 bees per replicates, 3 replicates per treatments, from 3 different colonies (one colony per cage for each treatment)) with 10^9 genome equivalent of Black Queen Cell Virus (BQCV) in 10µl of sugar solution and/or 10^5 fresh Nosema ceranae spores (control bees were given a similar bee extract in PBS, without pathogen). Bees were kept in cages of 30 bees in incubator (30°C/50%RH). At day 13 p.i., bees were flash frozen, and stored at -80°C. Brain mRNA profiles of 15 old bees were generated by deep sequencing, in triplicates except for bees infected by both Nosema ceranae and Black Queen Cell Virus (duplicates)
Project description:The aim of this study was to explore epigenetic variations between sugar beet genotypes with distinct bolting tolerance levels and to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction. Overall design: Two condition experiment on sugar beet shoot apical meristems after 9 weeks of vernalization treatment at 4°C. Experiment was performed one time using six sugar beet genotypes. Genotypes 1, 4 and 7 correspond to the group of bolting resistant genotypes and genotypes 2, 3, 5 correspond to the group of bolting sensitive genotypes. Methylated DNA was compared to the corresponding genomic DNA for each genotype.
Project description:We constructed two independent small RNA libraries from leaves of mock and Cucumber mosaic virus (CMV) infected tomatoes, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 known miRNAs (32 families) and 568 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 known miRNAs and 154 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed 79 miRNAs (including 15 novel tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries. Among these virus responsive miRNAs, expression patters of some novel tomato miRNAs and PC-miRNAs in mock and in CMV-Fny infected tomatoes were further validated by qRT-PCR. Moreover, we revealed 563 potential targets for 66 tomato miRNAs by the recently developed degradome sequencing approach, including 124 targets for 7 new tomato miRNAs and 97 targets for 24 PC-miRNAs. Target annotation for the newly identified miRNA and PC-miRNAs indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that stress response- and photosynthesis-related genes were most affected in CMV-Fny infected tomatoes. Examination of small RNAs and their targets in mock and CMV-Fny infected tomatoes.
Project description:To study the induction of the genes encoding known and putative enzymes from the pectinolytic system of A. niger, the transcriptional profiles of 58 selected known or putative pectinolytic genes were monitored by microarray experiments. For this purpose, A. niger was cultivated on the complex substrates, sugar beet pectin and polygalacturonic acid as primary carbon sources. Galacturonic acid, rhamnose and xylose were used to assess the effects on gene expression caused by simple well-defined carbon sources, representing the most abundant sugar residues present in the backbone of pectin. Fructose, as a strong repressor of the expression of genes that are under carbon catabolite regulation, and sorbitol, as a non-inducing sugar-like alcohol, which does not affect the carbon catabolite regulation mechanisms were selected as control substrates. Mycelia of A. niger were pregrown for 18 h on 2% fructose, transferred to medium containing the different pectic and control substrates, and sampled at four time points during 24 h of incubation.
Project description:The aim of this study was to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction. Overall design: Gene expression in sugar beet shoot apical meristem was measured after 9 weeks of vernalization treatment at 4°C. Experiment was performed one time using six different sugar beet genotypes named 1, 2, 3, 4, 5 and 7. Genotypes 3 and 7 were both hybridized on two different arrays to have technical replicates.