Project description:In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. The filtered 21- to 24-nt was mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism. Evaluation of the vd-sRNA production in PSTVd infected tomato plants by high-throughput sequencing of small RNAs.
Project description:In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. The filtered 21- to 24-nt was mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism.
Project description:In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid- RG1 strain (PSTVd-RG1) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-RG1. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.
Project description:In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid-intermediate strain (PSTVd-I) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-I. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.
Project description:In order to verify the production of viroid specific small RNAs (vd-sRNA) by viroids upon infecting plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with Potato spindle tuber viroid (PSTVd) variants. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. Obtained data was analyzed for the presence of PSTVd specific small RNAs.
Project description:Rice stripe virus (RSV) causes the general chlorosis symptom and influences expression of numberous chloropalst-related genes at transcriotional level in Nicotiana benthamiana plants, but the mechanism are not well understood. Small RNAs (sRNAs), including virus-derived siRNA (vsiRNA) play roles in modulating genes expression post-transcriptionally. This present work presents multi-omics analysis of the transcriptome, sRNAome and degradome in RSV-infected N.benthamiana plants. Transcriptome-seq profiled 4127 N. benthamiana genes, with differentially expressed genes (DEGs) enriched in functional categories such as metabolic process, protein phosphorylation, regulation of transcription, carotenoid biosynthetic process. We identified 400863, 203874 and 244713 reads of vsiRNA from 3 sRNA libraries of RSV-infected N.benthamiana plants respectively. The degradome-seq report discovered a significant number of N.benthamiana genes that might be regulated by vsiRNAs post-transcriptionally. Based on integrated analysis of the three omics, we provide a substantial amount of novel information on the transcriptional and post-transcriptional networks in RSV-infected N.benthamiana, which will extends our horizon about the interactions between virus and their hosts.
Project description:In order to compare the small RNA (sRNA) population between the control and Potato spindle tuber viroid (PSTVd) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were mock inoculated. At 21 dpi,tTotal RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.
Project description:WT plants (at the five-leaf stage) were infected with PSTVd strain NB by agroinfiltration. Three weeks post infection (3 wpi) young leaves were collected from infected and uninfected (control) WT plants and used in a custom genome-wide gene expression microarray (4x 180K Sureprint G3 microarray, Agilent)