High-throughput transcriptome and small RNA analysis for studying phytoplasma infection on Catharanthus roseus using Next Generation Sequencing
Date Issued
2011
Date
2011
Author(s)
Tseng, Hsin-I
Abstract
Phytoplasmas are special bacteria that are obligated parasites on plants and cause severe damage on economical crops worldwide. The peanut witches-broom (PnWB) phytoplasma were caused significant floral malformation such as virescence, phyllody and petal discoloration in a numerous phytoplasma ideal host plant periwinkle (Catharanthus roseus). Studying of phytoplasmas-host interaction, however, is limited due to the lack of genome information of periwinkle plant. Next generation sequencing (NGS) is a new high-throughput sequencing technology that is rapid and economic on the genomic project, especially on non-model species. In this study, the whole transcriptome and small RNA profiles of the flower organs of the healthy and PnWB phytoplasma-infected periwinkles were investigated by NGS. The 85.9% successful rate of de novo assembly from periwinkle sequence reads are generated 60,580 contigs. The sequence analysis results showed the periwinkle sequences are similar to those in Arabidopsis coding sequence (CDS) database and more complete compared with Catharanthus EST database. Based on the gene ontology (GO) on classification roles with Arabidopsis CDS database, gene related to defense, photosynthesis, chloroplast, and karrikin were highly expressed in transcriptome of PnWB phytoplasma-infected flower profiles. In addition, the total number of 24-nt small RNA displayed dramatic decrease in PnWB phytoplasma-infected flower. Moreover, there were 414 candidate genes in periwinkle transcriptome that were likely associated with the 24-nt small RNAs and RNA-directed DNA methylation (RdDM); those genes were highly expressed in diseased organs and were associated with defense and chloroplast development. This results were consistent with the morphological phenotype between healthy and PnWB phytoplasma-infected flower organs that photosynthesis and chloroplast were developed in the phyllody of floral organ. Furthermore, the 200-600 nt non-coding RNA (ncRNA) were indentified in contigs that might involve in the histone methlyation of periwinkle. The results suggested that PnWB phytoplasma might inhibit the 24-nt small RNA biogenesis that caused the suppression of RdDM pathway to reactative the methlyated genes. In conclusion, this study provides a new vision to understand the disease mechanism between host and phytoplasma in the periwinkle plant by bioinformatics with powerful and fast high throughput technique.
Subjects
next generation sequencing (NGS)
Catharanthus roseus
transcriptome
Type
thesis
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