Articles
IRREGULAR DISTRIBUTION OF SHARKA (PLUM POX VIRUS) SYMPTOMS IN PEACH IS RELATED TO DIFFERENTIAL GENE EXPRESSION EVIDENCED BY RNA-SEQ
Article number
1063_20
Pages
143 – 146
Language
English
Abstract
Plum pox virus (PPV, sharka disease) is a serious limiting factor for temperate fruit production (mainly apricots, plums, prunes and peaches) in those areas that are affected.
Many studies demonstrated the irregular distribution of sharka symptoms in the woody plants infected with PPV. However, to date, the causes of this erratic distribution are not well known.
In this study, differences in gene expression were studied following Plum pox virus (PPV) infection in peach cultivar GF305. Leaves from plants, with or without PPV symptoms, were assayed using high-throughput Illumina RNA sequencing (RNA-Seq). We conducted high-throughput Illumina RNA sequencing by 105 nt paired-end sequencing.
An intensive bioinformatics data analysis was performed, generating approximately 2.72×108 high quality (HQ) reads.
Reads were mapped to the publicly available peach reference genome sequence, allowing estimation of the expression levels from
RNA-Seq data.
For each of the samples, >80% of all reads were aligned on the peach reference genome, with a tolerance of 2 bp mismatches.
We gained a number of significantly differentially expressed mRNAs in leaves with and without symptoms.
Target predictions of the differentially expressed mRNAs resulted in 1,564 target genes.
Gene ontology (GO) annotation revealed that high-ranking mRNA target genes are those implicated in the developmental process, the regulation of transcription, and response to PPV infection.
Novel transcript isoforms can be found by high throughput sequencing since present databases may be incomplete.
Many studies demonstrated the irregular distribution of sharka symptoms in the woody plants infected with PPV. However, to date, the causes of this erratic distribution are not well known.
In this study, differences in gene expression were studied following Plum pox virus (PPV) infection in peach cultivar GF305. Leaves from plants, with or without PPV symptoms, were assayed using high-throughput Illumina RNA sequencing (RNA-Seq). We conducted high-throughput Illumina RNA sequencing by 105 nt paired-end sequencing.
An intensive bioinformatics data analysis was performed, generating approximately 2.72×108 high quality (HQ) reads.
Reads were mapped to the publicly available peach reference genome sequence, allowing estimation of the expression levels from
RNA-Seq data.
For each of the samples, >80% of all reads were aligned on the peach reference genome, with a tolerance of 2 bp mismatches.
We gained a number of significantly differentially expressed mRNAs in leaves with and without symptoms.
Target predictions of the differentially expressed mRNAs resulted in 1,564 target genes.
Gene ontology (GO) annotation revealed that high-ranking mRNA target genes are those implicated in the developmental process, the regulation of transcription, and response to PPV infection.
Novel transcript isoforms can be found by high throughput sequencing since present databases may be incomplete.
Publication
Authors
M. Rubio , A.R. Ballester, L. Rodríguez-Moreno, M. Castro de Moura, A. Mascarell-Creus, P. Martínez-Gómez
Keywords
PPV, sharka, Prunus, pathogenesis, symptoms, RNA-Seq
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