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Metagenomic analysis of phytoplasma infected apple trees

ABSTRACT: Apple is one of the most important fruits that is propagated vegetatively, facilitating frequent transmission of viruses. The causative agent of the apple rubbery wood disease, apple rubbery wood virus 2 (ARWV2), can infect apple and pear. The branches of ARWV2-infected, symptomatic trees are flexible due to the decreased lignification of the xylem. In this research, we reanalysed our sRNA HTS datasets to survey the presence of ARWV2 in Hungary. Validation of HTS using RT-PCR revealed infection in several cultivars. The following RT-PCR-based survey revealed the infection of 15 trees, including pear and quince, without showing any rubbery wood symptoms. Analysis of the sRNA datasets allowed us to profile the sRNA pattern of ARWV2-infected and non-infected trees, and characterise the differential expression pattern of vsiRNAs and miRNAs targeting the lignin biosynthetic pathway. The results confirmed that neither the symptoms nor the gene-expression changes in the ARWV2-infected trees can be directly correlated with the presence of the virus, which can explain its frequent latent presence. Its variable concentration, sequence, and the mixed-infection status of the trees, make difficult its reliable diagnostics, which, although it would be highly needed, could be achieved as a result of further research.

ORGANISM(S): Malus domestica

PROVIDER: GSE306190 | GEO | 2025/12/03

REPOSITORIES: GEO

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Project description:Woody plant material represents a vast renewable resource that has the potential to produce biofuels and other bio-based products with favourable net CO2 emissions1,2. Its potential has been demonstrated in a recent study that generated novel structural materials from flexible mouldable wood3. The study of viral infection in plants has largely focussed on detrimental symptoms, such as leaf yellowing or cell death that result in reduced crop yields. Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility4. While ARW disease is associated with the presence of an RNA virus5 (ARWV), the mechanism underlying the development of its unique symptoms is not known. We demonstrate that ARWV symptoms arise from reduced lignification within the secondary cell wall of xylem fibres, while the mid-lamellae region and xylem ray cells are largely unaffected, and results in increased wood digestibility. Gene expression and proteomic data from symptomatic xylem clearly show the downregulation of phenylalanine ammonia lyase (PAL), the enzyme catalysing the first committed step in the phenylpropanoid pathway leading 2 to lignin biosynthesis. PAL downregulation is the likely cause of the decreased lignification, which is consistent with a large increase in soluble phenolics, including the lignin precursor phenylalanine, seen in symptomatic xylem. ARWV-infection results in the accumulation of many host-derived viral activated small interfering RNAs (vasiRNAs). PAL-derived vasiRNAs are among the most abundant vasiRNAs in symptomatic xylem and are likely the cause of reduced PAL activity. Apparently, the mechanism used by the virus to alter lignin exhibits similarities to the RNAi strategy that has been used to alter lignin in genetically modified trees to generate comparable improvements in wood properties6–8. CRISPR technology was recently used to increase yields in maize by introducing the naturally occurring waxy mutation into maize9. A similar biomimetic approach for biomass improvement based upon our understanding of ARWV symptoms offers a promising route to improve wood properties and provides important context for the genetic manipulation of trees.

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Metagenomic analysis of phytoplasma infected apple trees

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