Articles
Whole-genome bisulfite sequencing and methylome profiling of homo- and hetero-grafted peach rootstocks uncovers a burst of DNA methylation events with potential impact on gene expression
Article number
1352_21
Pages
157 – 162
Language
English
Abstract
DNA methylation has been described as an efficient epigenetic regulation mechanism together with the histone post-translational modifications involved in different process in fruit trees.
In addition, new sequencing technologies have enabled researchers to analyze DNA methylation in the whole genome in a single experiment.
In this context, aiming to identify genomic regions with differential methylation states in response to intra and interspecific grafting in peach [Prunus persica (L.) Batsch] rootstocks, we carried out an Illumina reduced-representation genome sequencing on bisulfite-treated DNA. Bisulfite sequencing uses enzymatic digestion for reducing genome complexity and allows detection of marks to study DNA methylation.
We analyzed GF305′ peach seedlings used as rootstock for our grafting experiments with the own GF305′ (intraspecific control grafting) and the almond cultivar Garrigues’ (interspecific grafting). A total amount of 283,072,597 reads were obtained and mapped using the v.2 peach reference genome.
The mapping rate was of 70.4% providing information about differentially methylated genic and promoter regions in the different studied comparisons and the three contexts CG, CHG and CHH. Such epigenetic modifications, among this DNA methylation, represented a potential mechanism contributing to gene expression regulation.
Further biological RNA-Seq experiments will contribute to correlate these DNA methylated regions with the differentially expressed genes.
In addition, new sequencing technologies have enabled researchers to analyze DNA methylation in the whole genome in a single experiment.
In this context, aiming to identify genomic regions with differential methylation states in response to intra and interspecific grafting in peach [Prunus persica (L.) Batsch] rootstocks, we carried out an Illumina reduced-representation genome sequencing on bisulfite-treated DNA. Bisulfite sequencing uses enzymatic digestion for reducing genome complexity and allows detection of marks to study DNA methylation.
We analyzed GF305′ peach seedlings used as rootstock for our grafting experiments with the own GF305′ (intraspecific control grafting) and the almond cultivar Garrigues’ (interspecific grafting). A total amount of 283,072,597 reads were obtained and mapped using the v.2 peach reference genome.
The mapping rate was of 70.4% providing information about differentially methylated genic and promoter regions in the different studied comparisons and the three contexts CG, CHG and CHH. Such epigenetic modifications, among this DNA methylation, represented a potential mechanism contributing to gene expression regulation.
Further biological RNA-Seq experiments will contribute to correlate these DNA methylated regions with the differentially expressed genes.
Publication
Authors
M. Rubio, P.J. Martínez-García, P. Martínez-Gómez
Keywords
peach, Prunus, antiviral resistance, Plum pox virus, cross-protection
Groups involved
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