Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.)
Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be...
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MDPI AG
2022-06-01
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| Series: | Biology |
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| author | Pratima Verma Amrita Singh Supriya Purru Kangila Venkataramana Bhat Suman Lakhanpaul |
| author_facet | Pratima Verma Amrita Singh Supriya Purru Kangila Venkataramana Bhat Suman Lakhanpaul |
| author_sort | Pratima Verma |
| collection | DOAJ |
| description | Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be identified. Cytosine methylation profiles of healthy and infected sesame plants studied using Whole Genome Bisulfite Sequencing (WGBS) and Quantitative analysis of DNA methylation with the real-time PCR (qAMP) technique revealed altered DNA methylation patterns upon infection. Phyllody was associated with global cytosine hypomethylation, though predominantly in the CHH (where H = A, T or C) context. Interestingly, comparable cytosine methylation levels were observed between healthy and little leaf-affected plant samples in CG, CHG and CHH contexts. Among the different genomic fractions, the highest number of differentially methylated Cytosines was found in the intergenic regions, followed by promoter, exonic and intronic regions in decreasing order. Further, most of the differentially methylated genes were hypomethylated and were mainly associated with development and defense-related processes. Loci for STOREKEEPER protein-like, a DNA-binding protein and PP2-B15, an F-Box protein, responsible for plugging sieve plates to maintain turgor pressure within the sieve tubes were found to be hypomethylated by WGBS, which was confirmed by methylation-dependent restriction digestion and qPCR. Likewise, serine/threonine-protein phosphatase-7 homolog, a positive regulator of cryptochrome signaling involved in hypocotyl and cotyledon growth and probable O-methyltransferase 3 locus were determined to be hypermethylated. Phytoplasma infection-associated global differential methylation as well as the defense and development-related loci reported here for the first time significantly elucidate the mechanism of phytoplasma-associated disease development. |
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| spelling | doaj.art-17a728d772e24eef83e4ce28f89f51a72023-12-03T14:39:58ZengMDPI AGBiology2079-77372022-06-0111795410.3390/biology11070954Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.)Pratima Verma0Amrita Singh1Supriya Purru2Kangila Venkataramana Bhat3Suman Lakhanpaul4Department of Botany, University of Delhi, New Delhi 110007, IndiaDepartment of Botany, Gargi College, University of Delhi, New Delhi 110049, IndiaICAR-NAARM, Rajender Nagar, Hyderabad 500030, IndiaICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, IndiaDepartment of Botany, University of Delhi, New Delhi 110007, IndiaPhytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be identified. Cytosine methylation profiles of healthy and infected sesame plants studied using Whole Genome Bisulfite Sequencing (WGBS) and Quantitative analysis of DNA methylation with the real-time PCR (qAMP) technique revealed altered DNA methylation patterns upon infection. Phyllody was associated with global cytosine hypomethylation, though predominantly in the CHH (where H = A, T or C) context. Interestingly, comparable cytosine methylation levels were observed between healthy and little leaf-affected plant samples in CG, CHG and CHH contexts. Among the different genomic fractions, the highest number of differentially methylated Cytosines was found in the intergenic regions, followed by promoter, exonic and intronic regions in decreasing order. Further, most of the differentially methylated genes were hypomethylated and were mainly associated with development and defense-related processes. Loci for STOREKEEPER protein-like, a DNA-binding protein and PP2-B15, an F-Box protein, responsible for plugging sieve plates to maintain turgor pressure within the sieve tubes were found to be hypomethylated by WGBS, which was confirmed by methylation-dependent restriction digestion and qPCR. Likewise, serine/threonine-protein phosphatase-7 homolog, a positive regulator of cryptochrome signaling involved in hypocotyl and cotyledon growth and probable O-methyltransferase 3 locus were determined to be hypermethylated. Phytoplasma infection-associated global differential methylation as well as the defense and development-related loci reported here for the first time significantly elucidate the mechanism of phytoplasma-associated disease development.https://www.mdpi.com/2079-7737/11/7/954<i>Sesamum indicum</i> L.DNA methylationWhole Genome Bisulfite Sequencing (WGBS)phytoplasmaphyllodylittle leaf and McrBC |
| spellingShingle | Pratima Verma Amrita Singh Supriya Purru Kangila Venkataramana Bhat Suman Lakhanpaul Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.) Biology <i>Sesamum indicum</i> L. DNA methylation Whole Genome Bisulfite Sequencing (WGBS) phytoplasma phyllody little leaf and McrBC |
| title | Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.) |
| title_full | Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.) |
| title_fullStr | Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.) |
| title_full_unstemmed | Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.) |
| title_short | Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (<i>Sesamum indicum</i> L.) |
| title_sort | comparative dna methylome of phytoplasma associated retrograde metamorphosis in sesame i sesamum indicum i l |
| topic | <i>Sesamum indicum</i> L. DNA methylation Whole Genome Bisulfite Sequencing (WGBS) phytoplasma phyllody little leaf and McrBC |
| url | https://www.mdpi.com/2079-7737/11/7/954 |
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