A tool for rapid, automated characterization of population epigenomics in plants
Abstract Epigenetic variation in plant populations is an important factor in determining phenotype and adaptation to the environment. However, while advances have been made in the molecular and computational methods to analyze the methylation status of a given sample of DNA, tools to profile and com...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-38356-7 |
| _version_ | 1797559838872436736 |
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| author | Jack M. Colicchio Cynthia L. Amstutz Nelson Garcia Keerthana N. Prabhu Thomas M. Cairns Melis Akman Thomas Gottilla Twyla Gollery Shawn L. Stricklin Travis S. Bayer |
| author_facet | Jack M. Colicchio Cynthia L. Amstutz Nelson Garcia Keerthana N. Prabhu Thomas M. Cairns Melis Akman Thomas Gottilla Twyla Gollery Shawn L. Stricklin Travis S. Bayer |
| author_sort | Jack M. Colicchio |
| collection | DOAJ |
| description | Abstract Epigenetic variation in plant populations is an important factor in determining phenotype and adaptation to the environment. However, while advances have been made in the molecular and computational methods to analyze the methylation status of a given sample of DNA, tools to profile and compare the methylomes of multiple individual plants or groups of plants at high resolution and low cost are lacking. Here, we describe a computational approach and R package (sounDMR) that leverages the benefits of long read nanopore sequencing to enable robust identification of differential methylation from complex experimental designs, as well as assess the variability within treatment groups and identify individual plants of interest. We demonstrate the utility of this approach by profiling a population of Arabidopsis thaliana exposed to a demethylating agent and identify genomic regions of high epigenetic variability between individuals. Given the low cost of nanopore sequencing devices and the ease of sample preparation, these results show that high resolution epigenetic profiling of plant populations can be made more broadly accessible in plant breeding and biotechnology. |
| first_indexed | 2024-03-10T17:50:58Z |
| format | Article |
| id | doaj.art-7f915e5bba5a4598b5210893df270d21 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T17:50:58Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-7f915e5bba5a4598b5210893df270d212023-11-20T09:21:36ZengNature PortfolioScientific Reports2045-23222023-08-0113111110.1038/s41598-023-38356-7A tool for rapid, automated characterization of population epigenomics in plantsJack M. Colicchio0Cynthia L. Amstutz1Nelson Garcia2Keerthana N. Prabhu3Thomas M. Cairns4Melis Akman5Thomas Gottilla6Twyla Gollery7Shawn L. Stricklin8Travis S. Bayer9Sound Agriculture CompanySound Agriculture CompanySound Agriculture CompanySound Agriculture CompanySound Agriculture CompanySound Agriculture CompanySound Agriculture CompanySound Agriculture CompanySound Agriculture CompanySound Agriculture CompanyAbstract Epigenetic variation in plant populations is an important factor in determining phenotype and adaptation to the environment. However, while advances have been made in the molecular and computational methods to analyze the methylation status of a given sample of DNA, tools to profile and compare the methylomes of multiple individual plants or groups of plants at high resolution and low cost are lacking. Here, we describe a computational approach and R package (sounDMR) that leverages the benefits of long read nanopore sequencing to enable robust identification of differential methylation from complex experimental designs, as well as assess the variability within treatment groups and identify individual plants of interest. We demonstrate the utility of this approach by profiling a population of Arabidopsis thaliana exposed to a demethylating agent and identify genomic regions of high epigenetic variability between individuals. Given the low cost of nanopore sequencing devices and the ease of sample preparation, these results show that high resolution epigenetic profiling of plant populations can be made more broadly accessible in plant breeding and biotechnology.https://doi.org/10.1038/s41598-023-38356-7 |
| spellingShingle | Jack M. Colicchio Cynthia L. Amstutz Nelson Garcia Keerthana N. Prabhu Thomas M. Cairns Melis Akman Thomas Gottilla Twyla Gollery Shawn L. Stricklin Travis S. Bayer A tool for rapid, automated characterization of population epigenomics in plants Scientific Reports |
| title | A tool for rapid, automated characterization of population epigenomics in plants |
| title_full | A tool for rapid, automated characterization of population epigenomics in plants |
| title_fullStr | A tool for rapid, automated characterization of population epigenomics in plants |
| title_full_unstemmed | A tool for rapid, automated characterization of population epigenomics in plants |
| title_short | A tool for rapid, automated characterization of population epigenomics in plants |
| title_sort | tool for rapid automated characterization of population epigenomics in plants |
| url | https://doi.org/10.1038/s41598-023-38356-7 |
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