AI Article Synopsis
- Polyploidy is a significant evolutionary process, but the role of epigenetic mechanisms like DNA methylation in regulating gene expression of duplicated genes is not well understood.
- The study focuses on Tragopogon miscellus, a naturally formed allotetraploid, examining its DNA methylation patterns compared to its parent species using whole-genome bisulfite sequencing.
- Results indicated that T. miscellus exhibited intermediate global methylation levels between its parents, with unique nonadditive methylation patterns and novel differentially methylated regions and genes emerging soon after its formation.
Article Abstract
Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome-wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95-100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole-genome bisulfite sequencing. Genome-wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized. This study provides the first assessment of both overall and locus-specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.
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| http://dx.doi.org/10.1111/nph.19655 | DOI Listing |
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