Abstract Detail



Functional Genetics/Genomics

Shan, Shengchen [1], Gitzendanner, Matt [2], Boatwright, J. Lucas [3], Ethridge, Christina L. [4], Ji, Lexiang [4], Soltis, Pamela [5], Schmitz, Robert J. [4], Soltis, Douglas [6].

Methylation Dynamics Following Recent Genome Doubling in Allotetraploid Tragopogon miscellus (Asteraceae).

DNA methylation, the addition of a methyl group to cytosine (C), plays a significant role in heterochromatin formation, transposable element silencing, and regulation of gene expression. In plants, DNA methylation occurs at three cytosine contexts: CG, CHG (H represents either A, T, or C), and CHH. Despite its importance, however, DNA methylation changes immediately following polyploidy remain unclear. Furthermore, high-throughput genome-wide DNA methylation studies of young polyploids are rare. One of the best-studied recently formed natural polyploid systems involves two polyploids in the genus Tragopogon (Asteraceae). Allotetraploids T. miscellus and T. mirus are only 80–90 years old with clearly documented parentage. Although the dynamic genetic changes of the two newly formed Tragopogon polyploids have been well documented, the epigenetic consequences of polyploidy in Tragopogon remain unknown. In this study, genome-wide DNA methylation patterns were examined in allopolyploid T. miscellus (the short-liguled form) and its diploid parents (T. dubius and T. pratensis). In all cytosine contexts, T. dubius had a higher genome-wide weighted methylation level than T. pratensis, and the methylation level of T. miscellus is intermediate to that of its diploid parents. The contributions of cytosine methylation from different contexts to the total number of methylated cytosines were examined in Tragopogon. In both diploid and polyploid species, most methylated cytosines were CG contexts, followed by CHG and CHH. Using more than 30,000 protein-coding genes, weighted methylation levels were analyzed within gene bodies and their flanking regions across all cytosine contexts. Non-additive methylation levels were identified in T. miscellus, which indicated dynamic epigenetic changes following polyploidy in Tragopogon. In all cytosine contexts, the number of differentially methylated regions (DMRs) between the two diploid parents largely decreased compared to that between the two subgenomes within the allopolyploid. These results indicated that the original methylation divergence between the two parental genomes was mitigated in the 80–90 years old polyploid Tragopogon. Additionally, de novo DMRs were identified in T. miscellus. In summary, genome-wide methylation levels of T. miscellus were intermediate between those of the diploid parents. However, non-additive methylation patterns in T. miscellus indicated dynamic epigenetic changes following polyploidy in Tragopogon. Future studies will attempt to correlate gene expression dynamics with the observed DNA methylation patterns in polyploid Tragopogon. In addition, methylation analysis of synthetic lines of T. miscellus will provide insight into how quickly the methylation divergence between the two diploid parents will diminish in the polyploids through time. Overall, methylation studies in Tragopogon contribute to a better understanding of the epigenetic changes following polyploidy, a pivotal evolutionary force in plant evolution.


1 - Florida Museum of Natural History, 1659 Museum Rd, Gainesville, FL, 32611, United States
2 - University Of Florida, Florida Museum Of Natural History, Po Box 117800, Gainsville, FL, 32611, United States
3 - Clemson University, Plant and Environmental Sciences Department
4 - University of Georgia, Department of Genetics
5 - University Of Florida, Florida Museum Of Natural History, Gainesville, FL, 32611.0, United States
6 - University of Florida, Florida Museum of Natural History,, 3215 Hull Road, P. O. Box 2710, Gainesville, FL, 32611, USA

Keywords:
Methylation
polyploidy
Tragopogon.

Presentation Type: Oral Paper
Session: FGG2, Functional Genetics/Genomics II
Location: Tikahtnu Ballroom C /Dena'ina Center
Date: Wednesday, July 27th, 2022
Time: 5:00 PM(EDT)
Live or Virtual Live
Number: FGG2006
Abstract ID:858
Candidate for Awards:None


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