Inference of ancient polyploidy from genomic data
- Author
- Hengchi Chen (UGent) and Arthur Zwaenepoel
- Organization
- Project
- Abstract
- Whole-genome sequence data have revealed that numerous eukaryotic organisms derive from distant polyploid ancestors, even when these same organisms are genetically and karyotypically diploid. Such ancient whole-genome duplications (WGDs) have been important for long-term genome evolution and are often speculatively associated with important evolutionary events such as key innovations, adaptive radiations, or survival after mass extinctions. Clearly, reliable methods for unveiling ancient WGDs are key toward furthering understanding of the long-term evolutionary significance of polyploidy. In this chapter, we describe a set of basic established comparative genomics approaches for the inference of ancient WGDs from genomic data based on empirical age distributions and collinearity analyses, explain the principles on which they are based, and illustrate a basic workflow using the software “wgd,” geared toward a typical exploratory analysis of a newly obtained genome sequence.
- Keywords
- Ancient whole-genome duplication; Collinearity; Comparative genomics; Paranome age distribution; Synteny
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01GS5BF5XF60149B5BW6WQ0SW4
- MLA
- Chen, Hengchi, and Arthur Zwaenepoel. “Inference of Ancient Polyploidy from Genomic Data.” Polyploidy : Methods and Protocols, edited by Yves Van de Peer, vol. 2545, Humana, 2023, pp. 3–18, doi:10.1007/978-1-0716-2561-3_1.
- APA
- Chen, H., & Zwaenepoel, A. (2023). Inference of ancient polyploidy from genomic data. In Y. Van de Peer (Ed.), Polyploidy : methods and protocols (Vol. 2545, pp. 3–18). https://doi.org/10.1007/978-1-0716-2561-3_1
- Chicago author-date
- Chen, Hengchi, and Arthur Zwaenepoel. 2023. “Inference of Ancient Polyploidy from Genomic Data.” In Polyploidy : Methods and Protocols, edited by Yves Van de Peer, 2545:3–18. New York, NY, USA: Humana. https://doi.org/10.1007/978-1-0716-2561-3_1.
- Chicago author-date (all authors)
- Chen, Hengchi, and Arthur Zwaenepoel. 2023. “Inference of Ancient Polyploidy from Genomic Data.” In Polyploidy : Methods and Protocols, ed by. Yves Van de Peer, 2545:3–18. New York, NY, USA: Humana. doi:10.1007/978-1-0716-2561-3_1.
- Vancouver
- 1.Chen H, Zwaenepoel A. Inference of ancient polyploidy from genomic data. In: Van de Peer Y, editor. Polyploidy : methods and protocols. New York, NY, USA: Humana; 2023. p. 3–18.
- IEEE
- [1]H. Chen and A. Zwaenepoel, “Inference of ancient polyploidy from genomic data,” in Polyploidy : methods and protocols, vol. 2545, Y. Van de Peer, Ed. New York, NY, USA: Humana, 2023, pp. 3–18.
@incollection{01GS5BF5XF60149B5BW6WQ0SW4,
abstract = {{Whole-genome sequence data have revealed that numerous eukaryotic organisms derive from distant polyploid ancestors, even when these same organisms are genetically and karyotypically diploid. Such ancient whole-genome duplications (WGDs) have been important for long-term genome evolution and are often speculatively associated with important evolutionary events such as key innovations, adaptive radiations, or survival after mass extinctions. Clearly, reliable methods for unveiling ancient WGDs are key toward furthering understanding of the long-term evolutionary significance of polyploidy. In this chapter, we describe a set of basic established comparative genomics approaches for the inference of ancient WGDs from genomic data based on empirical age distributions and collinearity analyses, explain the principles on which they are based, and illustrate a basic workflow using the software “wgd,” geared toward a typical exploratory analysis of a newly obtained genome sequence.}},
author = {{Chen, Hengchi and Zwaenepoel, Arthur}},
booktitle = {{Polyploidy : methods and protocols}},
editor = {{Van de Peer, Yves}},
isbn = {{9781071625606}},
issn = {{1064-3745}},
keywords = {{Ancient whole-genome duplication; Collinearity; Comparative genomics; Paranome age distribution; Synteny}},
language = {{eng}},
pages = {{3--18}},
publisher = {{Humana}},
series = {{Methods in Molecular Biology}},
title = {{Inference of ancient polyploidy from genomic data}},
url = {{http://doi.org/10.1007/978-1-0716-2561-3_1}},
volume = {{2545}},
year = {{2023}},
}
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