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Inference of ancient polyploidy using transcriptome data

Jia Li (UGent) , Yves Van de Peer (UGent) and Zhen Li (UGent)
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Abstract
Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and likely enabled adaptation under harsh conditions. Besides genomic data, transcriptome data have been widely employed to detect WGDs, due to their efficient accessibility to the gene space of a species. Age distributions based on synonymous substitutions (so-called KS age distributions) for paralogs assembled from transcriptome data have identified numerous WGDs in plants, paving the way for further studies on the importance of WGDs for the evolution of seed and flowering plants. However, it is still unclear how transcriptome-based age distributions compare to those based on genomic data. In this chapter, we implemented three different de novo transcriptome assembly pipelines with two popular assemblers, i.e., Trinity and SOAPdenovo-Trans. We selected six plant species with published genomes and transcriptomes to evaluate how assembled transcripts from different pipelines perform when using KS distributions to detect previously documented WGDs in the six species. Further, using genes predicted in each genome as references, we evaluated the effects of missing genes, gene family clustering, and de novo assembled transcripts on the transcriptome-based KS distributions. Our results show that, although the transcriptome-based KS distributions differ from the genome-based ones with respect to their shapes and scales, they are still reasonably reliable for unveiling WGDs, except in species where most duplicates originated from a recent WGD. We also discuss how to overcome some possible pitfalls when using transcriptome data to identify WGDs.
Keywords
Ancient polyploidy; KS age distribution; RNA-Seq; Transcriptome assembly; WGD

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MLA
Li, Jia, et al. “Inference of Ancient Polyploidy Using Transcriptome Data.” Polyploidy : Methods and Protocols, edited by Yves Van de Peer, vol. 2545, Humana, 2023, pp. 47–76, doi:10.1007/978-1-0716-2561-3_3.
APA
Li, J., Van de Peer, Y., & Li, Z. (2023). Inference of ancient polyploidy using transcriptome data. In Y. Van de Peer (Ed.), Polyploidy : methods and protocols (Vol. 2545, pp. 47–76). https://doi.org/10.1007/978-1-0716-2561-3_3
Chicago author-date
Li, Jia, Yves Van de Peer, and Zhen Li. 2023. “Inference of Ancient Polyploidy Using Transcriptome Data.” In Polyploidy : Methods and Protocols, edited by Yves Van de Peer, 2545:47–76. New York: Humana. https://doi.org/10.1007/978-1-0716-2561-3_3.
Chicago author-date (all authors)
Li, Jia, Yves Van de Peer, and Zhen Li. 2023. “Inference of Ancient Polyploidy Using Transcriptome Data.” In Polyploidy : Methods and Protocols, ed by. Yves Van de Peer, 2545:47–76. New York: Humana. doi:10.1007/978-1-0716-2561-3_3.
Vancouver
1.
Li J, Van de Peer Y, Li Z. Inference of ancient polyploidy using transcriptome data. In: Van de Peer Y, editor. Polyploidy : methods and protocols. New York: Humana; 2023. p. 47–76.
IEEE
[1]
J. Li, Y. Van de Peer, and Z. Li, “Inference of ancient polyploidy using transcriptome data,” in Polyploidy : methods and protocols, vol. 2545, Y. Van de Peer, Ed. New York: Humana, 2023, pp. 47–76.
@incollection{01GS5BJ5JAW72EM2S3N9ESVYMY,
  abstract     = {{Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and likely enabled adaptation under harsh conditions. Besides genomic data, transcriptome data have been widely employed to detect WGDs, due to their efficient accessibility to the gene space of a species. Age distributions based on synonymous substitutions (so-called KS age distributions) for paralogs assembled from transcriptome data have identified numerous WGDs in plants, paving the way for further studies on the importance of WGDs for the evolution of seed and flowering plants. However, it is still unclear how transcriptome-based age distributions compare to those based on genomic data. In this chapter, we implemented three different de novo transcriptome assembly pipelines with two popular assemblers, i.e., Trinity and SOAPdenovo-Trans. We selected six plant species with published genomes and transcriptomes to evaluate how assembled transcripts from different pipelines perform when using KS distributions to detect previously documented WGDs in the six species. Further, using genes predicted in each genome as references, we evaluated the effects of missing genes, gene family clustering, and de novo assembled transcripts on the transcriptome-based KS distributions. Our results show that, although the transcriptome-based KS distributions differ from the genome-based ones with respect to their shapes and scales, they are still reasonably reliable for unveiling WGDs, except in species where most duplicates originated from a recent WGD. We also discuss how to overcome some possible pitfalls when using transcriptome data to identify WGDs.}},
  author       = {{Li, Jia and Van de Peer, Yves and Li, Zhen}},
  booktitle    = {{Polyploidy : methods and protocols}},
  editor       = {{Van de Peer, Yves}},
  isbn         = {{9781071625606}},
  issn         = {{1064-3745}},
  keywords     = {{Ancient polyploidy; KS age distribution; RNA-Seq; Transcriptome assembly; WGD}},
  language     = {{eng}},
  pages        = {{47--76}},
  publisher    = {{Humana}},
  series       = {{Methods in Molecular Biology}},
  title        = {{Inference of ancient polyploidy using transcriptome data}},
  url          = {{http://doi.org/10.1007/978-1-0716-2561-3_3}},
  volume       = {{2545}},
  year         = {{2023}},
}

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