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Sequencing and Assembly of Polyploid Genomes

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Polyploidy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2545))

Abstract

Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations often result in highly complex genome structures, posing challenges to genome assembly and phasing. Recent advances in sequencing technologies and genome assembly algorithms have enabled high-quality, near-complete chromosome-level assemblies of polyploid genomes. Advances in novel sequencing technologies include highly accurate single-molecule sequencing with HiFi reads, chromosome conformation capture with Hi-C technique, and linked reads sequencing. Additionally, new computational approaches have also significantly improved the precision and reliability of polyploid genome assembly and phasing, such as HiCanu, hifiasm, ALLHiC, and PolyGembler. Herein, we review recently published polyploid genomes and compare the various sequencing, assembly, and phasing approaches that are utilized in these genome studies. Finally, we anticipate that accurate and telomere-to-telomere chromosome-level assembly of polyploid genomes could ultimately become a routine procedure in the near future.

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Author notes

  1. Yibin Wang and Jiaxin Yu contributed equally with all other contributors.

Authors and Affiliations

  1. Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China

    Yibin Wang, Jiaxin Yu, Mengwei Jiang, Wenlong Lei & Haibao Tang

  2. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

    Xingtan Zhang

Authors
  1. Yibin Wang
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  2. Jiaxin Yu
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  3. Mengwei Jiang
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  4. Wenlong Lei
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  5. Xingtan Zhang
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  6. Haibao Tang
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Editor information

Editors and Affiliations

  1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Yves Van de Peer

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Wang, Y., Yu, J., Jiang, M., Lei, W., Zhang, X., Tang, H. (2023). Sequencing and Assembly of Polyploid Genomes. In: Van de Peer, Y. (eds) Polyploidy. Methods in Molecular Biology, vol 2545. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2561-3_23

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  • DOI: https://doi.org/10.1007/978-1-0716-2561-3_23

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2560-6

  • Online ISBN: 978-1-0716-2561-3

  • eBook Packages: Springer Protocols

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