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A Comprehensive Guide to Potato Transcriptome Assembly

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Solanum tuberosum

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2354))

Abstract

We have witnessed a rapid advancement in high-throughput genome sequencing and the maturation of long-read technologies. However, an accurate assembly of polyploid potato genomes still remains challenging. Sequencing the double-monoploid genome of Solanum tuberosum Group Phureja (Xu et al., Nature 475:189–195, 2011) has enabled functional studies of polyploid potato cultivars using RNA sequencing (RNA-Seq) technologies, although with the limitation of not covering cultivar-specific gene expression. The accumulated RNA-Seq datasets from these cultivars can be leveraged to assemble tetraploid potato transcriptomes that enable the analysis of genes that are not limited to reference genome annotations. To increase transcriptomes’ quality, short-read assemblies are nowadays complemented with full-length transcriptome sequencing using Pacific Biosciences or Oxford Nanopore platforms. In this chapter we give a detailed guide on a pipeline for de novo transcriptome assembly of polyploid potato genotypes and their integration into a pan-transcriptome.

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Acknowledgments

The authors would like to thank the coworkers from the Department of Biotechnology and Systems Biology of the National Institute of Biology for providing raw RNA-Seq datasets, Henrik Krnec for BLAST output parser, and the Omics bioinformatics team for critical discussions. This project was supported by the Slovenian Research Agency (grants P4-0165, J4-1777, J4-4165, J4-7636, J4-8228, J4-9302, and Z7-1888), and COST actions CA15110 (CHARME) and CA15109 (COSTNET).

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Authors and Affiliations

  1. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Maja Zagorščak & Marko Petek

Authors
  1. Maja Zagorščak
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  2. Marko Petek
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Corresponding author

Correspondence to Maja Zagorščak .

Editor information

Editors and Affiliations

  1. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    David Dobnik

  2. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Kristina Gruden

  3. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Živa Ramšak

  4. Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

    Anna Coll

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Zagorščak, M., Petek, M. (2021). A Comprehensive Guide to Potato Transcriptome Assembly. In: Dobnik, D., Gruden, K., Ramšak, Ž., Coll, A. (eds) Solanum tuberosum. Methods in Molecular Biology, vol 2354. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1609-3_8

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  • DOI: https://doi.org/10.1007/978-1-0716-1609-3_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1608-6

  • Online ISBN: 978-1-0716-1609-3

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