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Strategies for Sequencing and Assembling Grapevine Genomes

  • Rosa Figueroa-Balderas
  • Andrea Minio
  • Abraham Morales-Cruz
  • Amanda M. Vondras
  • Dario CantuEmail author
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Though grape transcriptomics has expanded dramatically over the last ten years, few additional novel genomic resources were developed since the release of the PN40024 reference genome in 2007. This is partly because of the difficulty associated with assembling grape genomes. Despite a relatively small genome size of ~500 Mb and modest repeat content, high sequence and structural heterozygosity makes assembling grape genomes particularly challenging. Without assemblies representative of the genetic diversity within the cultivated germplasm, identifying cultivar-specific functions not represented in the PN40024 genome has remained elusive. Now, third-generation sequencing technologies and long-range scaffolding methods have made it possible to relatively inexpensively and rapidly generate highly contiguous and complete grape genomes. This chapter will describe the challenges associated with the isolation of high-quality nucleic acids suitable for long-read sequencing and provide an overview of the sequencing and assembling approaches that can be used to successfully reconstruct grape genomes.

Keywords

Genome assembling Sequencing technologies Grapevine nucleic acid isolation 

Notes

Acknowledgements

This work was supported by J. Lohr Vineyards and Wines, E. & J. Gallo Winery, Dolce Winery, the Louis P. Martini Endowment in Viticulture, and the NSF Grant #1741627. Part of this work was carried out in collaboration with UC Davis Chile and funded by the Chilean Economic Development Agency (CORFO).

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Rosa Figueroa-Balderas
    • 1
  • Andrea Minio
    • 1
  • Abraham Morales-Cruz
    • 1
  • Amanda M. Vondras
    • 1
  • Dario Cantu
    • 1
    Email author
  1. 1.Department of Viticulture and EnologyUniversity of California DavisDavisUSA

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