A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3B - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Conference Papers Year : 2012

A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3B

Michael M. Alaux
Hadi Quesneville
Patrick Wincker

Abstract

Because of an extra-large (17 Gb) hexaploid genome, wheat genomics has been lagging behind the one of the other major crops. Despite the major increases of sequencing throughput made these last years, short read length limits our ability to assemble a reference wheat genome sequence using whole genome shotgun approaches. To overcome these limitations, the International Wheat Genome Sequencing Consortium established a strategy aiming at reducing the genome complexity, first, by sorting chromosomes individually and, then, by building BAC-based physical maps of individual chromosomes. Following the establishment of the first physical map of a wheat chromosome, the 3B (1 Gb), we have undertaken its complete sequencing by combining Roche/454 8 kb long paired-end sequencing of 8500 BACs following an optimized pooling strategy, with a whole 3B shotgun Illumina sequencing. A specific workflow was established in order to increase scaffolding accuracy of 454 contigs and to use Illumina reads for gap filling and homopolymer error correction in the objective of getting a high quality reference pseudomolecule. This enables direct application in gene cloning, marker development and genomics breeding. It also allows us to study the organization, composition and evolution of a giant polyploid genome at a scale never reached before.

Domains

Vegetal Biology
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Dates and versions

hal-02809032 , version 1 (06-06-2020)

Identifiers

  • HAL Id : hal-02809032 , version 1
  • PRODINRA : 308443

Cite

Frédéric Choulet, Sébastien Theil, Josquin Daron, Natasha Marie Glover, Nicolas N. Guilhot, et al.. A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3B. TGAC/ESF-LESC workshop, Strategies for de novo assemblies of complex crop genomes, Genome Analysis Centre (TGAC). Norwich, GBR., Oct 2012, Norwich, United Kingdom. ⟨hal-02809032⟩
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