Choulet, F., Caccamo, M., Wright, J., Alaux, M., Šimková, H., Šafář, J., Leroy, P., Doležel, J., Rogers, J., Eversole, K., Feuillet, C.
Genomics of plant genetic resources : 405-438, 2014

Keywords: Wheat, Polyploid, Chromosome, Flowsorting, Physical map, Genome sequence, Next generation sequencing, Assembly, Annotation, Transposable elements, Database, Data integration
Abstract: Despite its socio-economic importance and the overall recognition that a reference genome sequence has great value for crop improvement, sequencing the wheat genome has long been considered “impossible” because of the sequencing cost and bioinformatic challenges associated with the assembly of the mostly repetitive 17 Gb hexaploid genome. In the past 5 years, however, new platforms and technologies have emerged that enabled the launching of an international effort to tackle the bread wheat genome sequence using a chromosome-by-chromosome approach. In this chapter, we review the features of the wheat genome as well as the tools and technologies that can be used to sequence, assemble, and annotate a large, complex, polyploid genome.We describe the strategies and current status of the efforts towards achieving a reference sequence for the 21 chromosomes of bread wheat. Finally, we present the databases that were established to support the integration of the sequence information with other genetic and biological information.
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IEB authors: Jaroslav Doležel, Jan Šafář, Hana Šimková