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Book Sections Year : 2024

Structural and Functional Annotation of the Wheat Genome

Xi Wang
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  • PersonId : 1312530
Manuel Spannagl
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  • PersonId : 1312531
David Swarbreck
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  • PersonId : 1312532

Abstract

Wheat genome sequencing has passed through major steps in a decade, starting from the sequencing of large contiguous sequences obtained from chromosome-specific BAC libraries, to reach high-quality genome assemblies of a dozen of bread wheat varieties and wild relatives. While access to an assembled genome sequence is crucial for research, the resource that is mainly used by the community is not the sequence itself, but rather the annotated features, i.e., genes and transposable elements. In this chapter, we describe the work performed to predict the repertoire of 107 k high-confidence genes and 4 million TE copies in the hexaploid wheat genome (cultivar CHINESE SPRING; IWGSC RefSeq) and the procedures established to transfer the annotation through the different releases of genome assembly. Limitations and implications for building a wheat pangenome are discussed, as well as the possibilities for future improvements of structural annotation, and opportunities offered by novel approaches for functional annotation.
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hal-04297331 , version 1 (21-11-2023)

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Frédéric Choulet, Xi Wang, Manuel Spannagl, David Swarbreck, Hélène Rimbert, et al.. Structural and Functional Annotation of the Wheat Genome. Rudi Appels, Kellye Eversole, Catherine Feuillet, Dusti Gallagher. The Wheat Genome, Springer International Publishing, pp.51-73, 2024, Compendium of Plant Genomes, ⟨10.1007/978-3-031-38294-9_4⟩. ⟨hal-04297331⟩
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