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Garg, V.* ; Bohra, A.* ; Mascher, M.* ; Spannagl, M. ; Xu, X.* ; Bevan, M.W.* ; Bennetzen, J.L.* ; Varshney, R.K.*

Unlocking plant genetics with telomere-to-telomere genome assemblies.

Nat. Genet., DOI: 10.1038/s41588-024-01830-7 (2024)
DOI PMC
Open Access Green as soon as Postprint is submitted to ZB.
Contiguous genome sequence assemblies will help us to realize the full potential of crop translational genomics. Recent advances in sequencing technologies, especially long-read sequencing strategies, have made it possible to construct gapless telomere-to-telomere (T2T) assemblies, thus offering novel insights into genome organization and function. Plant genomes pose unique challenges, such as a continuum of ancient to recent polyploidy and abundant highly similar and long repetitive elements. Owing to progress in sequencing approaches, for most crop plants, chromosome-scale reference genome assemblies are available, but T2T assembly construction remains challenging. Here we describe methods for haplotype-resolved, gapless T2T assembly construction in plants, including various crop species. We outline the impact of T2T assemblies in elucidating the roles of repetitive elements in gene regulation, as well as in pangenomics, functional genomics, genome-assisted breeding and targeted genome manipulation. In conjunction with sequence-enriched germplasm repositories, T2T assemblies thus hold great promise for basic and applied plant sciences.
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Publication type Article: Journal article
Document type Review
Corresponding Author
Keywords De-novo Domestication; Transposable Elements; Evolution; Crop; Sequence; Dna; Rearrangement; Improvement; Expression; Maize
ISSN (print) / ISBN 1061-4036
e-ISSN 1546-1718
Journal Nature Genetics
Publisher Nature Publishing Group
Publishing Place New York, NY
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)
Grants Hort Innovation
Grains Research & Development Corporation
Food Futures Institute (FFI) of Murdoch University