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Unlocking plant genetics with telomere-to-telomere genome assemblies

Nature Genetics volume 56, pages 1788–1799 (2024)Cite this article

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Abstract

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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Fig. 1: Overview of different strategies for developing T2T genome assemblies.
Fig. 2: Applications of T2T genome assemblies for crop improvement.

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Acknowledgements

R.K.V. acknowledges financial support from the Food Futures Institute (FFI) of Murdoch University, as well as the Grains Research & Development Corporation and Hort Innovation supporting research projects on development of genome assemblies in wheat (UMU2404-003RTX, WSU2303-001RTX), legume (UMU2403-009RTX, UMU2303-003RTX) and horticultural crops (AS21006, AS23003). We thank the Pawsey Supercomputing Research Centre for the use of its computing resources in developing genome assemblies at the Centre for Crop & Food Innovation, Murdoch University.

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Authors and Affiliations

  1. WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia

    Vanika Garg, Abhishek Bohra, Manuel Spannagl, Xun Xu & Rajeev K. Varshney

  2. ICAR-Indian Institute of Pulses Research, Kanpur, India

    Abhishek Bohra

  3. Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Seeland, Germany

    Martin Mascher

  4. Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany

    Manuel Spannagl

  5. BGI-Shenzhen, Shenzhen, China

    Xun Xu

  6. John Innes Centre, Norwich, UK

    Michael W. Bevan

  7. Department of Genetics, University of Georgia, Athens, GA, USA

    Jeffrey L. Bennetzen

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  1. Vanika Garg
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  8. Rajeev K. Varshney
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Contributions

R.K.V. conceptualized the idea. V.G. and A.B. developed the first draft with inputs from M.M., M.S., X.X., M.W.B., J.L.B. and R.K.V. V.G., A.B., M.M., J.L.B. and R.K.V. revised the manuscript. V.G. created the schematics for the original figures. All authors read and approved the final manuscript.

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Correspondence to Rajeev K. Varshney.

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Nature Genetics thanks Roberto Tuberosa and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Garg, V., Bohra, A., Mascher, M. et al. Unlocking plant genetics with telomere-to-telomere genome assemblies. Nat Genet 56, 1788–1799 (2024). https://doi.org/10.1038/s41588-024-01830-7

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