Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves higher resolution for research and breeding

Aury, J.-M.; Engelen, S.; Istace, B.; Monat, C.; Lasserre-Zuber, P.; Belser, C.; Cruaud, C.; Rimbert, H.; Leroy, P.; Arribat, S.; Dufau, I.; Bellec, A.; Grimbichler, D.; Papon, N.; Paux, E.; Ranoux, M.; Alberti, A.; Wincker, P.; Choulet, F.

doi:10.1101/2021.08.24.457458

bioRxiv · 10.1101/2021.08.24.457458

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves higher resolution for research and breeding

Aury, J.-M.·Engelen, S.·Istace, B.·Monat, C.·Lasserre-Zuber, P.·Belser, C.·Cruaud, C.·Rimbert, H.·Leroy, P.·Arribat, S.·Dufau, I.·Bellec, A.·Grimbichler, D.·Papon, N.·Paux, E.·Ranoux, M.·Alberti, A.·Wincker, P.·Choulet, F.

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Abstract

The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years due to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost. Here, we report on an optimized procedure based on long-reads produced on the ONT (Oxford Nanopore Technology) PromethION device to assemble the genome of the French bread wheat cultivar Renan. We provide the most contiguous and complete chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-Seq data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

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Aury, J.-M., Engelen, S., Istace, B., Monat, C., Lasserre-Zuber, P., Belser, C., Cruaud, C., Rimbert, H., Leroy, P., Arribat, S., Dufau, I., Bellec, A., Grimbichler, D., Papon, N., Paux, E., Ranoux, M., Alberti, A., Wincker, P., Choulet, F.. 2021-08-24. Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves higher resolution for research and breeding. https://doi.org/10.1101/2021.08.24.457458

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