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

Jean-Marc Aury (1) , Stefan Engelen (1) , Benjamin Istace (1) , Cécile Monat (2) , Pauline Lasserre-Zuber (2) , Caroline Belser (1) , Corinne Cruaud (3) , Hélène Rimbert (2) , Philippe Leroy (2) , Sandrine Arribat (4) , Isabelle Dufau (4) , Arnaud Bellec (4) , David Grimbichler (5) , Nathan Papon (2) , Etienne Paux (2) , Marion Ranoux (2) , Adriana A. Alberti (6) , Patrick Wincker (6) , Frédéric Choulet (2)

1 LBGB - Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
2 GDEC - Génétique Diversité et Ecophysiologie des Céréales
3 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
4 CNRGV - Centre National de Ressources Génomiques Végétales
5 Mésocentre Clermont Auvergne
6 UMR 8030 - Génomique métabolique

Background:The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing 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. Results: Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan. Conclusions: We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing 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.

Keywords: introgressions; long-reads; nanopore sequencing; wheat; genome assembly; haplotype characterization; hexaploid genome; introgressions

Domains: Life Sciences [q-bio]; Vegetal Biology; Cellular Biology; Plants genetics

Jean-Marc Aury, Stefan Engelen, Benjamin Istace, Cécile Monat, Pauline Lasserre-Zuber, et al.. Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. GigaScience, 2022, 11, pp.1-18. ⟨10.1093/gigascience/giac034⟩. ⟨hal-03658639⟩