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

Abstract

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.

A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance

“…Few outliers were however identified, namely East Asian accessions in Group 2, and African accessions in Group 3. For a better interpretation of the observed genetic diversity within the LandracePLUS panel, wheat accessions with high-quality genome sequences, namely the 10+ wheat reference genomes (25,36), Fielder (40) and Renan (41) were included in the analysis with 27,016 out of the 29,556 SNPs that mapped unambiguously to chromosomes of these genomes. Most of the high-quality sequenced genomes clustered in Group 2 of the LandracePLUS panel, while Norin61 and Chinese Spring were on the edge of Group 4 (Fig 2A).…”

Wheat Omics: Advancements and Opportunities

“…In the past decade, several reference genomes sequences have been released for wheat, including durum wheat ( Triticum turgidum ssp. durum ;) [ 35 , 36 ] bread wheat ( T. aestivum ) [ 9 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 ] and its progenitor species including wild emmer ( T. turgidum spp. dicoccoides ) [ 35 ] wild goatgrass ( Aegilops tauschii ) [ 45 , 46 , 47 ] and T. urartu [ 48 ].…”

All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity

“…We thus compared the fully assembled sequences of the A genomes, the B genomes, and also the D genomes between di-, tetra-, and hexaploids: T. urartu (AA; Ling et al, 2013), Ae. tauschii (DD; Jia et al, 2013), T. dicoccoides (AABB; Avni et al, 2017), T. durum (AABB; Maccaferri et al, 2019), and 13 T. aestivum (AABBDD; Aury et al, 2022;IWGSC, 2018;Walkowiak et al, 2020). The evolutionary time scale studied here is thus limited to the recent evolution corresponding to the early stages of TE turnover: 0.01 million year (Myr) for comparisons within hexaploids and between T. durum and T. aestivum, ∼0.8 Myr between T. dicoccoides and T. aestivum, and 1.3 Myr for T. urartu which diverged from the A genome donor ∼0.5 Myr before tetraploidization.…”

“…ipk-gatersleben.de/ (Walkowiak et al, 2020). We also used the Renan genome sequence that we published previously (GCA_937894285) (Aury et al, 2022), and that of Tibetan wheat Zang1817 (Guo et al, 2020).…”