[DOI] 10.5524/102205 [Title] Supporting data for "Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding" [Release Date] 2022-03-15 [Citation] Aury, J; 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 (2022): Supporting data for "Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding" GigaScience Database. http://dx.doi.org/10.5524/102205 [Data Type] Genomic,Transcriptomic [Dataset Summary] 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 whole genome 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 chromosome-scale assembly of a bread wheat genome to date, a resource that will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide the methodological standards to generate high-quality assemblies of complex genomes. [File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/102205/ [File name] - [File Description] TaeRenan_refseq_v2.1.stats - Metrics of Triticum aestivum Renan genome assembly TaeRenan.cds.fasta - Coding sequence of Triticum aestivum Renan TaeRenan.gff - Annotation of Triticum aestivum Renan TaeRenan.pep.fasta - Protein sequence of Triticum aestivum Renan haplotypic_map.tar.gz - Scripts and alignment files of Triticum aestivum Chinese Spring and Triticum aestivum Renan (BED format) used to generate haplotypic maps shown in the manuscript renan_prediction_full_table.tsv - BUSCO output of Triticum aestivum Renan. Gene Prediction - Full table output renan_prediction_missing_busco_list.tsv - BUSCO output of Triticum aestivum Renan. Gene Prediction - Missing BUSCO output ChineseSpring_merqury.qv - Merqury Quality Value file for Chinese Spring Renan_genes_merqury.qv - Merqury Quality Value file for Renan genes Renan_merqury.qv - Merqury Quality Value file for Renan TaeRenan_refseq_v2.1_clariTE.gff3.gz - Annotation of Triticum aestivum Renan transposable elements readme_102205.txt - None Renan-associated-data-main.zip - Archival copy of the GitHub repository https://github.com/institut-de-genomique/Renan-associated-data downloaded 24-Feb-2022. Renan-associated-data - all data and scripts used to produce the main figures as well as the haplotypic blocks and graphical visualisations in the accompanying manuscript. This project is licensed under the GPL-3.0 license. Please refer to the GitHub repo for most recent updates. TaeRenan_refseq_v2.1.fa - Genome assembly of of Triticum aestivum Renan chinese_spring_short_summary.txt - BUSCO output of Triticum aestivum Chinese Spring. Genome Assembly - Short summary output chinese_spring_full_table.tsv - BUSCO output of Triticum aestivum Chinese Spring. Genome Assembly - Full table output chinese_spring_missing_busco_list.tsv - BUSCO output of Triticum aestivum Chinese Spring. Genome Assembly - Missing BUSCO output renan_short_summary.txt - BUSCO output of Triticum aestivum Renan. Genome Assembly - Short summary output renan_full_table.tsv - BUSCO output of Triticum aestivum Renan. Genome Assembly - Full table output renan_missing_busco_list.tsv - BUSCO output of Triticum aestivum Renan. Genome Assembly - Missing BUSCO output chinese_spring_prediction_short_summary.txt - BUSCO output of Triticum aestivum Chinese Spring. Gene Prediction - Short summary output chinese_spring_prediction_full_table.tsv - BUSCO output of Triticum aestivum Chinese Spring. Gene Prediction - Full table output chinese_spring_prediction_missing_busco_list.tsv - BUSCO output of Triticum aestivum Chinese Spring. Gene Prediction - Missing BUSCO output renan_prediction_short_summary.txt - BUSCO output of Triticum aestivum Renan. Gene Prediction - Short summary output [License] All files and data are distributed under the Creative Commons Attribution-CC0 License unless specifically stated otherwise, see http://gigadb.org/site/term for more details. [Comments] [End]