Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding.
genome assembly
haplotype characterization
hexaploid genome
introgressions
long-reads
nanopore sequencing
wheat
Journal
GigaScience
ISSN: 2047-217X
Titre abrégé: Gigascience
Pays: United States
ID NLM: 101596872
Informations de publication
Date de publication:
28 04 2022
28 04 2022
Historique:
received:
27
09
2021
revised:
17
12
2021
accepted:
15
03
2022
entrez:
28
4
2022
pubmed:
29
4
2022
medline:
3
5
2022
Statut:
ppublish
Résumé
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. 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. 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.
Sections du résumé
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.
Identifiants
pubmed: 35482491
pii: 6575388
doi: 10.1093/gigascience/giac034
pmc: PMC9049114
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press GigaScience.
Références
Gigascience. 2020 Dec 15;9(12):
pubmed: 33319909
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
Gigascience. 2020 Dec 15;9(12):
pubmed: 33319912
PeerJ. 2020 Nov 05;8:e10150
pubmed: 33194395
Genome Res. 2017 May;27(5):737-746
pubmed: 28100585
Nat Genet. 2021 Apr;53(4):574-584
pubmed: 33737755
Bioinformatics. 2020 Aug 1;36(15):4350-4352
pubmed: 32637988
Commun Biol. 2020 Nov 25;3(1):712
pubmed: 33239669
Bioinformatics. 2005 May 1;21(9):1859-75
pubmed: 15728110
Science. 2007 Jun 29;316(5833):1862-6
pubmed: 17600208
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14330-5
pubmed: 18794528
Gigascience. 2022 Apr 28;11:
pubmed: 35482491
Genome Res. 2017 May;27(5):885-896
pubmed: 28420692
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
Nature. 2020 Dec;588(7837):277-283
pubmed: 33239791
Genomics Proteomics Bioinformatics. 2020 Jun;18(3):221-229
pubmed: 32561470
Proc Biol Sci. 2012 Dec 22;279(1749):5048-57
pubmed: 22977152
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Commun Biol. 2021 Sep 7;4(1):1047
pubmed: 34493830
Genome Biol. 2020 Sep 14;21(1):245
pubmed: 32928274
Genome Biol. 2015 Jan 31;16:26
pubmed: 25637298
Sci Data. 2020 Nov 17;7(1):399
pubmed: 33203859
Front Genet. 2020 Aug 18;11:891
pubmed: 33014014
Front Plant Sci. 2020 Mar 06;11:252
pubmed: 32211007
Nature. 2020 Sep;585(7823):79-84
pubmed: 32663838
Bioinformatics. 2018 Mar 1;34(5):867-868
pubmed: 29096012
Nat Biotechnol. 2019 May;37(5):540-546
pubmed: 30936562
Science. 2014 Jul 18;345(6194):1250092
pubmed: 25035499
Front Plant Sci. 2012 Jan 31;3:5
pubmed: 22645565
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
NAR Genom Bioinform. 2021 May 03;3(2):lqab034
pubmed: 33987534
Genome Biol. 2020 Sep 17;21(1):249
pubmed: 32943081
Genome Biol. 2020 May 20;21(1):121
pubmed: 32434565
Science. 2018 Aug 17;361(6403):
pubmed: 30115783
Plant Physiol. 2016 Aug;171(4):2294-316
pubmed: 27288366
Nucleic Acids Res. 2019 Dec 2;47(21):10994-11006
pubmed: 31584084
Sci Data. 2017 Aug 01;4:170093
pubmed: 28763055
Genome Res. 2002 Apr;12(4):656-64
pubmed: 11932250
Nat Methods. 2020 Feb;17(2):155-158
pubmed: 31819265
Nat Commun. 2020 Jan 7;11(1):17
pubmed: 31911615
Gigascience. 2017 Nov 1;6(11):1-7
pubmed: 29069494
Genome Biol. 2019 Jun 24;20(1):129
pubmed: 31234903
Genome Biol. 2014;15(12):546
pubmed: 25476263
Genome Res. 2011 Jun;21(6):974-84
pubmed: 21324876
Front Plant Sci. 2018 May 23;9:673
pubmed: 29875781
Genome Biol. 2018 Aug 17;19(1):103
pubmed: 30115100
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nat Plants. 2018 Nov;4(11):879-887
pubmed: 30390080
PLoS One. 2018 Jan 2;13(1):e0186329
pubmed: 29293495
Biology (Basel). 2021 Jul 30;10(8):
pubmed: 34439964
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
PeerJ Comput Sci. 2020 Jan 20;6:e251
pubmed: 33816903
Plant J. 2021 Jul;107(1):303-314
pubmed: 33893684
Science. 2008 Apr 25;320(5875):486-8
pubmed: 18436778