Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety.
chromosome-scale
elite potato variety
genome divergence
intragenomic diversity
reference sequence
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
08 12 2021
08 12 2021
Historique:
received:
31
05
2021
accepted:
08
09
2021
pubmed:
18
9
2021
medline:
8
1
2022
entrez:
17
9
2021
Statut:
ppublish
Résumé
Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The objectives of this study were (1) to create a high-quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (2) to evaluate the new assembly's usefulness for various genomic methods; and (3) to assess the performance of phasing in diploid and tetraploid clones, using linked-read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.
Identifiants
pubmed: 34534288
pii: 6371871
doi: 10.1093/g3journal/jkab330
pmc: PMC8664475
pii:
doi:
Banques de données
figshare
['10.6084/m9.figshare.14604780']
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) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
Références
Gigascience. 2020 Jan 1;9(1):
pubmed: 31919520
Nucleic Acids Res. 2010 Dec;38(22):e199
pubmed: 20880995
Front Plant Sci. 2019 May 29;10:670
pubmed: 31191581
Nat Genet. 2019 Mar;51(3):374-378
pubmed: 30643248
Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14694-9
pubmed: 16203994
Genomics. 2017 Jul;109(3-4):186-191
pubmed: 28286147
Genome Biol. 2020 Aug 3;21(1):189
pubmed: 32746918
PLoS One. 2013 May 08;8(5):e62355
pubmed: 23667470
Nat Plants. 2017 Sep;3(9):696-703
pubmed: 28827752
Nat Protoc. 2016 Jan;11(1):1-9
pubmed: 26633127
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811
pubmed: 30395283
Nat Commun. 2019 Jan 16;10(1):260
pubmed: 30651564
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Curr Opin Plant Biol. 2017 Apr;36:64-70
pubmed: 28231512
Bioinformatics. 2018 Mar 1;34(5):725-731
pubmed: 29069293
Plant Cell. 2015 Apr;27(4):954-68
pubmed: 25873387
Biotechniques. 2016 Oct 1;61(4):203-205
pubmed: 27712583
Genome Res. 2018 Feb 9;:
pubmed: 29440222
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
BMC Genomics. 2017 Jul 12;18(1):527
pubmed: 28701198
Int J Mol Sci. 2021 Feb 11;22(4):
pubmed: 33670420
Bioinformatics. 2010 Mar 1;26(5):589-95
pubmed: 20080505
Commun Biol. 2020 Feb 18;3(1):78
pubmed: 32071408
G3 (Bethesda). 2016 Aug 09;6(8):2617-28
pubmed: 27342736
Philos Trans R Soc Lond B Biol Sci. 2010 Jan 12;365(1537):61-71
pubmed: 20008386
Plant Cell. 2016 Jul;28(7):1510-20
pubmed: 27335450
Curr Protoc Bioinformatics. 2014 Dec 12;48:4.11.1-39
pubmed: 25501943
Nucleic Acids Res. 2016 Nov 2;44(19):e147
pubmed: 27458204
Genome Biol. 2015 Aug 21;16:170
pubmed: 26294115
Nat Genet. 2020 Oct;52(10):1018-1023
pubmed: 32989320
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Ann Hum Genet. 2020 Mar;84(2):125-140
pubmed: 31711268
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
BMC Bioinformatics. 2018 Nov 29;19(1):460
pubmed: 30497373
G3 (Bethesda). 2013 Nov 06;3(11):2031-47
pubmed: 24062527
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Genome Biol. 2018 Mar 23;19(1):40
pubmed: 29571299
G3 (Bethesda). 2020 Oct 5;10(10):3489-3495
pubmed: 32759330
Nature. 2018 Nov;563(7732):501-507
pubmed: 30429615
Nat Biotechnol. 2016 Mar;34(3):303-11
pubmed: 26829319
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Nat Commun. 2019 Jan 2;10(1):4
pubmed: 30602775
Sci Rep. 2020 Oct 7;10(1):15980
pubmed: 33028920
PLoS Comput Biol. 2018 Jan 26;14(1):e1005944
pubmed: 29373581
Plant Sci. 2019 Oct;287:110207
pubmed: 31481198
Gigascience. 2020 Apr 1;9(4):
pubmed: 32236524
Gigascience. 2015 Aug 04;4:35
pubmed: 26244089
Nucleic Acids Res. 2016 Jul 8;44(12):e113
pubmed: 27131372
Genome Biol. 2020 Sep 21;21(1):252
pubmed: 32951599
Nat Plants. 2017 Sep;3(9):742-748
pubmed: 28848243
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Nat Methods. 2016 Dec;13(12):1050-1054
pubmed: 27749838
Nat Commun. 2016 Jun 24;7:11706
pubmed: 27339290
Nature. 2011 Jul 10;475(7355):189-95
pubmed: 21743474
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Front Plant Sci. 2018 Mar 07;9:159
pubmed: 29563919
Plant J. 2018 May;94(3):562-570
pubmed: 29405524
Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9999-E10008
pubmed: 29087343
Gigascience. 2020 Sep 23;9(9):
pubmed: 32964225
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
BMC Bioinformatics. 2018 Oct 26;19(1):393
pubmed: 30367597
Sci Data. 2020 Mar 11;7(1):88
pubmed: 32161269
BMC Bioinformatics. 2004 May 14;5:59
pubmed: 15144565