A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist").
Rubus
Hi-C
Rosaceae
Rosoideae
annotation
annual flowering
biennial flowering
blackberry
chromosome-length genome assembly
primocane-fruiting
repetitive content
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
09 02 2023
09 02 2023
Historique:
received:
12
05
2022
accepted:
03
10
2022
pubmed:
5
11
2022
medline:
14
2
2023
entrez:
4
11
2022
Statut:
ppublish
Résumé
Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession "Hillquist" (R. argutus). "Hillquist" is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The "Hillquist" assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the "Hillquist" genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
Identifiants
pubmed: 36331334
pii: 6798616
doi: 10.1093/g3journal/jkac289
pmc: PMC9911083
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NHGRI NIH HHS
ID : UM1 HG009375
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : RM1 HG011016
Pays : United States
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.
Déclaration de conflit d'intérêts
Conflicts of interest None declared.
Références
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
PLoS Genet. 2012;8(3):e1002512
pubmed: 22457632
Plant Cell Physiol. 2007 Jun;48(6):822-32
pubmed: 17504813
Development. 2007 May;134(10):1931-41
pubmed: 17470967
Nat Commun. 2019 Apr 2;10(1):1494
pubmed: 30940818
Nat Genet. 2017 Jul;49(7):1099-1106
pubmed: 28581499
Plant Cell. 1997 Aug;9(8):1327-38
pubmed: 9286110
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811
pubmed: 30395283
EMBO J. 2007 Apr 4;26(7):1934-41
pubmed: 17363895
Curr Biol. 2012 Jun 19;22(12):1095-101
pubmed: 22608508
G3 (Bethesda). 2020 Jan 7;10(1):281-292
pubmed: 31732504
PLoS One. 2022 Mar 16;17(3):e0265096
pubmed: 35294470
Gigascience. 2018 Feb 1;7(2):1-7
pubmed: 29253147
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Hortic Res. 2018 Feb 7;5:8
pubmed: 29423238
Plant Biotechnol J. 2016 Sep;14(9):1852-61
pubmed: 26940366
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Nat Commun. 2020 Oct 12;11(1):5118
pubmed: 33046692
J Exp Bot. 2013 Apr;64(7):1837-48
pubmed: 23554259
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
Hortic Res. 2014 Jan 22;1:1
pubmed: 26504527
Front Plant Sci. 2019 Oct 25;10:1341
pubmed: 31708950
Plant Physiol. 2012 Jul;159(3):1043-54
pubmed: 22566495
Nat Genet. 2019 Mar;51(3):541-547
pubmed: 30804557
Plant J. 2011 Nov;68(4):681-92
pubmed: 21771123
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Front Plant Sci. 2019 Dec 20;10:1615
pubmed: 31921259
Bioinformatics. 2020 Dec 15;:
pubmed: 33320174
Brief Bioinform. 2021 Sep 2;22(5):
pubmed: 33822850
Nat Cell Biol. 2005 Dec;7(12):1256-60
pubmed: 16299497
BMC Bioinformatics. 2018 Nov 29;19(1):460
pubmed: 30497373
Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457
pubmed: 32300014
BMC Bioinformatics. 2008 Jan 14;9:18
pubmed: 18194517
Plant Physiol. 2009 Feb;149(2):1196-204
pubmed: 19091875
PLoS Genet. 2013;9(10):e1003861
pubmed: 24130508
Planta. 2012 Jun;235(6):1239-51
pubmed: 22203321
Nat Genet. 2018 Jun;50(6):772-777
pubmed: 29713014
Methods Mol Biol. 2019;1962:227-245
pubmed: 31020564
DNA Res. 2018 Feb 1;25(1):61-70
pubmed: 29036429
Tree Physiol. 2012 Oct;32(10):1288-301
pubmed: 23022687
Nat Genet. 2010 Oct;42(10):833-9
pubmed: 20802477
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
Plant J. 2021 Sep;107(5):1466-1477
pubmed: 34174125
Nucleic Acids Res. 2019 Jan 8;47(D1):D1137-D1145
pubmed: 30357347
BMC Bioinformatics. 2006 Feb 09;7:62
pubmed: 16469098
Bioinformatics. 2005 May 1;21(9):1859-75
pubmed: 15728110
Nucleic Acids Res. 2016 Jan 4;44(D1):D1167-71
pubmed: 26476447
Plant J. 2016 Sep;87(6):535-47
pubmed: 27228578
Front Plant Sci. 2018 Aug 21;9:1166
pubmed: 30186293
Plant J. 2011 Feb;65(3):418-29
pubmed: 21265895
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Gigascience. 2018 Aug 1;7(8):
pubmed: 30107523
Nat Genet. 2013 May;45(5):487-94
pubmed: 23525075
J Mol Biol. 2016 Feb 22;428(4):726-731
pubmed: 26585406
NAR Genom Bioinform. 2020 Jun;2(2):lqaa026
pubmed: 32440658
PLoS Comput Biol. 2018 Jan 26;14(1):e1005944
pubmed: 29373581
Nucleic Acids Res. 2014 Sep;42(15):e119
pubmed: 24990371
Plant Cell. 2008 Mar;20(3):568-79
pubmed: 18375658
Bioinformatics. 2001 Sep;17(9):847-8
pubmed: 11590104
Theor Appl Genet. 2013 Oct;126(10):2521-32
pubmed: 23856741
Nat Methods. 2016 Dec;13(12):1050-1054
pubmed: 27749838
Bioinformatics. 2011 Mar 15;27(6):863-4
pubmed: 21278185
Nat Protoc. 2020 Nov;15(11):3745-3776
pubmed: 33097925
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Mob DNA. 2019 Jan 03;10:1
pubmed: 30622655
Proc Natl Acad Sci U S A. 2016 May 24;113(21):6065-70
pubmed: 27114519
Nat Genet. 2011 Feb;43(2):109-16
pubmed: 21186353
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122
pubmed: 28460117
Hortic Res. 2021 Sep 1;8(1):197
pubmed: 34465760
Plant J. 2007 Dec;52(5):899-913
pubmed: 17908157
Genetics. 2007 Jun;176(2):1359-62
pubmed: 17579240