Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa.
Grape
Muscadine grape
Pangenome
Pierce’s disease
Transcriptome
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
20 Jul 2023
20 Jul 2023
Historique:
received:
04
04
2023
accepted:
13
07
2023
medline:
24
7
2023
pubmed:
21
7
2023
entrez:
20
7
2023
Statut:
epublish
Résumé
Muscadine grape (Vitis rotundifolia) is resistant to many of the pathogens that negatively impact the production of common grape (V. vinifera), including the bacterial pathogen Xylella fastidiosa subsp. fastidiosa (Xfsf), which causes Pierce's Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf, but the mechanism is unknown. We assembled and annotated a new, long-read genome assembly for 'Carlos', a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the 'Carlos' and common grape genomes indicates an expansion of resistance (R) genes in 'Carlos.' We further identified genes involved in Xfsf response by transcriptome sequencing 'Carlos' plants inoculated with Xfsf. We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf, we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome. Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf, within and between muscadine and common grape.
Sections du résumé
BACKGROUND
BACKGROUND
Muscadine grape (Vitis rotundifolia) is resistant to many of the pathogens that negatively impact the production of common grape (V. vinifera), including the bacterial pathogen Xylella fastidiosa subsp. fastidiosa (Xfsf), which causes Pierce's Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf, but the mechanism is unknown.
RESULTS
RESULTS
We assembled and annotated a new, long-read genome assembly for 'Carlos', a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the 'Carlos' and common grape genomes indicates an expansion of resistance (R) genes in 'Carlos.' We further identified genes involved in Xfsf response by transcriptome sequencing 'Carlos' plants inoculated with Xfsf. We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf, we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome.
CONCLUSIONS
CONCLUSIONS
Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf, within and between muscadine and common grape.
Identifiants
pubmed: 37474911
doi: 10.1186/s12864-023-09514-y
pii: 10.1186/s12864-023-09514-y
pmc: PMC10357881
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
409Subventions
Organisme : USDA-ARS
ID : 6062-21000-010-013
Organisme : USDA-ARS
ID : 6062-21000-010-000-D
Organisme : USDA-ARS
ID : 6062-21000-010-000-D
Organisme : USDA-ARS
ID : 6062-21000-010-000-D
Organisme : USDA-ARS
ID : 6062-21000-010-000-D
Organisme : USDA-ARS
ID : 6062-21000-010-000-D
Organisme : USDA-ARS
ID : 6062-21000-010-013
Informations de copyright
© 2023. The Author(s).
Références
Nature. 2007 Sep 27;449(7161):463-7
pubmed: 17721507
Genome Biol. 2019 Dec 16;20(1):277
pubmed: 31842948
Nat Genet. 2019 Jun;51(6):1044-1051
pubmed: 31086351
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Bioinformatics. 2022 May 13;38(10):2922-2926
pubmed: 35561173
3 Biotech. 2015 Apr;5(2):129-151
pubmed: 28324581
Theor Appl Genet. 2019 May;132(5):1571-1585
pubmed: 30756127
Methods Mol Biol. 2019;1962:1-14
pubmed: 31020551
Nat Plants. 2020 Aug;6(8):914-920
pubmed: 32690893
Front Plant Sci. 2019 May 08;10:583
pubmed: 31134119
Int J Mol Sci. 2022 Jan 19;23(3):
pubmed: 35163008
Science. 2021 Aug 6;373(6555):655-662
pubmed: 34353948
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Theor Appl Genet. 2019 Apr;132(4):1073-1087
pubmed: 30535509
Front Plant Sci. 2018 Jun 08;9:771
pubmed: 29937771
Theor Appl Genet. 2012 Dec;125(8):1663-75
pubmed: 22865124
J Proteomics Bioinform. 2015;8(9):217-224
pubmed: 27019567
Front Plant Sci. 2022 Mar 28;13:852130
pubmed: 35419015
Mol Ecol Resour. 2020 Mar;20(2):591-604
pubmed: 31628884
BMC Evol Biol. 2013 Jul 05;13:141
pubmed: 23826735
Mol Plant Microbe Interact. 2013 Jun;26(6):676-85
pubmed: 23441576
FASEB J. 2011 Oct;25(10):3290-305
pubmed: 21746866
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
BMC Bioinformatics. 2014 Jun 12;15:182
pubmed: 24925680
Curr Protein Pept Sci. 2017;18(4):323-334
pubmed: 27455971
Plant Dis. 2002 Oct;86(10):1056-1066
pubmed: 30818496
Front Plant Sci. 2017 Jul 04;8:1185
pubmed: 28725237
Appl Biochem Biotechnol. 2010 Mar;160(3):932-44
pubmed: 19412582
BMC Plant Biol. 2021 Aug 20;21(1):385
pubmed: 34416864
Sci Data. 2020 Nov 17;7(1):399
pubmed: 33203859
Mol Ecol Resour. 2022 May;22(4):1284-1302
pubmed: 34748273
Methods Mol Biol. 2019;1962:161-177
pubmed: 31020559
Commun Biol. 2023 May 30;6(1):580
pubmed: 37253933
Plant Cell. 2004 Jun;16(6):1604-15
pubmed: 15155877
PLoS Pathog. 2017 Nov 13;13(11):e1006724
pubmed: 29131851
Elife. 2022 Sep 09;11:
pubmed: 36083267
Anticancer Res. 2019 Aug;39(8):4043-4053
pubmed: 31366486
Genome Biol. 2021 Jan 4;22(1):3
pubmed: 33397434
Heliyon. 2019 Jan 16;5(1):e01128
pubmed: 30705983
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
G3 (Bethesda). 2022 Nov 4;12(11):
pubmed: 35904764
Methods Mol Biol. 2019;1962:227-245
pubmed: 31020564
Nat Methods. 2017 Nov;14(11):1072-1074
pubmed: 28945707
Sci Data. 2020 Apr 7;7(1):113
pubmed: 32265447
Food Nutr Res. 2017 Dec 10;61(1):1412795
pubmed: 29249924
Plant J. 2013 Nov;76(4):661-74
pubmed: 24033846
Hortic Res. 2022 Jan 18;:
pubmed: 35040982
Plant Cell Rep. 2020 Jul;39(7):839-849
pubmed: 32529484
Nat Genet. 2018 Feb;50(2):278-284
pubmed: 29335547
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Phytopathology. 2005 Jan;95(1):44-52
pubmed: 18943835
J Exp Bot. 2017 Jun 15;68(13):3287-3301
pubmed: 28472349
Biochem Biophys Res Commun. 2009 Feb 20;379(4):1038-42
pubmed: 19146828
Nucleic Acids Res. 2018 Jan 4;46(D1):D1197-D1201
pubmed: 29156057
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Gigascience. 2020 Sep 1;9(9):
pubmed: 32893860
Plant Cell. 2021 Jul 19;33(6):1888-1906
pubmed: 33710295
J Mol Biol. 2016 Feb 22;428(4):726-731
pubmed: 26585406
Nat Commun. 2018 Jan 26;9(1):390
pubmed: 29374171
Microbiol Resour Announc. 2020 Jun 18;9(25):
pubmed: 32554794
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genome Biol. 2019 Oct 28;20(1):224
pubmed: 31661016
Front Plant Sci. 2016 Jun 08;7:806
pubmed: 27375660
Genomics Proteomics Bioinformatics. 2019 Jun;17(3):305-310
pubmed: 31437583
G3 (Bethesda). 2021 Apr 15;11(4):
pubmed: 33824960
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
PeerJ Comput Sci. 2020 Jan 20;6:e251
pubmed: 33816903
Nucleic Acids Res. 2007;35(9):3100-8
pubmed: 17452365