A cattle graph genome incorporating global breed diversity.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
17 02 2022
17 02 2022
Historique:
received:
29
10
2020
accepted:
20
01
2022
entrez:
18
2
2022
pubmed:
19
2
2022
medline:
4
3
2022
Statut:
epublish
Résumé
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.
Identifiants
pubmed: 35177600
doi: 10.1038/s41467-022-28605-0
pii: 10.1038/s41467-022-28605-0
pmc: PMC8854726
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
910Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/T019468/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/D/10002070
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R015155/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/P024025/1
Pays : United Kingdom
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2022. The Author(s).
Références
Sci Rep. 2015 Dec 07;5:17875
pubmed: 26639839
Data Brief. 2018 May 10;19:236-239
pubmed: 29892639
Nat Commun. 2012;3:1202
pubmed: 23149746
Genome Res. 2017 May;27(5):737-746
pubmed: 28100585
Genome Res. 2018 Nov;28(11):1720-1732
pubmed: 30341161
Nat Commun. 2020 Dec 10;11(1):6327
pubmed: 33303762
Mob DNA. 2018 May 1;9:15
pubmed: 29743957
Nat Biotechnol. 2018 Oct 22;:
pubmed: 30346939
Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2757-61
pubmed: 8146187
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Sci Rep. 2017 Feb 24;7:43169
pubmed: 28233799
Bioinformatics. 2018 Jul 1;34(13):i142-i150
pubmed: 29949969
Bioinformatics. 2015 Oct 15;31(20):3350-2
pubmed: 26099265
Nat Commun. 2019 Jan 16;10(1):260
pubmed: 30651564
Bioinformatics. 2012 Sep 15;28(18):i333-i339
pubmed: 22962449
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9
pubmed: 16845043
Sci Rep. 2015 Nov 25;5:16923
pubmed: 26603754
Parasite. 2018;25:44
pubmed: 30117802
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Genome Biol. 2018 Dec 17;19(1):220
pubmed: 30558649
Bioinformatics. 2013 May 15;29(10):1341-2
pubmed: 23505295
BMC Genomics. 2017 Oct 18;18(1):799
pubmed: 29047335
PLoS Comput Biol. 2019 Feb 19;15(2):e1006731
pubmed: 30779737
Vet Immunol Immunopathol. 1987 Dec;17(1-4):125-34
pubmed: 2963429
J Comput Biol. 2006 Jun;13(5):1028-40
pubmed: 16796549
Bioinformatics. 2006 Jan 15;22(2):134-41
pubmed: 16287941
Genet Sel Evol. 2017 Sep 18;49(1):68
pubmed: 28923017
Nucleic Acids Res. 2016 Nov 2;44(19):e147
pubmed: 27458204
Genome Biol. 2020 Jul 27;21(1):184
pubmed: 32718320
Genome Biol. 2020 Sep 14;21(1):245
pubmed: 32928274
Gigascience. 2020 Jun 1;9(6):
pubmed: 32543654
Genet Sel Evol. 2019 May 15;51(1):21
pubmed: 31092189
Nat Biotechnol. 2018 Oct;36(9):875-879
pubmed: 30125266
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
PLoS Genet. 2019 Jul 26;15(7):e1008302
pubmed: 31348818
Genome Biol. 2020 Feb 12;21(1):35
pubmed: 32051000
Proc Natl Acad Sci U S A. 2021 May 18;118(20):
pubmed: 33972446
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
PLoS Comput Biol. 2021 Sep 27;17(9):e1009444
pubmed: 34570769
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
Genome Biol. 2017 Feb 20;18(1):34
pubmed: 28219390
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
G3 (Bethesda). 2020 Apr 9;10(4):1361-1374
pubmed: 32071071
Nature. 2020 Nov;587(7833):246-251
pubmed: 33177663
Gigascience. 2019 Jan 1;8(1):
pubmed: 30576505
Bioinformatics. 2021 Jan 29;36(21):5139-5144
pubmed: 33040146
Evol Appl. 2018 Jul 23;12(1):123-136
pubmed: 30622640
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Genome Biol. 2020 May 25;21(1):124
pubmed: 32450900
PLoS One. 2012;7(2):e31002
pubmed: 22319599
F1000Res. 2018 Sep 3;7:1391
pubmed: 30613392
Nat Commun. 2020 Sep 21;11(1):4739
pubmed: 32958756
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
Nat Methods. 2016 Dec;13(12):1050-1054
pubmed: 27749838
Nat Methods. 2017 Oct;14(10):959-962
pubmed: 28846090
Nat Genet. 2019 Jan;51(1):30-35
pubmed: 30455414
BMC Genomics. 2017 Jun 29;18(1):495
pubmed: 28662691
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842
Mol Biol Evol. 2018 Mar 1;35(3):543-548
pubmed: 29220515
Gigascience. 2020 Mar 1;9(3):
pubmed: 32191811
Nat Genet. 2017 Apr;49(4):643-650
pubmed: 28263316