A Reference Genome Assembly of American Bison, Bison bison bison.
Genome resources
bovine
interspecies hybrid
nanopore sequencing
trio binning
Journal
The Journal of heredity
ISSN: 1465-7333
Titre abrégé: J Hered
Pays: United States
ID NLM: 0375373
Informations de publication
Date de publication:
29 03 2021
29 03 2021
Historique:
received:
21
11
2020
accepted:
13
01
2021
pubmed:
18
2
2021
medline:
21
10
2021
entrez:
17
2
2021
Statut:
ppublish
Résumé
Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
Identifiants
pubmed: 33595645
pii: 6141414
doi: 10.1093/jhered/esab003
pmc: PMC8006816
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
Pagination
174-183Subventions
Organisme : NHGRI NIH HHS
ID : T32 HG008345
Pays : United States
Informations de copyright
© The American Genetic Association. 2021.
Références
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Am J Vet Res. 1967 Sep;28(126):1319-25
pubmed: 6053538
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
J Hered. 2007 Jan-Feb;98(1):1-12
pubmed: 17172633
Nature. 2011 Nov 02;479(7373):359-64
pubmed: 22048313
PLoS One. 2012;7(12):e52210
pubmed: 23284938
Science. 2004 Nov 26;306(5701):1561-5
pubmed: 15567864
Nature. 2021 Apr;592(7856):737-746
pubmed: 33911273
Nat Rev Genet. 2018 Apr;19(4):220-234
pubmed: 29335644
J Anim Sci. 2016 Nov;94(11):4491-4497
pubmed: 27898962
Nat Methods. 2020 Feb;17(2):155-158
pubmed: 31819265
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Conserv Biol. 2008 Apr;22(2):252-66
pubmed: 18402580
J Hered. 2013 Jul-Aug;104(4):500-9
pubmed: 23667052
BMC Genomics. 2017 Jul 12;18(1):527
pubmed: 28701198
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Bioinformatics. 2020 Dec 15;:
pubmed: 33320174
J Hered. 2009 Jul-Aug;100(4):411-20
pubmed: 19414501
Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):3457-3462
pubmed: 28289222
Genome Biol. 2020 Sep 14;21(1):245
pubmed: 32928274
Nat Ecol Evol. 2018 Jul;2(7):1139-1145
pubmed: 29784979
Q Rev Biol. 1970 Mar;45(1):1-15
pubmed: 5446770
Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8057-63
pubmed: 27274051
Mol Ecol. 2008 Dec;17(23):4963-77
pubmed: 19017265
Elife. 2014 Jun 04;3:
pubmed: 24898754
Environ Manage. 2019 Nov;64(5):553-563
pubmed: 31578626
Sci Rep. 2019 Nov 12;9(1):16637
pubmed: 31719547
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Genome Biol. 2014 Jun 26;15(6):R84
pubmed: 24970577
Nat Biotechnol. 2019 Oct;37(10):1155-1162
pubmed: 31406327
J Hered. 2021 Mar 29;112(2):184-191
pubmed: 33438035
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Commun Biol. 2018 Oct 19;1:169
pubmed: 30374461
Nat Biotechnol. 2018 Oct 22;:
pubmed: 30346939
PLoS One. 2019 Jul 10;14(7):e0218899
pubmed: 31291291
PeerJ. 2018 Jun 4;6:e4958
pubmed: 29888139
Nat Commun. 2020 Apr 29;11(1):2071
pubmed: 32350247
Bioinformatics. 2020 May 1;36(9):2896-2898
pubmed: 31971576
Nat Biotechnol. 2018 Apr;36(4):338-345
pubmed: 29431738
Mol Biol Evol. 2016 Nov;33(11):2801-2814
pubmed: 27436010
Anim Genet. 2001 Apr;32(2):89-91
pubmed: 11421943
Nat Commun. 2019 Apr 16;10(1):1784
pubmed: 30992455
Nat Methods. 2015 Aug;12(8):733-5
pubmed: 26076426
PLoS Genet. 2017 Jan 3;13(1):e1006529
pubmed: 28045893
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
BMC Biol. 2016 Oct 21;14(1):93
pubmed: 27769298
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Gigascience. 2020 Apr 1;9(4):
pubmed: 32242610
Trends Biotechnol. 2019 Sep;37(9):973-982
pubmed: 30902345
Gigascience. 2020 Mar 1;9(3):
pubmed: 32191811
Nat Genet. 2017 Apr;49(4):643-650
pubmed: 28263316