A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison).
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
16 12 2022
16 12 2022
Historique:
received:
13
06
2022
accepted:
05
12
2022
entrez:
16
12
2022
pubmed:
17
12
2022
medline:
21
12
2022
Statut:
epublish
Résumé
Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.
Identifiants
pubmed: 36526733
doi: 10.1038/s42003-022-04341-5
pii: 10.1038/s42003-022-04341-5
pmc: PMC9757699
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1381Informations de copyright
© 2022. The Author(s).
Références
Gene. 2012 Dec 10;511(1):66-72
pubmed: 22982743
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
J Hered. 2021 Nov 1;112(6):549-557
pubmed: 34036348
Front Genet. 2020 Apr 02;11:231
pubmed: 32300354
Gigascience. 2018 Jan 1;7(1):1-6
pubmed: 29220494
Nat Methods. 2021 Feb;18(2):170-175
pubmed: 33526886
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
pubmed: 11917018
Genome Res. 2020 Sep;30(9):1291-1305
pubmed: 32801147
Nat Commun. 2019 Jan 16;10(1):260
pubmed: 30651564
BMC Genet. 2017 Jan 26;18(1):7
pubmed: 28122512
Mol Ecol. 2004 Feb;13(2):483-90
pubmed: 14717902
Int J Plant Genomics. 2008;2008:619832
pubmed: 18483572
Genome Biol. 2016 Oct 11;17(1):211
pubmed: 27802837
PLoS Genet. 2020 Oct 22;16(10):e1008926
pubmed: 33090996
BMC Biol. 2020 Jan 8;18(1):3
pubmed: 31915011
Methods Mol Biol. 2020;2117:65-78
pubmed: 31960372
J Anim Sci. 2018 Jun 29;96(7):2596-2606
pubmed: 29726960
BMC Genet. 2018 Nov 12;19(1):103
pubmed: 30419805
Bioinformatics. 2006 Jan 15;22(2):134-41
pubmed: 16287941
Sci Data. 2020 Jun 19;7(1):187
pubmed: 32561793
Genome Biol. 2020 Sep 24;21(1):253
pubmed: 32972461
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Front Genet. 2020 Mar 13;11:223
pubmed: 32231688
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63
pubmed: 24259432
Conserv Biol. 2018 Dec;32(6):1301-1312
pubmed: 29935028
Nat Rev Genet. 2011 Jun;12(6):443-51
pubmed: 21587300
Genome Biol. 2020 Jun 2;21(1):129
pubmed: 32487205
Genes (Basel). 2021 Feb 11;12(2):
pubmed: 33670138
Mol Biol Evol. 2021 Sep 27;38(10):4647-4654
pubmed: 34320186
Animals (Basel). 2021 Jan 12;11(1):
pubmed: 33445704
PLoS Genet. 2013 Nov;9(11):e1003942
pubmed: 24244198
Front Vet Sci. 2015 Sep 08;2:29
pubmed: 26664958
Lancet Infect Dis. 2021 Jan;21(1):18-19
pubmed: 33227234
Emerg Infect Dis. 2021 Feb;27(2):547-551
pubmed: 33207152
Nat Biotechnol. 2019 May;37(5):540-546
pubmed: 30936562
Gigascience. 2020 Dec 21;9(12):
pubmed: 33347571
Genomics. 2009 Sep;94(3):204-10
pubmed: 19520153
Sci Rep. 2017 Nov 6;7(1):14564
pubmed: 29109430
Mol Phylogenet Evol. 2009 Sep;52(3):632-42
pubmed: 19501660
Gigascience. 2017 Oct 1;6(10):1-16
pubmed: 29020750
Proc Natl Acad Sci U S A. 2020 May 26;117(21):11727-11734
pubmed: 32376634
Genome Biol. 2020 Jun 18;21(1):148
pubmed: 32552806
Mob DNA. 2018 Nov 10;9:32
pubmed: 30455747
Sci Data. 2019 Sep 30;6(1):187
pubmed: 31570724
BMC Biol. 2008 Feb 14;6:10
pubmed: 18275614
Mol Ecol. 2014 Apr;23(8):2072-92
pubmed: 24629132
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
PLoS Pathog. 2021 Nov 12;17(11):e1009952
pubmed: 34767598
Front Microbiol. 2021 Sep 20;12:675528
pubmed: 34616371
Nat Methods. 2020 Feb;17(2):155-158
pubmed: 31819265
Eur J Med Res. 2021 May 20;26(1):46
pubmed: 34016183
Future Oncol. 2020 Sep;16(27):2029-2033
pubmed: 32658591
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Annu Rev Anim Biosci. 2017 Feb 8;5:309-327
pubmed: 27860491
PLoS Comput Biol. 2020 Jun 26;16(6):e1007981
pubmed: 32589667
Nature. 2013 Jul 25;499(7459):471-5
pubmed: 23823723
PLoS One. 2016 Jun 22;11(6):e0157972
pubmed: 27333328
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Am J Med Genet. 1989 Mar;32(3):325-9
pubmed: 2543222
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Front Microbiol. 2021 Apr 01;12:663815
pubmed: 33868218
BMC Genomics. 2017 Jun 29;18(1):495
pubmed: 28662691
Nat Genet. 2017 Apr;49(4):643-650
pubmed: 28263316
Nature. 2011 Jul 13;475(7357):493-6
pubmed: 21753753
Anim Genet. 2014 Feb;45(1):105-10
pubmed: 24303917
J Anim Ecol. 2017 Sep;86(5):1179-1191
pubmed: 28609555
Sci Rep. 2021 Feb 3;11(1):2944
pubmed: 33536540
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500