Comparative Genomic Analysis of Warthog and Sus Scrofa Identifies Adaptive Genes Associated with African Swine Fever.
African swine fever
Kenyan domestic pig
genome assembly
lactate dehydrogenase B
warthog
Journal
Biology
ISSN: 2079-7737
Titre abrégé: Biology (Basel)
Pays: Switzerland
ID NLM: 101587988
Informations de publication
Date de publication:
14 Jul 2023
14 Jul 2023
Historique:
received:
24
05
2023
revised:
01
07
2023
accepted:
12
07
2023
medline:
29
7
2023
pubmed:
29
7
2023
entrez:
29
7
2023
Statut:
epublish
Résumé
As warthogs ( Here, we present two completed new genomes of one warthog and one Kenyan domestic pig as fundamental genomic references to elucidate the genetic mechanisms of ASF tolerance. Multiple genomic variations, including gene losses, independent contraction, and the expansion of specific gene families, likely molded the warthog genome to adapt to the environment. Importantly, the analysis of the presence and absence of genomic sequences revealed that the DNA sequence of the warthog genome had an absence of the gene lactate dehydrogenase B ( Our results will help improve the understanding of genetic resistance to ASF in pigs.
Sections du résumé
BACKGROUND
BACKGROUND
As warthogs (
METHODS
METHODS
Here, we present two completed new genomes of one warthog and one Kenyan domestic pig as fundamental genomic references to elucidate the genetic mechanisms of ASF tolerance.
RESULTS
RESULTS
Multiple genomic variations, including gene losses, independent contraction, and the expansion of specific gene families, likely molded the warthog genome to adapt to the environment. Importantly, the analysis of the presence and absence of genomic sequences revealed that the DNA sequence of the warthog genome had an absence of the gene lactate dehydrogenase B (
CONCLUSION
CONCLUSIONS
Our results will help improve the understanding of genetic resistance to ASF in pigs.
Identifiants
pubmed: 37508430
pii: biology12071001
doi: 10.3390/biology12071001
pmc: PMC10376286
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : National Key Research and Development Program of China
ID : 2021YFD1200801
Organisme : National Natural Science Foundation of China
ID : 31661143013
Organisme : National Natural Science Foundation of China
ID : 31972563
Organisme : Beijing Municipal Science and Technology Commission
ID : Z211100004621005
Organisme : Earmarked Fund for China Agriculture Research System
ID : No. CARS-36-05B
Références
Nature. 2021 May;593(7857):37
pubmed: 33947991
J Clin Invest. 2017 Mar 1;127(3):987-1004
pubmed: 28192372
Emerg Microbes Infect. 2022 Dec;11(1):2021-2033
pubmed: 35912875
J Biol Chem. 1998 Feb 27;273(9):5405-11
pubmed: 9479002
Science. 2011 Feb 4;331(6017):540-2
pubmed: 21292958
Autophagy. 2021 Sep;17(9):2305-2324
pubmed: 32924761
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811
pubmed: 30395283
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Am J Hum Genet. 2015 Sep 3;97(3):389-403
pubmed: 26279205
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
BMC Bioinformatics. 2015 Jul 25;16:230
pubmed: 26209068
Sci Rep. 2017 Apr 24;7:46747
pubmed: 28436458
Nucleic Acids Res. 2008 Apr;36(7):2284-94
pubmed: 18287116
Anim Genet. 2015 Aug;46(4):433-6
pubmed: 26011180
Brief Bioinform. 2007 Nov;8(6):382-92
pubmed: 17932080
Nat Biotechnol. 2015 Jun;33(6):623-30
pubmed: 26006009
Mol Biol Evol. 2022 Dec 5;39(12):
pubmed: 36413509
Transbound Emerg Dis. 2018 Dec;65(6):1482-1484
pubmed: 30102848
PLoS One. 2018 Jan 22;13(1):e0190080
pubmed: 29357367
Bull Epizoot Dis Afr. 1969 Jun;17(2):179-83
pubmed: 5386390
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Sci Data. 2019 Oct 1;6(1):188
pubmed: 31575853
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Int J Mol Sci. 2022 May 26;23(11):
pubmed: 35682650
J Biol Chem. 2018 Oct 12;293(41):15947-15961
pubmed: 30158244
Nucleic Acids Res. 2005 Nov 28;33(20):6494-506
pubmed: 16314312
Gigascience. 2018 May 1;7(5):
pubmed: 29790964
Philos Trans R Soc Lond B Biol Sci. 2015 Mar 5;370(1663):20140064
pubmed: 25602068
Eur J Immunol. 2008 Mar;38(3):619-30
pubmed: 18286572
Front Microbiol. 2020 Jun 04;11:1203
pubmed: 32655518
J Thorac Dis. 2018 Jul;10(7):4387-4395
pubmed: 30174887
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Oncogene. 2013 Feb 7;32(6):747-58
pubmed: 22450746
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259
pubmed: 30931475
Am J Hum Genet. 2011 Jan 7;88(1):76-82
pubmed: 21167468
Nucleic Acids Res. 2021 Jan 8;49(D1):D545-D551
pubmed: 33125081
Bioinformatics. 2016 Jun 15;32(12):1895-7
pubmed: 27153702
BMC Genomics. 2014 Sep 26;15:816
pubmed: 25260959
Sci Immunol. 2019 Oct 25;4(40):
pubmed: 31653718
Bioinformatics. 2008 Nov 1;24(21):2438-44
pubmed: 18728043
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
Nat Genet. 2014 Aug;46(8):919-25
pubmed: 24952747
Sci China Life Sci. 2020 May;63(5):623-634
pubmed: 32124180
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Comput Appl Biosci. 1997 Oct;13(5):555-6
pubmed: 9367129
Gigascience. 2019 Jan 1;8(1):
pubmed: 30576505
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Gigascience. 2020 Sep 1;9(9):
pubmed: 32893860
NAR Genom Bioinform. 2020 Jun;2(2):lqaa026
pubmed: 32440658
Annu Rev Anim Biosci. 2016;4:61-85
pubmed: 26526544
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Prev Vet Med. 2013 Jun 1;110(2):198-205
pubmed: 23219357
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W465-7
pubmed: 15980513
Sci Rep. 2016 Jan 05;6:18501
pubmed: 26729041
Bioinformatics. 2006 May 15;22(10):1269-71
pubmed: 16543274
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Compr Physiol. 2018 Mar 26;8(2):555-583
pubmed: 29687889
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Gene. 2003 Jul 17;312:207-13
pubmed: 12909357
Vaccines (Basel). 2020 Dec 14;8(4):
pubmed: 33327488
PLoS Pathog. 2008 Feb 8;4(2):e16
pubmed: 18248090
J Anim Sci Biotechnol. 2020 Jan 17;11:10
pubmed: 31969983
J Virol. 2013 Jan;87(1):257-72
pubmed: 23077300
Brief Bioinform. 2008 Jul;9(4):299-306
pubmed: 18417537
J Anim Sci. 2018 Jun 4;96(6):2074-2085
pubmed: 29669012
EMBO J. 2001 May 1;20(9):2140-51
pubmed: 11331580
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Syst Biol. 2010 May;59(3):307-21
pubmed: 20525638