The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs.
adaptation
chromosomal rearrangement
de novo genome assembly
domestication
speciation
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
02 06 2022
02 06 2022
Historique:
pubmed:
2
6
2022
medline:
10
6
2022
entrez:
1
6
2022
Statut:
ppublish
Résumé
It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks postzygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent postdivergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.
Identifiants
pubmed: 35642310
pii: 6596366
doi: 10.1093/molbev/msac110
pmc: PMC9178973
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
Références
Nat Commun. 2019 Oct 25;10(1):4872
pubmed: 31653862
PLoS Comput Biol. 2010 Dec 02;6(12):e1001025
pubmed: 21152010
Science. 2010 Jan 15;327(5963):302-5
pubmed: 20007865
Gigascience. 2020 Jun 1;9(6):
pubmed: 32543654
Chem Senses. 1999 Jun;24(3):301-16
pubmed: 10400449
Nucleic Acids Res. 2018 Jul 2;46(W1):W296-W303
pubmed: 29788355
Bioinformatics. 2006 May 15;22(10):1269-71
pubmed: 16543274
Hereditas. 1980;92(2):283-9
pubmed: 7390871
BMC Genomics. 2012 Nov 15;13:584
pubmed: 23153364
Curr Biol. 2014 Mar 31;24(7):R288-94
pubmed: 24698381
G3 (Bethesda). 2017 Jul 5;7(7):2171-2184
pubmed: 28500056
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Physiol Behav. 1980 Mar;24(3):601-5
pubmed: 7375580
Cell Syst. 2019 Jun 26;8(6):494-505.e14
pubmed: 31229558
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9
pubmed: 16845043
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:Unit 4.10
pubmed: 19274634
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7686-91
pubmed: 20404179
BMC Biol. 2019 Dec 30;17(1):108
pubmed: 31884969
Nat Genet. 2015 Oct;47(10):1141-8
pubmed: 26323058
Genome Biol Evol. 2017 Oct 1;9(10):2592-2603
pubmed: 29016799
Integr Comp Biol. 2010 Oct;50(4):515-27
pubmed: 21558220
Nat Plants. 2019 Aug;5(8):833-845
pubmed: 31383970
Bioinformatics. 2003 Jan 22;19(2):301-2
pubmed: 12538260
Bioinformatics. 2017 Jul 15;33(14):2202-2204
pubmed: 28369201
Nat Methods. 2012 Jul 30;9(8):772
pubmed: 22847109
Nat Commun. 2018 Jan 15;9(1):189
pubmed: 29335486
Methods Mol Biol. 2019;1962:65-95
pubmed: 31020555
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Cytogenet Genome Res. 2005;110(1-4):462-7
pubmed: 16093699
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
Bioinformatics. 2014 Jun 15;30(12):i319-i328
pubmed: 24932000
Chem Senses. 2010 Feb;35(2):121-33
pubmed: 20032112
Genome Res. 2004 Apr;14(4):708-15
pubmed: 15060014
Nat Struct Mol Biol. 2019 Mar;26(3):164-174
pubmed: 30778236
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Am Nat. 2000 Oct;156(4):390-415
pubmed: 29592141
BMC Genomics. 2015 Apr 22;16:330
pubmed: 25896665
Sci Rep. 2015 Nov 24;5:17118
pubmed: 26597053
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Annu Rev Genet. 2014;48:187-214
pubmed: 25421598
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Mol Ecol. 2016 May;25(10):2130-43
pubmed: 26923504
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Mol Ecol. 2014 Nov;23(22):5566-74
pubmed: 25294645
Zoo Biol. 2008 Jul;27(4):305-19
pubmed: 19360626
Nature. 2006 Aug 24;442(7105):934-8
pubmed: 16929298
Nucleic Acids Res. 2017 May 5;45(8):e57
pubmed: 28053114
Cytogenet Cell Genet. 1996;75(1):32-5
pubmed: 8995485
Brief Bioinform. 2011 Jan;12(1):41-51
pubmed: 21278375
Science. 2005 Mar 11;307(5715):1618-21
pubmed: 15761152
Trends Ecol Evol. 2009 Sep;24(9):487-96
pubmed: 19500875
Mol Ecol Resour. 2021 Oct;21(7):2455-2470
pubmed: 34097816
Mol Biol Evol. 2015 Mar;32(3):820-32
pubmed: 25540451
Mol Biol Evol. 2014 Feb;31(2):303-9
pubmed: 24202612
Genome Res. 2000 Apr;10(4):547-8
pubmed: 10779496
Genetica. 1991;83(3):189-94
pubmed: 1879688
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W720-4
pubmed: 16845106
Bioessays. 2008 May;30(5):470-9
pubmed: 18404703
Nature. 2012 Nov 15;491(7424):393-8
pubmed: 23151582
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Genome Biol. 2013;14(9):R107
pubmed: 24070215
Genome Biol. 2011 Nov 08;12(11):R112
pubmed: 22067484
Cytogenet Genome Res. 2010;129(4):305-9
pubmed: 20606389
Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):9045-50
pubmed: 27450087
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8
pubmed: 16381938
Nucleic Acids Res. 2019 Jun 20;47(11):e63
pubmed: 30864657
Genome Res. 2017 May;27(5):865-874
pubmed: 27646534
Nucleic Acids Res. 2014 Sep;42(15):e119
pubmed: 24990371
Cytogenetics. 1966;5(1):75-81
pubmed: 5958872
Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12
pubmed: 25348405
PLoS One. 2011;6(5):e20007
pubmed: 21625513
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Cytogenet Cell Genet. 1996;73(3):203-8
pubmed: 8697808
Gigascience. 2012 Nov 15;1(1):16
pubmed: 23587058
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Nat Genet. 2016 Jan;48(1):84-8
pubmed: 26569123
Nat Commun. 2014 Jul 15;5:4392
pubmed: 25025832
Toxicol Appl Pharmacol. 2013 Jul 15;270(2):149-57
pubmed: 23602889
Nat Commun. 2019 Apr 30;10(1):1992
pubmed: 31040280
Nat Genet. 2013 Dec;45(12):1431-8
pubmed: 24162736
Horm Behav. 2004 Sep;46(3):247-56
pubmed: 15325226
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12569-74
pubmed: 16891422
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Genome Res. 2016 Mar;26(3):342-50
pubmed: 26848124
Annu Rev Nutr. 2007;27:389-414
pubmed: 17444812