Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika (Ochotona princeps).
Lagomorpha
UV radiation
cold tolerance
comparative genomics
hypoxia
local adaptation
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
04 11 2022
04 11 2022
Historique:
received:
13
06
2022
accepted:
07
09
2022
pubmed:
11
9
2022
medline:
9
11
2022
entrez:
10
9
2022
Statut:
ppublish
Résumé
High-elevation environments have lower atmospheric oxygen content, reduced temperatures, and higher levels of UV radiation than found at lower elevations. As such, species living at high elevations must overcome these challenges to survive, grow, and reproduce. American pikas (Ochotona princeps) are alpine lagomorphs that are habitat specialists typically found at elevations >2,000 m. Previous research has shown putative evidence for high-elevation adaptation; however, investigations to date have been limited to a fraction of the genome. Here, we took a comparative genomics approach to identify putative regions under selection using a chromosomal reference genome assembly for the American pika relative to 8 other mammalian species targeted based on phylogenetic relatedness and (dis)similarity in ecology. We first identified orthologous gene groups across species and then extracted groups containing only American pika genes as well as unclustered pika genes to inform functional enrichment analyses; among these, we found 141 enriched terms with many related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. We identified 15 significantly expanded gene families within the American pika across all orthologous gene groups that displayed functionally enriched terms associated with hypoxia adaptation. We further detected 196 positively selected genes, 41 of which have been associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. In particular, OXNAD1, NRDC, and those genes critical in DNA repair represent important targets for future research to examine their functional implications in the American pika, especially as they may relate to adaptation to rapidly changing environments.
Identifiants
pubmed: 36087005
pii: 6695220
doi: 10.1093/g3journal/jkac241
pmc: PMC9635661
pii:
doi:
Types de publication
Review
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 Genetics Society of America.
Références
Front Genet. 2020 Feb 14;10:1404
pubmed: 32117428
Biochim Biophys Acta. 2013 Dec;1834(12):2750-60
pubmed: 24140568
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
BMC Res Notes. 2013 Apr 22;6:160
pubmed: 23607317
Can J Zool. 1974 Mar;52(3):353-8
pubmed: 4819475
Bioinformatics. 2011 Feb 1;27(3):431-2
pubmed: 21149340
Syst Biol. 2007 Aug;56(4):564-77
pubmed: 17654362
Natl Sci Rev. 2020 Jan;7(1):113-127
pubmed: 34692022
J Anim Ecol. 2022 Jun;91(6):1180-1195
pubmed: 34716929
Ecol Appl. 2010 Jan;20(1):164-78
pubmed: 20349838
Sci Rep. 2019 Feb 26;9(1):2753
pubmed: 30808882
Cell. 1999 Mar 5;96(5):645-53
pubmed: 10089880
Front Physiol. 2019 Jan 11;9:1916
pubmed: 30687126
Expert Opin Biol Ther. 2007 Sep;7(9):1437-47
pubmed: 17727332
Comput Struct Biotechnol J. 2019 Nov 17;18:9-19
pubmed: 31890139
Acta Cir Bras. 2012 Nov;27(11):773-82
pubmed: 23117609
J Proteomics. 2019 Jun 15;201:27-36
pubmed: 30954612
Mar Biotechnol (NY). 2015 Oct;17(5):576-92
pubmed: 26017776
Genes Dev. 2010 Sep 1;24(17):1939-50
pubmed: 20810650
Comp Biochem Physiol A Mol Integr Physiol. 2020 Apr;242:110653
pubmed: 31926299
BMC Genomics. 2013 May 10;14:311
pubmed: 23663654
Mol Ecol. 2011 Nov;20(21):4503-20
pubmed: 21980951
Mol Biol Evol. 2021 Sep 27;38(10):4268-4285
pubmed: 34021753
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Mol Biol Evol. 2007 Jan;24(1):26-53
pubmed: 17047029
Comp Biochem Physiol Part D Genomics Proteomics. 2011 Dec;6(4):370-81
pubmed: 21885357
BMC Evol Biol. 2015 Jun 02;15:101
pubmed: 26031664
Mol Biol Evol. 2020 Jun 1;37(6):1577-1592
pubmed: 32027372
BMC Evol Biol. 2008 Nov 26;8:321
pubmed: 19036132
Nucleic Acids Res. 2008 Jun;36(10):3420-35
pubmed: 18445632
BMC Evol Biol. 2018 Dec 7;18(1):187
pubmed: 30526493
J Hered. 2021 Nov 1;112(6):549-557
pubmed: 34036348
Life (Basel). 2021 Sep 13;11(9):
pubmed: 34575108
EMBO J. 2011 Nov 16;30(22):4554-70
pubmed: 21915097
Mar Genomics. 2016 Feb;25:95-102
pubmed: 26683592
Sci Rep. 2018 Jun 14;8(1):9113
pubmed: 29904092
Animals (Basel). 2021 Sep 28;11(10):
pubmed: 34679854
Mol Biol Rep. 2019 Jun;46(3):2857-2866
pubmed: 30982215
Heredity (Edinb). 2012 Apr;108(4):354-61
pubmed: 21934702
Int J Mol Sci. 2020 Oct 01;21(19):
pubmed: 33019598
Am J Hum Biol. 2000 Mar;12(2):214-220
pubmed: 11534018
Mar Biotechnol (NY). 2014 Jun;16(3):277-88
pubmed: 24091821
Horm Behav. 2022 Jun;142:105179
pubmed: 35477059
PLoS One. 2010 Mar 12;5(3):e9644
pubmed: 20300197
J Exp Biol. 2006 Jun;209(Pt 12):2328-36
pubmed: 16731809
Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):E10634-E10641
pubmed: 30348757
Genome Res. 2005 Aug;15(8):1153-60
pubmed: 16077014
Comp Biochem Physiol B Biochem Mol Biol. 2016 Aug;198:10-8
pubmed: 26969108
Mol Ecol Resour. 2021 Apr;21(3):641-652
pubmed: 33326691
Heredity (Edinb). 2021 Nov;127(5):443-454
pubmed: 34537819
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
pubmed: 16845082
Biochem Biophys Res Commun. 2004 Apr 2;316(2):565-72
pubmed: 15020255
Microbiol Res. 2021 Jun;247:126730
pubmed: 33662850
J Exp Zool A Ecol Genet Physiol. 2009 Feb 1;311(2):134-41
pubmed: 19048601
Semin Cell Dev Biol. 2005 Aug-Oct;16(4-5):462-73
pubmed: 15916908
FASEB J. 2019 Jul;33(7):7929-7941
pubmed: 30917010
Arch Insect Biochem Physiol. 2011 Nov;78(3):161-75
pubmed: 22006535
Am J Physiol Lung Cell Mol Physiol. 2020 Sep 1;319(3):L456-L470
pubmed: 32639867
J Biol Chem. 2010 Mar 19;285(12):8595-604
pubmed: 20061386
Nat Rev Mol Cell Biol. 2020 May;21(5):268-283
pubmed: 32144406
Sci Total Environ. 2017 May 15;586:890-899
pubmed: 28215807
Syst Biol. 2012 May;61(3):539-42
pubmed: 22357727
Nat Commun. 2014;5:3224
pubmed: 24492630
Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:Unit 6.12.1-19
pubmed: 21901743
Nucleic Acids Res. 2003 Jan 1;31(1):365-70
pubmed: 12520024
J Exp Biol. 2019 Mar 7;222(Pt 5):
pubmed: 30692167
Genetics. 2007 Nov;177(3):1941-9
pubmed: 17947411
Sci Rep. 2019 Jun 13;9(1):8592
pubmed: 31197188
Am J Bot. 2014 May;101(5):796-802
pubmed: 24748608
Science. 2011 Oct 28;334(6055):521-4
pubmed: 21940861
Biol Rev Camb Philos Soc. 2005 Nov;80(4):589-610
pubmed: 16221331
Mol Ecol. 2018 Jun;27(11):2512-2528
pubmed: 29693300
Bioinformatics. 2005 Aug 15;21(16):3448-9
pubmed: 15972284
Mol Biol Evol. 2021 Sep 27;38(10):4286-4300
pubmed: 34037784
Proc Natl Acad Sci U S A. 2018 Aug 14;115(33):8406-8411
pubmed: 30065117
Mol Cell. 2011 Oct 21;44(2):235-51
pubmed: 21963239
PeerJ. 2021 Jul 21;9:e11776
pubmed: 34327056
BMC Bioinformatics. 2004 Aug 19;5:113
pubmed: 15318951
Comp Biochem Physiol Part D Genomics Proteomics. 2021 Sep;39:100860
pubmed: 34126312
Mil Med. 2013 Nov;178(11):1256-63
pubmed: 24183776
Nat Genet. 2012 Jul 01;44(8):946-9
pubmed: 22751099
Exp Mol Med. 2020 Oct;52(10):1705-1714
pubmed: 33122806
PLoS One. 2020 Oct 12;15(10):e0240435
pubmed: 33044983
Cell Rep. 2017 Apr 4;19(1):162-174
pubmed: 28380355
Mol Biol Evol. 2021 Jun 25;38(7):3022-3027
pubmed: 33892491
Physiol Genomics. 2018 Aug 1;50(8):636-647
pubmed: 29799804
Bioinformatics. 2006 May 15;22(10):1269-71
pubmed: 16543274
Am J Hum Genet. 2014 Oct 2;95(4):394-407
pubmed: 25262650
Arch Insect Biochem Physiol. 2021 May;107(1):e21781
pubmed: 33687102
Mol Biol Evol. 2016 Oct;33(10):2576-92
pubmed: 27401233
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32559296
Cancer Treat Rev. 2010 Nov;36(7):518-27
pubmed: 20413225
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Gen Comp Endocrinol. 2011 Feb 1;170(3):604-12
pubmed: 21130089
PLoS One. 2018 Dec 12;13(12):e0207936
pubmed: 30540800
PeerJ. 2013 Sep 17;1:e167
pubmed: 24109552
Front Bioinform. 2021 Apr 01;1:638255
pubmed: 36303779
Genes (Basel). 2022 Feb 01;13(2):
pubmed: 35205335
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Cryobiology. 2019 Jun;88:54-63
pubmed: 30946844
Ann N Y Acad Sci. 2020 Sep;1476(1):5-22
pubmed: 30259990
Glob Chang Biol. 2016 Apr;22(4):1572-84
pubmed: 26667878
Evolution. 2009 Nov;63(11):2848-63
pubmed: 19663994
PLoS One. 2021 Feb 8;16(2):e0245494
pubmed: 33556109