Genomic insights into the host specific adaptation of the Pneumocystis genus.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
08 03 2021
08 03 2021
Historique:
received:
17
09
2020
accepted:
04
02
2021
entrez:
9
3
2021
pubmed:
10
3
2021
medline:
10
8
2021
Statut:
epublish
Résumé
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.
Identifiants
pubmed: 33686174
doi: 10.1038/s42003-021-01799-7
pii: 10.1038/s42003-021-01799-7
pmc: PMC7940399
doi:
Substances chimiques
Fungal Proteins
0
Types de publication
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
305Subventions
Organisme : BLRD VA
ID : I01 BX004441
Pays : United States
Organisme : BLRD VA
ID : IK6 BX005232
Pays : United States
Organisme : NIH HHS
ID : P51 OD011104
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL146266
Pays : United States
Références
mBio. 2012 Dec 26;4(1):e00428-12
pubmed: 23269827
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Mol Biol Evol. 2017 Mar 1;34(3):772-773
pubmed: 28013191
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Nat Protoc. 2016 Sep;11(9):1650-67
pubmed: 27560171
J Eukaryot Microbiol. 2003;50 Suppl:624-6
pubmed: 14736188
Infect Immun. 1990 Jun;58(6):1705-10
pubmed: 2160429
Mob DNA. 2015 Jun 02;6:11
pubmed: 26045719
BMC Genomics. 2015;16 Suppl 10:S10
pubmed: 26450642
Genetics. 2013 Nov;195(3):979-92
pubmed: 23979584
Bioinformatics. 2008 Jul 1;24(13):1538-9
pubmed: 18474506
Proc Assoc Am Physicians. 1999 Jul-Aug;111(4):347-56
pubmed: 10417743
PLoS Biol. 2019 Dec 4;17(12):e3000494
pubmed: 31800571
J Mol Evol. 1985;22(2):160-74
pubmed: 3934395
Bioinformatics. 2010 May 1;26(9):1145-51
pubmed: 20208069
Bioinformatics. 2005 May 1;21(9):1846-52
pubmed: 15691858
mBio. 2018 May 8;9(3):
pubmed: 29739910
Nat Methods. 2018 Jun;15(6):461-468
pubmed: 29713083
BMC Bioinformatics. 2019 Apr 15;20(1):184
pubmed: 30987585
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
J Clin Microbiol. 2002 May;40(5):1862-5
pubmed: 11980979
Genome Biol Evol. 2016 Aug 25;8(8):2340-50
pubmed: 27412607
Nucleic Acids Res. 2018 Mar 16;46(5):2699
pubmed: 29425356
Nature. 2005 Feb 17;433(7027):733-6
pubmed: 15716951
PLoS One. 2010 Jun 25;5(6):e11147
pubmed: 20593022
Genome Biol Evol. 2014 Apr;6(4):861-72
pubmed: 24682155
Nat Commun. 2016 Feb 22;7:10740
pubmed: 26899007
J Infect Dis. 1997 Mar;175(3):655-60
pubmed: 9041338
BMC Bioinformatics. 2011 Dec 22;12:491
pubmed: 22192575
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Mycologia. 2004 May-Jun;96(3):429-38
pubmed: 21148866
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
PLoS Biol. 2006 May;4(5):e88
pubmed: 16683862
J Eukaryot Microbiol. 2001;Suppl:113S-115S
pubmed: 11906016
Mol Biol Evol. 2006 Feb;23(2):254-67
pubmed: 16221896
Mol Biol Evol. 2008 Jul;25(7):1307-20
pubmed: 18367465
Metallomics. 2017 Mar 22;9(3):215-227
pubmed: 28217776
Bioinformatics. 2012 Oct 1;28(19):2520-2
pubmed: 22908215
Mol Microbiol. 1996 Jan;19(2):273-81
pubmed: 8825773
Infect Genet Evol. 2019 Nov;75:103934
pubmed: 31247340
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Genome Res. 2017 May;27(5):737-746
pubmed: 28100585
Infect Genet Evol. 2008 Sep;8(5):708-26
pubmed: 18565802
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
BMC Bioinformatics. 2013 Oct 02;14:289
pubmed: 24088262
Parasitology. 2018 Jun;145(7):885-900
pubmed: 29117878
Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25
pubmed: 14534192
Nucleic Acids Res. 2014 Apr;42(7):e59
pubmed: 24493737
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Syst Biol. 2012 Dec 1;61(6):1061-7
pubmed: 22780991
Bioinformatics. 2012 Sep 15;28(18):i409-i415
pubmed: 22962460
PLoS Comput Biol. 2014 Apr 10;10(4):e1003537
pubmed: 24722319
Bioinformatics. 2019 Nov 1;35(21):4453-4455
pubmed: 31070718
Bioinformatics. 2010 Aug 1;26(15):1897-8
pubmed: 20576622
Nat Rev Genet. 2010 Jan;11(1):47-59
pubmed: 19997068
Bioinformatics. 2007 May 1;23(9):1061-7
pubmed: 17332020
BMC Bioinformatics. 2017 Nov 21;18(1):507
pubmed: 29162056
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Nat Biotechnol. 2019 Apr;37(4):420-423
pubmed: 30778233
Bioinformatics. 2000 Feb;16(2):130-4
pubmed: 10842734
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Mol Biol Evol. 2018 Oct 1;35(10):2582-2584
pubmed: 30165589
Infect Immun. 1993 Jul;61(7):2886-90
pubmed: 8514391
Genome Res. 2004 Jun;14(6):1188-90
pubmed: 15173120
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Sci Adv. 2020 Nov 4;6(45):
pubmed: 33148650
PLoS One. 2015 Oct 02;10(10):e0139225
pubmed: 26431199
mBio. 2013 Apr 30;4(3):e00055-13
pubmed: 23631913
BMC Bioinformatics. 2008 Sep 23;9:392
pubmed: 18811934
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Genome Res. 2008 Dec;18(12):1979-90
pubmed: 18757608
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Nucleic Acids Res. 2009 Jul;37(13):4322-30
pubmed: 19454603
Genome Biol. 2007;8(10):R223
pubmed: 17949488
Mol Genet Genomics. 2010 Jan;283(1):63-72
pubmed: 19921262
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
mBio. 2017 Nov 7;8(6):
pubmed: 29114024
Mol Phylogenet Evol. 2014 Sep;78:386-98
pubmed: 24792086
Genetics. 2006 Apr;172(4):2665-81
pubmed: 16489234
Mol Biol Evol. 2005 Dec;22(12):2472-9
pubmed: 16107592
J Mol Biol. 2004 Mar 19;337(2):243-53
pubmed: 15003443
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
BMC Bioinformatics. 2014 Nov 25;15:356
pubmed: 25420514
Syst Biol. 2015 May;64(3):369-83
pubmed: 25398445
Curr Protoc Bioinformatics. 2014 Sep 08;47:11.12.1-34
pubmed: 25199790
Nucleic Acids Res. 2003 Nov 15;31(22):6633-9
pubmed: 14602924
Bioinformatics. 2010 Aug 1;26(15):1910-2
pubmed: 20551134
BMC Evol Biol. 2015 Sep 15;15:187
pubmed: 26373638
J Theor Biol. 2008 Aug 21;253(4):769-78
pubmed: 18538793
FASEB J. 2013 May;27(5):1962-72
pubmed: 23392351
PLoS One. 2014 Nov 19;9(11):e112963
pubmed: 25409509
mBio. 2020 Mar 3;11(2):
pubmed: 32127451
J Eukaryot Microbiol. 2006;53 Suppl 1:S89-91
pubmed: 17169080
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
Methods Mol Biol. 2014;1079:105-16
pubmed: 24170397
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Mol Phylogenet Evol. 2018 Nov;128:98-111
pubmed: 30030180
PLoS One. 2010 Dec 20;5(12):e15152
pubmed: 21188143
PLoS One. 2007 Apr 18;2(4):e384
pubmed: 17440620
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Sci Rep. 2019 Mar 5;9(1):3514
pubmed: 30837676
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Bioinformatics. 2002 Mar;18(3):492-3
pubmed: 11934753
Genome Biol. 2015 Aug 06;16:157
pubmed: 26243257
BMC Bioinformatics. 2004 May 14;5:59
pubmed: 15144565
PLoS Comput Biol. 2014 Oct 30;10(10):e1003929
pubmed: 25356683