Detecting sex-linked genes using genotyped individuals sampled in natural populations.
genetics of sex
hierarchical model
population genomics
probabilistic inference
sex chromosomes
Journal
Genetics
ISSN: 1943-2631
Titre abrégé: Genetics
Pays: United States
ID NLM: 0374636
Informations de publication
Date de publication:
24 06 2021
24 06 2021
Historique:
received:
04
02
2021
accepted:
21
03
2021
pubmed:
26
3
2021
medline:
22
2
2022
entrez:
25
3
2021
Statut:
ppublish
Résumé
We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans) and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.
Identifiants
pubmed: 33764439
pii: 6187941
doi: 10.1093/genetics/iyab053
pmc: PMC8225351
pii:
doi:
Banques de données
figshare
['10.25386/genetics.13704310']
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) 2021. Published by Oxford University Press on behalf of Genetics Society of America. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Références
Annu Rev Plant Biol. 2016 Apr 29;67:397-420
pubmed: 26653795
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6453-8
pubmed: 23547111
BMC Genomics. 2013 Apr 23;14:273
pubmed: 23617698
Nature. 2005 Mar 17;434(7031):325-37
pubmed: 15772651
Genetics. 2013 Jul;194(3):663-72
pubmed: 23733787
Nature. 2014 Apr 24;508(7497):488-93
pubmed: 24759410
Genetics. 1985 Jun;110(2):325-44
pubmed: 4007484
Genetics. 2014 Jun;197(2):531-41
pubmed: 24578352
PLoS Biol. 2013;11(8):e1001643
pubmed: 24015111
Genes (Basel). 2020 May 31;11(6):
pubmed: 32486434
BMC Plant Biol. 2014 Sep 03;14:229
pubmed: 25179565
Mol Biol Evol. 2021 Mar 9;38(3):805-818
pubmed: 32926156
Mol Biol Evol. 2017 May 1;34(5):1140-1154
pubmed: 28158772
Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13710-5
pubmed: 22869747
Heredity (Edinb). 2008 Jan;100(1):92-9
pubmed: 18000521
Nat Commun. 2018 Sep 28;9(1):3969
pubmed: 30266991
Annu Rev Genomics Hum Genet. 2012;13:83-108
pubmed: 22483277
Mol Biol Evol. 2000 Dec;17(12):1826-32
pubmed: 11110898
Curr Biol. 2018 Jun 4;28(11):1832-1838.e4
pubmed: 29804812
Genome Biol Evol. 2019 Feb 1;11(2):350-361
pubmed: 30649306
DNA Res. 2018 Aug 1;25(4):375-382
pubmed: 29617732
Nature. 2003 Jun 19;423(6942):825-37
pubmed: 12815422
Genome Biol Evol. 2016 Aug 29;8(8):2530-43
pubmed: 27492231
Genome Biol Evol. 2017 Mar 1;9(3):627-645
pubmed: 28391324
Mol Ecol. 2019 Nov;28(21):4709-4724
pubmed: 31538682
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
Trends Genet. 2018 Jul;34(7):492-503
pubmed: 29716744
Genetics. 2007 Jun;176(2):1049-57
pubmed: 17435246
BMC Genomics. 2014 Apr 15;15:285
pubmed: 24735434
Nature. 2014 Apr 24;508(7497):494-9
pubmed: 24759411
Genetics. 2019 Jul;212(3):815-835
pubmed: 31113811
Trends Genet. 2017 Apr;33(4):266-282
pubmed: 28236503
Nucleic Acids Res. 2012 Jun;40(11):4774-82
pubmed: 22362730
Heredity (Edinb). 2005 Aug;95(2):118-28
pubmed: 15931241
Mol Ecol Resour. 2021 Jul;21(5):1715-1731
pubmed: 33590960
Science. 1999 Oct 29;286(5441):964-7
pubmed: 10542153
Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):13021-6
pubmed: 26438872
Mol Ecol Resour. 2014 Nov;14(6):1141-59
pubmed: 24751186
Genome Res. 2013 Nov;23(11):1894-907
pubmed: 23921660
Nat Plants. 2018 Sep;4(9):677-680
pubmed: 30104649
Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11715-11720
pubmed: 29042518
Nat Protoc. 2018 Apr;13(4):787-809
pubmed: 29565902
PLoS Genet. 2013 Apr;9(4):e1003457
pubmed: 23593039
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Genome Biol. 2020 Sep 7;21(1):223
pubmed: 32892750
Bioinformatics. 2002 Feb;18(2):337-8
pubmed: 11847089
Genome Biol Evol. 2011;3:230-5
pubmed: 21317157
Genome Res. 2020 Feb;30(2):164-172
pubmed: 32033943
Heredity (Edinb). 2004 Jun;92(6):543-9
pubmed: 15100706
Curr Biol. 2011 Sep 13;21(17):1470-4
pubmed: 21889891
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Genes (Basel). 2020 Jul 13;11(7):
pubmed: 32668777
Evol Lett. 2019 Oct 01;3(6):586-597
pubmed: 31867120
PLoS Biol. 2014 Jul 01;12(7):e1001899
pubmed: 24983465