Orphan genes
annotation artifacts
de novo genes
frame-shift
taxonomically-restricted
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
09 07 2019
09 07 2019
Historique:
pubmed:
16
5
2019
medline:
16
1
2020
entrez:
16
5
2019
Statut:
epublish
Résumé
Homology is a fundamental concept in comparative biology. It is extensively used at the sequence level to make phylogenetic hypotheses and functional inferences. Nonetheless, the majority of eukaryotic genomes contain large numbers of orphan genes lacking homologs in other taxa. Generally, the fraction of orphan genes is higher in genomically undersampled clades, and in the absence of closely related genomes any hypothesis about their origin and evolution remains untestable. Previously, we sequenced ten genomes with an underlying ladder-like phylogeny to establish a phylogenomic framework for studying genome evolution in diplogastrid nematodes. Here, we use this deeply sampled data set to understand the processes that generate orphan genes in our focal species
Identifiants
pubmed: 31088903
pii: g3.119.400326
doi: 10.1534/g3.119.400326
pmc: PMC6643871
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2277-2286Informations de copyright
Copyright © 2019 Prabh, Rodelsperger.
Références
Mol Biol Evol. 2017 Apr 1;34(4):779-792
pubmed: 28053006
Nat Commun. 2018 Apr 19;9(1):1555
pubmed: 29674719
Nat Rev Genet. 2003 Nov;4(11):865-75
pubmed: 14634634
Nat Rev Genet. 2016 Sep;17(9):567-78
pubmed: 27452112
Genome Res. 2010 Jun;20(6):837-46
pubmed: 20237107
Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9935-9
pubmed: 16777968
Nat Ecol Evol. 2018 Oct;2(10):1626-1632
pubmed: 30201962
Genetics. 2014 Apr;196(4):1153-65
pubmed: 24443445
PLoS Biol. 2015 Feb 10;13(2):e1002061
pubmed: 25668728
PLoS One. 2012;7(11):e48650
pubmed: 23185269
PLoS Genet. 2011 Nov;7(11):e1002379
pubmed: 22102831
PLoS Genet. 2013 Jun;9(6):e1003569
pubmed: 23818866
PLoS Genet. 2015 Jun 18;11(6):e1005146
pubmed: 26087034
Cell Rep. 2017 Oct 17;21(3):834-844
pubmed: 29045848
Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3811-6
pubmed: 9108060
BMC Bioinformatics. 2016 May 31;17(1):226
pubmed: 27245157
PLoS Comput Biol. 2010 Mar 26;6(3):e1000734
pubmed: 20376170
BMC Evol Biol. 2015 Sep 15;15:185
pubmed: 26370559
Genome Res. 2009 Oct;19(10):1752-9
pubmed: 19726446
Genetics. 2001 Oct;159(2):589-98
pubmed: 11606536
Genome Res. 2018 Nov;28(11):1675-1687
pubmed: 30232198
Genome Biol. 2009;10(1):R8
pubmed: 19161630
PLoS Genet. 2012 Sep;8(9):e1002942
pubmed: 23028352
BMC Bioinformatics. 2005 Feb 15;6:31
pubmed: 15713233
Nat Rev Genet. 2013 Sep;14(9):645-60
pubmed: 23949544
Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9746-50
pubmed: 9275195
Dev Biol. 1996 Feb 1;173(2):396-407
pubmed: 8606000
RNA. 2014 Sep;20(9):1386-97
pubmed: 25015138
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Nat Genet. 2018 Mar;50(3):452-459
pubmed: 29459678
Trends Genet. 2019 Mar;35(3):186-198
pubmed: 30606460
Genome Res. 2018 Nov;28(11):1664-1674
pubmed: 30232197
BMC Evol Biol. 2016 Aug 22;16(1):165
pubmed: 27549405
Nature. 2011 Jan 6;469(7328):97-101
pubmed: 21085120
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
pubmed: 16845082
Trends Genet. 2009 Sep;25(9):404-13
pubmed: 19716618
Nat Rev Genet. 2011 Aug 31;12(10):692-702
pubmed: 21878963
Trends Genet. 2007 Nov;23(11):533-9
pubmed: 18029048
Elife. 2014 Feb 19;3:e01311
pubmed: 24554240
PLoS Comput Biol. 2007 May;3(5):e91
pubmed: 17511511
Mol Biol Evol. 2018 Mar 1;35(3):631-645
pubmed: 29220506
Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9489-93
pubmed: 1329098
Curr Biol. 2018 Oct 8;28(19):3123-3127.e5
pubmed: 30245109
Genetics. 2002 Sep;162(1):129-34
pubmed: 12242228
Nat Genet. 2018 Feb;50(2):285-296
pubmed: 29358651
Nature. 2012 Jul 19;487(7407):370-4
pubmed: 22722833
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Nat Ecol Evol. 2018 May;2(5):890-896
pubmed: 29556078
BMC Evol Biol. 2008 Jan 28;8:31
pubmed: 18226237
PLoS Genet. 2005 Aug;1(2):e18
pubmed: 16110341
PLoS Genet. 2015 Jul 15;11(7):e1005391
pubmed: 26177073
Proc Natl Acad Sci U S A. 1984 Apr;81(8):2421-5
pubmed: 6585807
Science. 1977 Jun 10;196(4295):1161-6
pubmed: 860134
Mol Biol Evol. 2012 Dec;29(12):3767-80
pubmed: 22821011
Genome Biol. 2018 Aug 14;19(1):115
pubmed: 30107805
Zoolog Sci. 2012 Jun;29(6):403-17
pubmed: 22639812
Genetics. 2008 May;179(1):487-96
pubmed: 18493065
Genome Biol. 2013 Apr 25;14(4):R36
pubmed: 23618408
FEBS J. 2018 Jul;285(14):2605-2625
pubmed: 29802682
Mol Biol Evol. 2011 Jul;28(7):2053-61
pubmed: 21245413
Genome Biol Evol. 2013;5(2):439-55
pubmed: 23348040
Sci China Life Sci. 2019 Apr;62(4):579-593
pubmed: 30919281
Trends Genet. 1996 Jul;12(7):263-70
pubmed: 8763498
Comput Biol Chem. 2005 Feb;29(1):1-12
pubmed: 15680581
Curr Biol. 2009 Sep 29;19(18):1527-31
pubmed: 19733073
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Nat Commun. 2011;2:323
pubmed: 21610726
Mol Biol Evol. 2010 Feb;27(2):221-4
pubmed: 19854763
PLoS One. 2010 Jan 28;5(1):e8861
pubmed: 20126624