Small effective population sizes and rare nonsynonymous variants in potyviruses.
Analysis of nucleotide sequence polymorphism in complete genomes of 12 species of potyviruses (single-stranded, positive-sense RNA viruses, family Potyviridae) revealed evidence that long-term effective population sizes of these viruses are on the order of 10(4). Comparison of nucleotide diversity in non-coding regions and at synonymous and nonsynonymous sites in coding regions showed that purifying selection has acted to eliminate numerous deleterious mutations both at nonsynonymous sites and in non-coding regions. The ratio of nonsynonymous to synonymous polymorphic sites increased as a function of the number of genomes sampled, whereas mean gene diversity at nonsynonymous polymorphic sites decreased with increasing sample size at a substantially faster rate than does mean gene diversity at synonymous polymorphic sites. Very similar relationships were observed both in available genomic sequences of 12 potyvirus species and in subsets created by randomly sampling from among 98 TuMV genomes. Taken together, these observations imply that a greater proportion of nonsynonymous than of synonymous variants are relatively rare as the result of ongoing purifying selection, and thus many nonsynonymous variants are unlikely to be discovered without extensive sampling.
Hughes
Austin L
AL
Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg., 715 Sumter St., Columbia SC 29208, USA. austin@biol.sc.edu
D016000:Cluster Analysis; D019143:Evolution, Molecular; D016679:Genome, Viral; D020125:Mutation, Missense; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017354:Point Mutation; D011110:Polymorphism, Genetic; D017800:Potyvirus / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics; D012641:Selection, Genetic; D017385:Sequence Homology
D012367:RNA, Viral
Nature. 1990 Nov 29;348(6300):454-5
2247152
J Gen Virol. 2004 Sep;85(Pt 9):2683-2696
15302962
Nature. 2008 Oct 2;455(7213):613-9
18833271
Genetics. 1931 Mar;16(2):97-159
17246615
J Virol. 2000 Apr;74(8):3566-71
10729131
Mol Biol Evol. 2001 Jun;18(6):987-94
11371587
Annu Rev Phytopathol. 2003;41:199-214
12730393
Vaccine. 2009 Mar 10;27(11):1685-90
19195493
Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1862-5
9050870
Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):6015-9
1321432
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15754-7
14660790
Naturwissenschaften. 1971 Oct;58(10):465-523
4942363
Genetics. 2002 Dec;162(4):1505-11
12524327
Gene. 2005 Mar 14;347(2):273-82
15777632
Evolution. 1975 Mar;29(1):1-10
28563291
Science. 2001 Jun 22;292(5525):2323-5
11423661
Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13910-3
10570172
Mol Biol Evol. 1987 Jul;4(4):406-25
3447015
J Mol Evol. 1993 Jan;36(1):96-9
8433381
Bioinformatics. 2002 Mar;18(3):502-4
11934758
Nature. 1973 Nov 9;246(5428):96-8
4585855
J Gen Virol. 2005 Feb;86(Pt 2):501-510
15659771
J Gen Virol. 2007 Jan;88(Pt 1):298-315
17170463
Proc Natl Acad Sci U S A. 1980 Nov;77(11):6710-4
16592920
Gene. 2007 May 1;392(1-2):266-72
17306473
Annu Rev Phytopathol. 2001;39:157-86
11701863
J Virol. 2006 Mar;80(5):2349-57
16474141
Mol Biol Evol. 2007 Aug;24(8):1596-9
17488738
Ann N Y Acad Sci. 2008;1133:162-79
18559820
Evolution. 1985 Jul;39(4):783-791
28561359
Arch Virol. 2008;153(8):1411-20
18566735
Gene. 2007 Dec 1;404(1-2):117-25
17928171
Annu Rev Microbiol. 1997;51:151-78
9343347
Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
9396791
J Gen Virol. 2008 Aug;89(Pt 8):1921-1929
18632963
Infect Genet Evol. 2008 Mar;8(2):130-8
18093882
Genetics. 2005 Feb;169(2):533-8
15545641
Comput Appl Biosci. 1992 Jun;8(3):275-82
1633570
J Gen Virol. 2007 Oct;88(Pt 10):2839-2845
17872538