Small effective population sizes and rare nonsynonymous variants in potyviruses

Abstract

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 104. 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.

The ‘emergence’ of turnip mosaic virus was probably a ‘gene-for-quasi-gene’ event

“…However, especially at the initial locale, it may have emerged on more than one occasion and followed more than one genetic trajectory, as found in recent well-sampled animal virus emergences (e.g. [32]); competition between emerging virus populations for a limited host population [33 ] probably selected among them.…”

Weak Selection and Protein Evolution

“…Numerous studies have reported PGIM patterns consistent with slightly deleterious amino acid changes. Excess rare polymorphisms and higher r pd for nonsynonymous compared to synonymous variation appear to be general patterns in viral (Edwards et al 2006;Pybus et al 2006;Hughes 2009) and bacterial genomes (Hughes 2005;Charlesworth and Eyre-Walker 2006;Rocha et al 2006;Hughes et al 2008) as well as in animal mtDNA (Ballard and Kreitman 1994;Nachman et al 1996;Rand and Kann 1996;Hasegawa et al 1998;Wise et al 1998;Weinreich and Rand 2000;Gerber et al 2001;Subramanian et al 2009). Similar patterns have been noted in nuclear genes from yeast (Doniger et al 2008;Liti et al 2009), Drosophila (Akashi 1996;Fay et al 2002;Loewe et al 2006;Andolfatto et al 2011), humans (Cargill et al 1999;Sunyaev et al 2000;Hughes et al 2003;Williamson et al 2005;Boyko et al 2008;Keightley and Halligan 2011;Subramanian 2012), mice (Halligan et al 2010), and plants (Bustamante et al 2002;Nordborg et al 2005;Foxe et al 2008;Fujimoto et al 2008;Gossmann et al 2010;Branca et al 2011;.…”

Time - the emerging dimension of plant virus studies

“…A large fraction (~70 %) of point substitutions are deleterious or lethal (Carrasco et al, 2007;Sanjuan et al, 2004) meaning that most mutations in RNA genomes are not likely to survive, particularly the non-synonymous changes (Hughes, 2009). Similar effects have been reported for animal viruses (Pybus et al, 2007).…”

“…A recent analysis (Hughes, 2009) of the population genetics of a large sample of complete potyvirus genomes has found that their effective populations are in the order of 10 4 . This, and the birth-death topology, suggest that despite large populations within individual infected plants, only small numbers survive the hazards of being transmitted to new hosts; there is probably strong selection for survival of the ecologically fittest.…”