Numerous studies have documented molecular variability in plant virus populations, but few have assessed the relative contribution of natural selection and genetic drift in generating the observed pattern of diversity. To this end, gene function, environment and phylogenetic history were examined to observe the effect on genetic diversity and population structure of the PAV and PAS species of Barley yellow dwarf virus (family Luteoviridae). Three functional classes of gene were analysed: transcription-related (RdRp), structural (CP) and movement-related (MP). The results indicate that there were no inherent differences, in terms of total diversity or diversity at synonymous or non-synonymous nucleotide sites, between functional classes of genes or populations. Rather, selective constraints on a gene may be more or less relaxed depending on its function and the phylogenetic history of the population sampled. The CP of the PAS species, but not the PAV species, was differentiated genetically between regions. This is probably due to genetic drift, as there was no evidence that any gene deviated from a neutral model of evolution or is under positive selection. In general, the MP was under considerably less functional constraint than structural or replication-related proteins and four positively selected codon sites were identified. Mutations at these sites differentiate species and geographical subpopulations, so presumably they have aided the virus in adaptation to its host environment and contributed to intra- and interspecies diversification.
AlicaiT.,
FenbyN. S.,
GibsonR. W.,
AdipalaE.,
VettenH. J.,
FosterG. D.,
SealS. E.1999; Occurrence of two serotypes of sweet potato chlorotic stunt virus in East Africa and their associated differences in coat protein and HSP70 homologue gene sequences. Plant Pathol 48:718–726[CrossRef]
BencharkiB.,
MuttererJ.,
El YamaniM.,
Ziegler-GraffV.,
ZaouiD.,
JonardG.1999; Severity of infection of Moroccan barley yellow dwarf virus PAV isolates correlates with variability in their coat protein sequences. Ann Appl Biol 134:89–99[CrossRef]
BisnieksM.,
KvarnhedenA.,
SigvaldR.,
ValkonenJ. P. T.2004; Molecular diversity of the coat protein-encoding region of Barley yellow dwarf virus-PAV and Barley yellow dwarf virus-MAV from Latvia and Sweden. Arch Virol 149:843–853[CrossRef]
ChayC. A.,
SmithD. M.,
VaughanR.,
GrayS. M.1996a; Diversity among isolates within the PAV serotype of barley yellow dwarf virus. Phytopathology 86:370–377[CrossRef]
ChayC. A.,
GunasingeU. B.,
Dinesh-KumarS. P.,
MillerW. A.,
GrayS. M.1996b; Aphid transmission and systemic plant infection determinants of barley yellow dwarf luteovirus-PAV are contained in the coat protein readthrough domain and 17-kDa protein, respectively. Virology 219:57–65[CrossRef]
ChoiI.-R.,
HallJ. S.,
HenryM.,
ZhangL.,
HeinG. L.,
FrenchR.,
StengerD. C.2001; Contributions of genetic drift and negative selection on the evolution of three strains of wheat streak mosaic tritimovirus. Arch Virol 146:619–628[CrossRef]
FilichkinS. A.,
ListerR. M.,
McGrathP. F.,
YoungM. J.1994; In vivo expression and mutational analysis of the barley yellow dwarf virus readthrough gene. Virology 205:290–299[CrossRef]
ListerR. M.,
RanieriR.1995; Distribution and economic importance of barley yellow dwarf. In Barley Yellow Dwarf: 40 Years of Progress pp 29–53 Edited by
D'ArcyC. J.,
BurnettP. A.
St Paul, MN: American Phytopathological Society;
Lucio-ZavaletaE.,
SmithD. M.,
GrayS. M.2001; Variation in transmission efficiency among Barley yellow dwarf virus -RMV isolates and clones of the normally inefficient aphid vector, Rhopalosiphum padi
. Phytopathology 91:792–796[CrossRef]
MalmstromC. M.,
HughesC. C.,
NewtonL. A.,
StonerC. J.2005a; Virus infection in remnant native bunchgrasses from invaded California grasslands. New Phytol 168:217–230[CrossRef]
MalmstromC. M.,
McCulloughA. J.,
JohnsonH. A.,
NewtonL. A.,
BorerE. T.2005b; Invasive annual grasses indirectly increase virus incidence in California native perennial bunchgrasses. Oecologia 145:153–164[CrossRef]
MishmarD.,
Ruiz-PesiniE.,
GolikP.& 10 other authors2003; Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A 100:171–176[CrossRef]
MouryB.,
CardinL.,
OnestoJ.-P.,
CandresseT.,
PoupetA.2001; Survey of Prunus necrotic ringspot virus in rose and its variability in rose and Prunus spp. Phytopathology 91:84–91[CrossRef]
MouryB.,
MorelC.,
JohansenE.,
JacquemondM.2002; Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. J Gen Virol 83:2563–2573
PowerA. G.,
GrayS. M.1995; Aphid transmission of barley yellow dwarf viruses: interactions between viruses, vectors, and host plants. In Barley Yellow Dwarf Virus: 40 Years of Progress pp 259–289 Edited by
D'ArcyC. J.,
BurnettP. A.
St Paul, MN: American Phytopathological Society;
RaybouldA. F.,
MaskellL. C.,
EdwardsM.-L.,
CooperJ. I.,
GrayA. J.1999; The prevalence and spatial distribution of viruses in natural populations of Brassica oleracea
. New Phytol 141:265–275[CrossRef]
RozasJ.,
Sánchez-DelBarrioJ. C.,
MesseguerX.,
RozasR.2003; DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinfomatics 19:2496–2497[CrossRef]
RubioL.,
Abou-JawdahY.,
LinH.-X.,
FalkB. W.2001; Geographically distant isolates of the crinivirus Cucurbit yellow stunting disorder virus show very low genetic diversity in the coat protein gene. J Gen Virol 82:929–933
SacristánS.,
FraileA.,
MalpicaJ. M.,
García-ArenalF.2005; An analysis of host adaptation and its relationship with virulence in Cucumber mosaic virus
. Phytopathology 95:827–833[CrossRef]
SmithG. R.,
BorgZ.,
LockhartB. E. L.,
BraithwaiteK. S.,
GibbsM. J.2000; Sugarcane yellow leaf virus: a novel member of the luteoviridae that probably arose by inter-species recombination. J Gen Virol 81:1865–1869
TackeE.,
PrüferD.,
SchmitzJ.,
RohdeW.1991; The potato leafroll luteovirus 17K protein is a single-stranded nucleic acid-binding protein. J Gen Virol 72:2035–2038[CrossRef]
TackeE.,
SchmitzJ.,
PrüferD.,
RohdeW.1993; Mutational analysis of the nucleic acid-binding 17 kDa phosphoprotein of potato leafroll luteovirus identifies an amphiphatic alpha-helix as the domain for protein/protein ineractions. Virology 197:274–282[CrossRef]
TomimuraK.,
GibbsA. J.,
JennerC. E.,
WalshJ. A.,
OhshimaK.2003; The phylogeny of Turnip mosaic virus ; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent ‘emergence’ in east Asia. Mol Ecol 12:2099–2111[CrossRef]
WangX.,
ChangS.,
JinZ.,
LiL.,
ZhouG.2001; Nucleotide sequences of the coat protein and readthrough protein genes of the Chinese GAV isolate of barley yellow dwarf virus. Acta Virol 45:249–252
YangZ.,
WongW. S. W.,
NielsenR.2005; Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118[CrossRef]