Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations

Ogawa, Tetsuji; Tomitaka, Yasuhiro; Nakagawa, Akio; Ohshima, Kazusato

doi:10.1016/j.virusres.2007.09.010

Cited by 106 publications

(83 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Here, population genetic analysis of PVX isolates from different countries was done based on the CP sequences because conserved nature of the CP gene makes it a suitable candidate for such studies. The CP gene in plant viruses is commonly used for investigation on genetic variation and molecular evolution [10,27,41,43] and was therefore selected for this study.…”

Section: Introductionmentioning

confidence: 99%

Population genetic analysis of potato virus X based on the CP gene sequence

Hajizadeh

Sokhandan-Bashir

2017

VirusDis.

View full text Add to dashboard Cite

To investigate the genetic variation and molecular evolution of potato virus X (PVX), 87 coat protein (CP) gene sequences were retrieved from GenBank and analyzed. Of the PVX isolates studied, one recombinant isolate (X3) was detected from South America population of the virus. The other isolates belonged to two lineages, Eurasia and America, with the significant F ST value (0.60). Non-synonymous nucleotide diversity to synonymous nucleotide diversity (x = dN/dS) was less than 1 indicating that the CP gene has been under negative selection or neutral evolution. Further analysis showed that all of the codons in both lineages were under negative selection pressure. No significant genetic differentiation was found between Chinese, Indian, Iranian, Japanese, and the UK populations whereas South America population was distinctly differentiated from other populations. Different evolutionary constraints found for the two lineages suggest that possible mutations and genetic drift were important evolutionary forces driving the genetic diversification of PVX population.

show abstract

Section: Introductionmentioning

confidence: 99%

Population genetic analysis of potato virus X based on the CP gene sequence

Hajizadeh

Sokhandan-Bashir

2017

VirusDis.

View full text Add to dashboard Cite

show abstract

“…The first RJ in the HC-Pro/P3 region is nearly identical to that of the PVY N -Wi RJ; in the 6K2-NIa N-terminal region, the sequence reverts to PVY Nlike sequence; and in the CP C-terminal region, there is another switch to a PVY O -type sequence (Boonham et al, 2002;Glais et al, 2002;Lorenzen et al, 2006). Other PVY recombination patterns were also described recently (Ogawa et al, 2008).…”

Section: Introductionmentioning

confidence: 62%

“…In PVY, different genes were reported to be under different selective constraints, e.g. P1 (Ogawa et al, 2008), CP and 6K2 (Moury et al, 2002) GC-rich (¢60 mol% GC content) and AU-rich (¢60 mol% AU) regions were termed 'homologousrecombination activators', which can influence homologous recombination (Nagy et al, 1999a). The upstream GCrich region and downstream AU-rich region were observed in RNA recombinants in CTV (Vives et al, 2005), noroviruses (Rohayem et al, 2005) and TuMV (Ohshima et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

Sequence characteristics of potato virus Y recombinants

Karasev

Brown

et al. 2009

Journal of General Virology

View full text Add to dashboard Cite

Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the physical and evolutionary mechanisms driving their emergence are not clear at the moment. The replicase-mediated template-switching model is considered the most likely mechanism for forming new RNA virus recombinants. Two factors, RNA secondary structure (especially stem-loop structures) and AU-rich regions, have been reported to affect recombination in this model. In this study, we investigated the influence of these two factors on PVY recombination from two perspectives: their distribution along the whole genome and differences between regions flanking the recombination junctions (RJs). Based on their distributions, only a few identified RJs in PVY genomes were located in lower negative FORS-D, i.e. having greater secondary-structure potential and higher AU-content regions, but most RJs had more negative FORS-D values upstream and/or higher AU content downstream. Our wholegenome analyses showed that RNA secondary structures and/or AU-rich regions at some sites may have affected PVY recombination, but in general they were not the main forces driving PVY recombination.

show abstract

“…There are many reports on the genetic structure of potyvirus populations, notably those on PVY (Ogawa et al, 2008;Karasev et al, 2011). These reports showed that virus populations were shaped by selection, founder effects and genetic recombination.…”

Section: Discussionmentioning

confidence: 99%

Biological, serological and molecular typing of potato virus Y (PVY) isolates from Tunisia

Tayahi

Gharsallah

Khamassy³

et al. 2016

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. In Tunisia, potato virus Y (PVY) currently presents a significant threat to potato production, reducing tuber yield and quality. Three hundred and eighty-five potato samples (six different cultivars) collected in autumn 2007 from nine regions in Tunisia were tested for PVY infection by DAS-ELISA. The virus was detected in all regions surveyed, with an average incidence of 80.26%. Subsequently, a panel of 82 Tunisian PVY isolates (PVY-TN) was subjected to systematic biological, serological and molecular typing using immunocapture reverse-transcription polymerase chain reaction and a series of PVY OCand PVY N -specific monoclonal antibodies. Combined analyses revealed ~67% of PVY NTN variants of which 17 were sequenced in the 5'NTR-P1 region to assess the genetic diversity and phylogenetic relationship of PVY-TN against other worldwide PVY isolates. To investigate whether selective constraints could act on viral genomic RNA, synonymous and non-synonymous substitution rates and their ratio were analyzed. Averages of all pairwise comparisons obtained in the 5'NTR-P1 region allowed more synonymous changes, suggesting selective constraint acting in this region. Selective neutrality test was significantly negative, suggesting a rapid expansion of PVY isolates. Pairwise mismatch distribution gave a bimodal pattern and pointed to an eventually early evolution characterizing these sequences. Genetic haplotype network topology provided evidence of the existence of a distinct geographical structure. This is the first report of such genetic analyses conducted on PVY isolates from Tunisia.

show abstract

Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations

Cited by 106 publications

References 66 publications

Population genetic analysis of potato virus X based on the CP gene sequence

Population genetic analysis of potato virus X based on the CP gene sequence

Sequence characteristics of potato virus Y recombinants

Biological, serological and molecular typing of potato virus Y (PVY) isolates from Tunisia

Contact Info

Product

Resources

About