Systematic Search for Recombination Events in plant Viruses and Viroids

Candresse, Thierry; Revers, Frédéric; Gall, Olivier Le; Kofalvi, S. A.; Marcos, José; Pallás, Vicente

doi:10.1007/978-3-662-03506-1_2

Cited by 7 publications

(5 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RECSITE and PHYLPRO analysis did not confirm these results and so it was difficult to consider them as putative recombinants. In particular, in agreement with Candresse et al (1997) , we found that the weight of particular point mutations in the subset of very close sequences could sometimes induce unreliable results. We will now discuss in more detail only the recombination events that were highlighted clearly by all the tests used.…”

Section: Resultssupporting

confidence: 93%

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

2000

View full text Add to dashboard Cite

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3h-untranslated region (3h-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis-Dioscorea rotundata and Dioscorea trifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3h-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complex D. cayenensis-D. rotundata, followed by independent transfers to D. alata and D. trifida during virus evolution.

show abstract

Section: Resultssupporting

confidence: 93%

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

2000

View full text Add to dashboard Cite

show abstract

“…1). These results reflect the facts that recombination events are more frequent than previously expected on HSVd and that intraspecific recombination could be a general mechanism in the evolution of viroids (Candresse et al , 1997 ). Finally, four out of the five variants from Morocco clustered into the plum-type group, confirming the homogeneous origin of the Moroccan isolates and showing their close relationship to the Spanish sequence variant isolated from the Bulida apricot, the most extended cultivar growth in the southeast of Spain having 81% HSVd infection (Cañizares et al , 1998 ).…”

Section: Resultssupporting

confidence: 81%

The molecular characterization of 16 new sequence variants of Hop stunt viroid reveals the existence of invariable regions and a conserved hammerhead-like structure on the viroid molecule

Amari

Gómez

Myrta

et al. 2001

Journal of General Virology

Self Cite

View full text Add to dashboard Cite

At present isolates of Hop stunt viroid (HSVd) are divided into five groups : three major groups (plum-type, hop-type and citrus-type) each containing isolates from only a limited number of isolation hosts and two minor groups that were presumed to derive from recombination events between members of the main groups. In this work we present the characterization of 16 new sequence variants of HSVd obtained from four Mediterranean countries (Cyprus, Greece, Morocco and Turkey) where this viroid had not previously been described. Molecular variability comparisons considering the totality of the sequence variants characterized so far revealed that most of the variability is found in the pathogenic and variable domains of the viroid molecule whereas both the terminal right (T R ) and left (T L ) domains are regions of low or no variability, respectively, suggesting the existence of constraints limiting the heterogeneity of the sequence variants. Phylogenetic analyses revealed that sequence variants belonging to the two minor recombinant subgroups are more frequent than previously thought. When the cruciform structure alternative to the typical rodlike conformation was considered it was observed that the upper part of this structure (hairpin I) was strictly conserved whereas in the lower part a reduced variability was found. The existence of a covariation in this lower part was notable. Interestingly, a hammerhead-like sequence was found within the T R domain of HSVd and it was strictly conserved in all the sequence variants. The evolutionary implications of the presence of this motif on the HSVd are discussed.

show abstract

“…Our study suggests that Tunisian HSVd variants was very heterogeneous, with 12 new mutations and a high value of minimum recombination event (Table 4), this is the highest value than those obtained from the other countries around the world. As assumed previously by Amari et al, (2001), recombination events are more frequent on HSVd and intra-specific recombination could be a general mechanism in the evolution of viroids (Candresse et al, 1997).…”

Section: Discussionsupporting

confidence: 51%

Insights on genetic diversity and phylogenetic analysis of Hop stunt viroid (HSVd) population from symptomatic citrus tree in Tunisia

Hamdi¹,

Elleuch²,

Bessaies³

et al. 2011

Afr. J. Microbiol. Res.

View full text Add to dashboard Cite

Hop stunt viroid (HSVd) variants from cachexia symptomatic citrus tree were subjected to retrotranscription and DNA amplification (RT-PCR), cloning and sequencing. Here we report genetic diversity and phylogenetic analysis of HSVd Tunisian isolate. Our study revealed obvious polymorphism within Tunisian isolates and high similarity with Japanese variants. Neighbor-joining analysis was carried out on the new HSVd-citrus sequences together with 44 previously described HSVd isolates from citrus and one from grapevine. The phylogenetic analysis showed that Tunisian isolates were clustered into 4 different groups (CVd-IIa, b, and c and grapevine group). Furthermore, the predicted secondary structure was scrutinized to be more understanding on how the nucleotide change affects variable (V) and pathogenicity domain (P).

show abstract

Systematic Search for Recombination Events in plant Viruses and Viroids

Cited by 7 publications

References 14 publications

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

The molecular characterization of 16 new sequence variants of Hop stunt viroid reveals the existence of invariable regions and a conserved hammerhead-like structure on the viroid molecule

Insights on genetic diversity and phylogenetic analysis of Hop stunt viroid (HSVd) population from symptomatic citrus tree in Tunisia

Contact Info

Product

Resources

About