Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: implication in virus taxonomy

Boulila, Moncef

doi:10.1590/s1415-47572011005000046

Cited by 15 publications

(14 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Unlike previous dN/dS-based analyses of MCMV, we detected significant positive selection in the genome: at sites in P50, P32, and P31, three proteins of unknown function 45 . This can be attributed to the greatly increased volume of sequence data included in the analysis.…”

Section: /10contrasting

confidence: 99%

A first global phylogeny ofMaize chlorotic mottle virus

Braidwood

Quito-Avila

Cabanas

et al. 2017

Preprint

View full text Add to dashboard Cite

Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of Maize chlorotic mottle virus with potyviridae viruses causes an aggressive synergistic viral condition -maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained Maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa.

show abstract

Section: /10contrasting

confidence: 99%

A first global phylogeny ofMaize chlorotic mottle virus

Braidwood

Quito-Avila

Cabanas

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Bootscan, Maxchi, LARD recombination events detected by only half of the nine methods in RDP4 were considered significant (25,26), and the results obtained by three programs, PHI test, Recco, and RDP4, were not consistent, we concluded that only limited HR occurred in sigB of Listeria sensu stricto.…”

Section: Resultsmentioning

confidence: 82%

“…PHI test was conducted in SplitsTree4 V4.14.2 (61). Recco (62) was used for the prediction of recombination events, recombinant sequences, and recombination breakpoints, as it uses a fast and sensitive algorithm (25). Parameter ␣, which represents the cost of mutation relative to recombination, yields additional information as to which sequence might be recombinant.…”

Section: Methodsmentioning

confidence: 99%

Genetic Stability and Evolution of thesigBAllele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference

Liao

Wiedmann

Kovač

2017

Appl Environ Microbiol

View full text Add to dashboard Cite

Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion of , which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverse isolates. In this study, evolutionary approaches were used to assess the validity of allelic typing for For a data set of 4,280 isolates, allelic typing showed a Simpson's index of diversity of 0.96. Analyses of 164 allelic types (ATs) found among the 6 species, representing these 4,280 isolates, indicate that neither frequent homologous recombination nor positive selection significantly contributed to the evolution of, confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; displayed the lowest diversity and was the only species in which evolved in a clocklike manner, implying a unique natural history. Among the four lineages, evolution followed a molecular clock only in lineage IV. Moreover, displayed a significant negative Tajima value in lineage II, suggesting a recent population bottleneck followed by lineage expansion. The absence of positive selection along with the violation of the molecular clock suggested a nearly neutral mechanism of evolution. While comparison with a whole-genome sequence-based phylogeny revealed that the phylogeny did not correctly reflect the ancestry of lineage IV, the availability of a large AT database allowed accurate species classification. allelic typing has been widely used for species delineation and subtyping of However, an informative evaluation of this method from an evolutionary perspective was missing. Our data indicate that the genetic stability of is affected by neither frequent homologous recombination nor positive selection, which supports that allelic typing provides reliable subtyping and classification of strains. However, multigene data are required for accurate phylogeny reconstruction of This study thus contributes to a better understanding of the evolution of and confirms the robustness of the subtyping system for.

show abstract

“…These findings indicate that the MNSV CP gene could have been acquired through recombination. In this regard, tombusviruses and carmoviruses have been predicted to be highly recombinant compared with viruses of the other genera in the Tombusviridae family (Boulila, ). Moreover, recombination may occur between viruses belonging to different genera, particularly in the CP‐encoding gene (Boulila, ).…”

Section: Discussionmentioning

confidence: 99%

“…In this regard, tombusviruses and carmoviruses have been predicted to be highly recombinant compared with viruses of the other genera in the Tombusviridae family (Boulila, ). Moreover, recombination may occur between viruses belonging to different genera, particularly in the CP‐encoding gene (Boulila, ). Such a recombinant event has been studied extensively for CNV and MNSV (Riviere and Rochon, ).…”

Section: Discussionmentioning

confidence: 99%

Dissecting the multifunctional role of the N‐terminal domain of the Melon necrotic spot virus coat protein in RNA packaging, viral movement and interference with antiviral plant defence

Serra-Soriano

Navarro

Pallás

2016

Molecular Plant Pathology

View full text Add to dashboard Cite

The coat protein (CP) of Melon necrotic spot virus (MNSV) is structurally composed of three major domains. The middle S-domain builds a robust protein shell around the viral genome, whereas the C-terminal protruding domain, or P-domain, is involved in the attachment of virions to the transmission vector. Here, we have shown that the N-terminal domain, or R-domain, and the arm region, which connects the R-domain and S-domain, are involved in different key steps of the viral cycle, such as cell-to-cell movement and the suppression of RNA silencing and pathogenesis through their RNA-binding capabilities. Deletion mutants revealed that the CP RNA-binding ability was abolished only after complete, but not partial, deletion of the R-domain and the arm region. However, a comparison of the apparent dissociation constants for the CP RNA-binding reaction of several partial deletion mutants showed that the arm region played a more relevant role than the R-domain in in vitro RNA binding. Similar results were obtained in in vivo assays, although, in this case, full-length CPs were required to encapsidate full-length genomes. We also found that the R-domain carboxyl portion and the arm region were essential for efficient cell-to-cell movement, for enhancement of Potato virus X pathogenicity, for suppression of systemic RNA silencing and for binding of small RNAs. Therefore, unlike other carmovirus CPs, the R-domain and the arm region of MNSV CP have acquired, in addition to other essential functions such as genome binding and encapsidation functions, the ability to suppress RNA silencing by preventing systemic small RNA transport.

show abstract

Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: implication in virus taxonomy

Cited by 15 publications

References 40 publications

A first global phylogeny ofMaize chlorotic mottle virus

A first global phylogeny ofMaize chlorotic mottle virus

Genetic Stability and Evolution of thesigBAllele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference

Dissecting the multifunctional role of the N‐terminal domain of the Melon necrotic spot virus coat protein in RNA packaging, viral movement and interference with antiviral plant defence

Contact Info

Product

Resources

About