Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

Rubio, Luís; Guerri, José; Moreno, Pedro

doi:10.3389/fmicb.2013.00151

Cited by 96 publications

(74 citation statements)

References 166 publications

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“…In contrast, divergence levels between isolates within each group were low. These findings are in agreement with previous studies, which showed that several viruses of the family Closteroviridae are composed of genetically distant groups of isolates although each group is very homogeneous (Rubio et al, 2013).…”

Section: Discussionsupporting

confidence: 94%

“…Previous analyses indicated frequent homologous recombination events between divergent virus isolates in several members of the Closteroviridae (CTV, GLRaV-2, RLMV, BYVaV, GLRaV-3, GLRaV-11, GLRaV-4, GLRa-5) (Karasev, 2000;Turturo et al, 2005;Farooq et al, 2013;Rubio et al, 2013). Thus, it is possible that RNA recombination also plays a significant role in LChV-1 variation and evolution.…”

Section: Discussionmentioning

confidence: 90%

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Insights into the genetic diversity and evolution of Little cherry virus 1

et al. 2014

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Little cherry virus 1 (LChV-1), a member of the recently proposed genus Velarivirus, is a sweet cherry pathogen that has been recently reported to infect other Prunus species and is associated with various plant disorders. In this work the incidence of the virus on its putative hosts and possible mechanisms driving its evolution were investigated. Due to problems encountered with LChV-1 detection, a new nested RT-PCR assay was developed and applied. The virus was found to be prevalent in cherry plantations in Greece and only occasionally detected in other Prunus species. Sequences corresponding to the partial RNA-dependent RNA polymerase (RdRp), heat-shock protein homologue (HSP70h) and coat protein (CP) genes were determined from Greek LChV-1 isolates originating from different hosts; these were analysed, along with published homologous genomic regions from other isolates. Phylogenetic analysis of the three genes revealed the segregation of four evolutionary distinct groups showing no host or geography-based clustering. Mean genetic distances among the four groups were high with the CP region showing the highest divergence, although intragroup variability levels were low. Nevertheless, estimations of the mean ratio of nonsynonymous substitutions per synonymous site to synonymous substitutions per synonymous site (dN/dS) for the partial RdRp, HSP70h and CP indicated that these genomic regions are under negative selection pressure. Interestingly, a recombination event was identified at the 3 0 end of RdRp on a Greek virus isolate, thus highlighting the role of this mechanism in the evolutionary history of LChV-1.

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Section: Discussionsupporting

confidence: 94%

Section: Discussionmentioning

confidence: 90%

Insights into the genetic diversity and evolution of Little cherry virus 1

et al. 2014

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“…1). This suggests long distance migration of some isolates and possibly genetic stability of different TSWV strains which might occupy distinct adaptive peaks as it has occurred in other plant viruses [8,26]. Potential genetic exchange was analyzed with the algorithms 3SeqBootScan, Chimaera, GENECON, Maxchi, RDP, SiScan, implemented in the RDP4 package [20].…”

mentioning

confidence: 99%

Complete sequence of three different biotypes of tomato spotted wilt virus (wild type, tomato Sw-5 resistance-breaking and pepper Tsw resistance-breaking) from Spain

Debreczeni

López

Aramburu³

et al. 2015

Arch Virol

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The 5'-and 3'-terminal sequences were determined using the 5'/3' RACE Kit 2ndGeneration (Roche). To avoid errors associated with RT-PCR and sequencing, each genomic region was amplified and sequenced at least twice in both directions. Table 2.The complete sequences of isolates LL-N.05, Pujol1TL3 and PVR were aligned and compared with all complete sequences available for TSWV retrieved from GenBank (Table 1) Phylogenetic trees of the nucleotide sequences of the five TSWV ORFs were inferred by the maximum likelihood (ML) method with the nucleotide substitution model best fit for each ORF and 1000 bootstrap replicates to estimate the statistical significance of each node, using the program MEGA V6.0. The phylogenetic relationships of the Spanish TSWV isolates changed for the three genomic segments, but they were very similar for the two ORFs within each segment (Fig. 1) The genetic distances among TSWV isolates were uncorrelated to biotypes (resistancebreakdown ability) or plant hosts (Fig. 1) isolates [16,19,29]. The probable cause is that resistance-breakdown seems to have occurred several times independently and involve a few nucleotide changes as for other plant viruses [4].With respect to plant hosts, some TSWV isolates were more closely related to isolates from other plant species than isolates from the same plant host. E.g isolate TSWV-4 from pepper was closely related to isolate TSWV-10 from Stellaria aquatica, and isolate TSWV-16 from tomato, but distantly related to isolate CY-CN1 from pepper ( Fig. 1). This could be due to that TSWV has similar fitness in different hosts or that only a few nucleotide changes are involved in host adaptation (fitness increase).The complete genome sequences of TSWV isolates with different ability to overcome resistance in tomato and pepper are useful for further studies to understand emergence and evolution of TSWV adaptation to new hosts genotypes which can be applied in breeding programs to develop durable and efficient resistance cultivars against TSWV.

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“…A few studies on the genetic diversity of natural populations of GLRaV-1 and -2, based on the partial HSP70h and CP gene sequences, revealed the existence of three phylogenetically distinct groups in GLRaV-1 (5) and six groups in GLRaV-2 (67). A recent study, based on CP sequences, reported the presence of distinct genetic groups within GLRaV-4 and its strains (120).…”

Section: Genetic Diversity Of the Grapevine Leafroll-associated Virusesmentioning

confidence: 99%

“…A few factors contribute to a scenario in which genetic variants of GLRaVs could be perpetuated in grapevines without being subjected to stringent selection pressures (102,120). The apparent absence of any natural virus resistance in Vitis spp.…”

Section: Genetic Diversity Of the Grapevine Leafroll-associated Virusesmentioning

confidence: 99%

Grapevine Leafroll Disease and Associated Viruses: A Unique Pathosystem

Naidu

Maree

Burger

2015

Annu. Rev. Phytopathol.

105

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Grapevine leafroll is the most complex and intriguing viral disease of grapevine (Vitis spp.). Several monopartite closteroviruses (family Closteroviridae) from grapevines have been molecularly characterized, yet their role in disease etiology is not completely resolved. Hence, these viruses are currently designated under the umbrella term of Grapevine leafroll-associated viruses (GLRaVs). This review examines our current understanding of the genetically divergent GLRaVs and highlights the emerging picture of several unique aspects of the leafroll disease pathosystem. A systems biology approach using contemporary technologies in molecular biology, -omics, and cell biology aids in exploring the comparative molecular biology of GLRaVs and deciphering the complex network of host-virus-vector interactions to bridge the gap between genomics and phenomics of leafroll disease. In addition, grapevine-infecting closteroviruses have a great potential as designer viruses to pursue functional genomics and for the rational design of novel disease intervention strategies in this agriculturally important perennial fruit crop.

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Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

Cited by 96 publications

References 166 publications

Insights into the genetic diversity and evolution of Little cherry virus 1

Insights into the genetic diversity and evolution of Little cherry virus 1

Complete sequence of three different biotypes of tomato spotted wilt virus (wild type, tomato Sw-5 resistance-breaking and pepper Tsw resistance-breaking) from Spain

Grapevine Leafroll Disease and Associated Viruses: A Unique Pathosystem

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