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A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family.

Varsani A, Shepherd DN, Dent K, Monjane AL, Rybicki EP, Martin DP - Virol. J. (2009)

Bottom Line: ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera.Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses.ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand. arvind.varsani@uct.ac.za

ABSTRACT

Background: We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera.

Results: Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses. Similarly, while ECSV has the same unusual TAAGATTCC virion strand replication origin nonanucleotide found in another recently described divergent geminivirus, Beet curly top Iran virus (BCTIV), the rest of the transcription and replication origin is structurally more similar to those found in begomoviruses and curtoviruses than it is to those found in BCTIV and mastreviruses. ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions.

Conclusion: Although it superficially resembles a chimaera of geminiviruses from different genera, the ECSV genome is not obviously recombinant, implying that the features it shares with other geminiviruses are those that were probably present within the last common ancestor of these viruses. In addition to inferring how the ancestral geminivirus genome may have looked, we use the discovery of ECSV to refine various hypotheses regarding the recombinant origins of the major geminivirus lineages.

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Degrees of genome-wide sequence identity shared between ECSV (in bold; isolate ECSV [Za-Gre3-g257-2007]) and 40 representative geminivirus genomes (or DNA-A or DNA-A like genome components in the case of the begomoviruses; virus names and GenBank accession numbers are given in the tree). Note that due to (i) recombination during the evolutionary histories of many of the represented viruses (ii) very high degrees of alignment uncertainty and (iii) the strong possibility that many regions of the aligned genomes are not homologous, the presented neighbour joining tree is simply intended as a graphical depiction of genome-wide nucleotide sequence identities rather than a credible representation of the evolutionary relatedness of these viruses. Numbers associated with tree branches indicate percentage of bootstrap support (from 1000 replicates) for those branches. Branches with less than either 50% bootstrap support or less than 90% interior branch length test support (as determined in MEGA 4.0) have been collapsed. The percentage genome-wide nucleotide sequence identities shared between ECSV and the other geminivirus genomes (with alignment gaps treated as missing data rather than a fifth character state) is presented on the right.
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Figure 2: Degrees of genome-wide sequence identity shared between ECSV (in bold; isolate ECSV [Za-Gre3-g257-2007]) and 40 representative geminivirus genomes (or DNA-A or DNA-A like genome components in the case of the begomoviruses; virus names and GenBank accession numbers are given in the tree). Note that due to (i) recombination during the evolutionary histories of many of the represented viruses (ii) very high degrees of alignment uncertainty and (iii) the strong possibility that many regions of the aligned genomes are not homologous, the presented neighbour joining tree is simply intended as a graphical depiction of genome-wide nucleotide sequence identities rather than a credible representation of the evolutionary relatedness of these viruses. Numbers associated with tree branches indicate percentage of bootstrap support (from 1000 replicates) for those branches. Branches with less than either 50% bootstrap support or less than 90% interior branch length test support (as determined in MEGA 4.0) have been collapsed. The percentage genome-wide nucleotide sequence identities shared between ECSV and the other geminivirus genomes (with alignment gaps treated as missing data rather than a fifth character state) is presented on the right.

Mentions: Attempts to align one of the ECSV genome sequences to those of 40 representative geminiviruses proved largely futile due to the large genetic distances separating ECSV from other currently described geminiviruses. Nevertheless, a neighbor joining phylogenetic tree constructed from this alignment using genetic distances calculated without any evolutionary model (called p-distances in MEGA) serves as a reasonable graphical depiction of the degrees of genome-wide sequence identity shared between the ECSV genome and those of other geminiviruses (Figure 2).


A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family.

Varsani A, Shepherd DN, Dent K, Monjane AL, Rybicki EP, Martin DP - Virol. J. (2009)

Degrees of genome-wide sequence identity shared between ECSV (in bold; isolate ECSV [Za-Gre3-g257-2007]) and 40 representative geminivirus genomes (or DNA-A or DNA-A like genome components in the case of the begomoviruses; virus names and GenBank accession numbers are given in the tree). Note that due to (i) recombination during the evolutionary histories of many of the represented viruses (ii) very high degrees of alignment uncertainty and (iii) the strong possibility that many regions of the aligned genomes are not homologous, the presented neighbour joining tree is simply intended as a graphical depiction of genome-wide nucleotide sequence identities rather than a credible representation of the evolutionary relatedness of these viruses. Numbers associated with tree branches indicate percentage of bootstrap support (from 1000 replicates) for those branches. Branches with less than either 50% bootstrap support or less than 90% interior branch length test support (as determined in MEGA 4.0) have been collapsed. The percentage genome-wide nucleotide sequence identities shared between ECSV and the other geminivirus genomes (with alignment gaps treated as missing data rather than a fifth character state) is presented on the right.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666655&req=5

Figure 2: Degrees of genome-wide sequence identity shared between ECSV (in bold; isolate ECSV [Za-Gre3-g257-2007]) and 40 representative geminivirus genomes (or DNA-A or DNA-A like genome components in the case of the begomoviruses; virus names and GenBank accession numbers are given in the tree). Note that due to (i) recombination during the evolutionary histories of many of the represented viruses (ii) very high degrees of alignment uncertainty and (iii) the strong possibility that many regions of the aligned genomes are not homologous, the presented neighbour joining tree is simply intended as a graphical depiction of genome-wide nucleotide sequence identities rather than a credible representation of the evolutionary relatedness of these viruses. Numbers associated with tree branches indicate percentage of bootstrap support (from 1000 replicates) for those branches. Branches with less than either 50% bootstrap support or less than 90% interior branch length test support (as determined in MEGA 4.0) have been collapsed. The percentage genome-wide nucleotide sequence identities shared between ECSV and the other geminivirus genomes (with alignment gaps treated as missing data rather than a fifth character state) is presented on the right.
Mentions: Attempts to align one of the ECSV genome sequences to those of 40 representative geminiviruses proved largely futile due to the large genetic distances separating ECSV from other currently described geminiviruses. Nevertheless, a neighbor joining phylogenetic tree constructed from this alignment using genetic distances calculated without any evolutionary model (called p-distances in MEGA) serves as a reasonable graphical depiction of the degrees of genome-wide sequence identity shared between the ECSV genome and those of other geminiviruses (Figure 2).

Bottom Line: ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera.Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses.ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand. arvind.varsani@uct.ac.za

ABSTRACT

Background: We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera.

Results: Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses. Similarly, while ECSV has the same unusual TAAGATTCC virion strand replication origin nonanucleotide found in another recently described divergent geminivirus, Beet curly top Iran virus (BCTIV), the rest of the transcription and replication origin is structurally more similar to those found in begomoviruses and curtoviruses than it is to those found in BCTIV and mastreviruses. ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions.

Conclusion: Although it superficially resembles a chimaera of geminiviruses from different genera, the ECSV genome is not obviously recombinant, implying that the features it shares with other geminiviruses are those that were probably present within the last common ancestor of these viruses. In addition to inferring how the ancestral geminivirus genome may have looked, we use the discovery of ECSV to refine various hypotheses regarding the recombinant origins of the major geminivirus lineages.

Show MeSH
Related in: MedlinePlus