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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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Maximum likelihood trees of (a) coat protein (JTT + G4 model) and (b) replication associated protein (RtRev + G4 model) amino acid sequences of ECSV (isolate ECSV [Za-Gre3-g257-2007]) and 40 other viruses representing the broadest breadth of currently sampled geminivirus diversity. Whereas the CP tree is unrooted, the Rep tree was rooted using the translated "master" rep sequence of Faba bean necrotic yellows virus (FBNYV; in grey). Viruses that are clearly members of the currently established geminivirus genera, Begomovirus, Topocuvirus, Curtovirus and Mastrevirus are indicated in green, orange, blue and pink respectively. Branches of the tree marked with filled circles were present in 90 or more maximum likelihood tree bootstrap replicates (performed in PHYML)and more than 99% of constructed trees from alignments sampled during the statistical alignment process (performed in STATALIGN). Open circles represent branches supported by 70 or more percent of the maximum likelihood tree bootstrap replicates and 95 or more percent of trees constructed during statistical alignment. Branches were collapsed if they were not supported in the consensus trees of either the maximum likelihood bootstrap replicates or the statistical alignment process. Branches were also collapsed if they were supported in less than either 50% of the bootstrap replicates or 90% of the trees generated during the statistical alignment.
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Figure 3: Maximum likelihood trees of (a) coat protein (JTT + G4 model) and (b) replication associated protein (RtRev + G4 model) amino acid sequences of ECSV (isolate ECSV [Za-Gre3-g257-2007]) and 40 other viruses representing the broadest breadth of currently sampled geminivirus diversity. Whereas the CP tree is unrooted, the Rep tree was rooted using the translated "master" rep sequence of Faba bean necrotic yellows virus (FBNYV; in grey). Viruses that are clearly members of the currently established geminivirus genera, Begomovirus, Topocuvirus, Curtovirus and Mastrevirus are indicated in green, orange, blue and pink respectively. Branches of the tree marked with filled circles were present in 90 or more maximum likelihood tree bootstrap replicates (performed in PHYML)and more than 99% of constructed trees from alignments sampled during the statistical alignment process (performed in STATALIGN). Open circles represent branches supported by 70 or more percent of the maximum likelihood tree bootstrap replicates and 95 or more percent of trees constructed during statistical alignment. Branches were collapsed if they were not supported in the consensus trees of either the maximum likelihood bootstrap replicates or the statistical alignment process. Branches were also collapsed if they were supported in less than either 50% of the bootstrap replicates or 90% of the trees generated during the statistical alignment.

Mentions: As cp and rep were the only ECSV genes that were obviously homologous to those of other geminiviruses we focused on these to explore the possible evolutionary relationships between ECSV and the other geminiviruses. We constructed phylogenetic trees for CP and Rep from translated amino acid sequences using two separate approaches. In the first we aligned the amino acid sequences using CLUSTALW, used PROTTEST to determine the best fit models of amino acid substitution, and constructed bootstrapped maximum likelihood phylogenetic trees using PHYML. As there is a large degree of uncertainty associated with aligning such divergent amino acid sequences, we also used the program STATALIGN to directly construct phylogenetic trees in which alignment uncertainty is explicitly accounted for. We then used the absolute consensus of the PHYML and STATALIGN trees, collapsing all tree branches that were: (i) Not retrieved in the consensus trees generated by both methods; (ii) were supported in less than 50% of the PHYML bootstrap replicates; or (iii) were only represented in less than 90% of the trees constructed from sampled alignments during the statistical alignment process (Figure 3).


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)

Maximum likelihood trees of (a) coat protein (JTT + G4 model) and (b) replication associated protein (RtRev + G4 model) amino acid sequences of ECSV (isolate ECSV [Za-Gre3-g257-2007]) and 40 other viruses representing the broadest breadth of currently sampled geminivirus diversity. Whereas the CP tree is unrooted, the Rep tree was rooted using the translated "master" rep sequence of Faba bean necrotic yellows virus (FBNYV; in grey). Viruses that are clearly members of the currently established geminivirus genera, Begomovirus, Topocuvirus, Curtovirus and Mastrevirus are indicated in green, orange, blue and pink respectively. Branches of the tree marked with filled circles were present in 90 or more maximum likelihood tree bootstrap replicates (performed in PHYML)and more than 99% of constructed trees from alignments sampled during the statistical alignment process (performed in STATALIGN). Open circles represent branches supported by 70 or more percent of the maximum likelihood tree bootstrap replicates and 95 or more percent of trees constructed during statistical alignment. Branches were collapsed if they were not supported in the consensus trees of either the maximum likelihood bootstrap replicates or the statistical alignment process. Branches were also collapsed if they were supported in less than either 50% of the bootstrap replicates or 90% of the trees generated during the statistical alignment.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Maximum likelihood trees of (a) coat protein (JTT + G4 model) and (b) replication associated protein (RtRev + G4 model) amino acid sequences of ECSV (isolate ECSV [Za-Gre3-g257-2007]) and 40 other viruses representing the broadest breadth of currently sampled geminivirus diversity. Whereas the CP tree is unrooted, the Rep tree was rooted using the translated "master" rep sequence of Faba bean necrotic yellows virus (FBNYV; in grey). Viruses that are clearly members of the currently established geminivirus genera, Begomovirus, Topocuvirus, Curtovirus and Mastrevirus are indicated in green, orange, blue and pink respectively. Branches of the tree marked with filled circles were present in 90 or more maximum likelihood tree bootstrap replicates (performed in PHYML)and more than 99% of constructed trees from alignments sampled during the statistical alignment process (performed in STATALIGN). Open circles represent branches supported by 70 or more percent of the maximum likelihood tree bootstrap replicates and 95 or more percent of trees constructed during statistical alignment. Branches were collapsed if they were not supported in the consensus trees of either the maximum likelihood bootstrap replicates or the statistical alignment process. Branches were also collapsed if they were supported in less than either 50% of the bootstrap replicates or 90% of the trees generated during the statistical alignment.
Mentions: As cp and rep were the only ECSV genes that were obviously homologous to those of other geminiviruses we focused on these to explore the possible evolutionary relationships between ECSV and the other geminiviruses. We constructed phylogenetic trees for CP and Rep from translated amino acid sequences using two separate approaches. In the first we aligned the amino acid sequences using CLUSTALW, used PROTTEST to determine the best fit models of amino acid substitution, and constructed bootstrapped maximum likelihood phylogenetic trees using PHYML. As there is a large degree of uncertainty associated with aligning such divergent amino acid sequences, we also used the program STATALIGN to directly construct phylogenetic trees in which alignment uncertainty is explicitly accounted for. We then used the absolute consensus of the PHYML and STATALIGN trees, collapsing all tree branches that were: (i) Not retrieved in the consensus trees generated by both methods; (ii) were supported in less than 50% of the PHYML bootstrap replicates; or (iii) were only represented in less than 90% of the trees constructed from sampled alignments during the statistical alignment process (Figure 3).

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