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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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Pairwise genome scans of local nucleotide sequence similarities (uncorrected by any evolutionary model – corresponding to p-distances in MEGA 4.0 with pairwise deletion of gaps) within a moving 100 nucleotide window between ECSV (isolate ECSV [Za-Gre3-g257-2007]), BCTIV and representatives of the four established geminivirus genera. Each coloured plot represents a different pairwise nucleotide sequence alignment (using CLUSTALW with a gap open penalty of 6 and gap extension penalty of 3) between a single representative of each of the six main geminivirus lineages and representatives of all the other lineages. The grey plots represent analogous scans between 20 geminivirus genome pairs in which the positions of nucleotides have been randomly reshuffled and aligned using the same settings used to align the unshuffled nucleotide sequences. The maximum and minimum bounds of these scans represent the degrees of sequence similarity expected following alignment amongst unrelated sequences with the same nucleotide composition as the real geminivirus sequences.
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Figure 4: Pairwise genome scans of local nucleotide sequence similarities (uncorrected by any evolutionary model – corresponding to p-distances in MEGA 4.0 with pairwise deletion of gaps) within a moving 100 nucleotide window between ECSV (isolate ECSV [Za-Gre3-g257-2007]), BCTIV and representatives of the four established geminivirus genera. Each coloured plot represents a different pairwise nucleotide sequence alignment (using CLUSTALW with a gap open penalty of 6 and gap extension penalty of 3) between a single representative of each of the six main geminivirus lineages and representatives of all the other lineages. The grey plots represent analogous scans between 20 geminivirus genome pairs in which the positions of nucleotides have been randomly reshuffled and aligned using the same settings used to align the unshuffled nucleotide sequences. The maximum and minimum bounds of these scans represent the degrees of sequence similarity expected following alignment amongst unrelated sequences with the same nucleotide composition as the real geminivirus sequences.

Mentions: While our analysis (Figure 4) supported the prevailing hypotheses that the curtoviruses and topocuviruses are inter-genus recombinants [27-29], it also indicated that BCTIV is probably not an inter-genus recombinant as suggested by Yazdi et al. [33]. BCTIV is instead identified as a close relative of the "mastrevirus-like" progenitor formerly proposed by Stanley et al. [28] and Rybicki [29] as the originator of the curtovirus coat protein gene. While our analysis also indicated that topocuviruses are the recombinant offspring of begomoviruses and curtoviruses, the identified recombination event in rep is within an extremely recombinogenic genome region such that it is very probable that either one or both of the identified parental sequences (i.e. the begomovirus CoGMV and the curtovirus Beet curly top virus [BCTV]) are also inter-species recombinants in this genome region [30-32]. The possibility of quite widespread ongoing rep sequence recombination amongst the begomoviruses, topocuviruses and begomoviruses is, for example, strongly supported by the fact that these lineages cannot be reliably resolved within the Rep amino acid sequence phylogeny (Figure 3b).


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)

Pairwise genome scans of local nucleotide sequence similarities (uncorrected by any evolutionary model – corresponding to p-distances in MEGA 4.0 with pairwise deletion of gaps) within a moving 100 nucleotide window between ECSV (isolate ECSV [Za-Gre3-g257-2007]), BCTIV and representatives of the four established geminivirus genera. Each coloured plot represents a different pairwise nucleotide sequence alignment (using CLUSTALW with a gap open penalty of 6 and gap extension penalty of 3) between a single representative of each of the six main geminivirus lineages and representatives of all the other lineages. The grey plots represent analogous scans between 20 geminivirus genome pairs in which the positions of nucleotides have been randomly reshuffled and aligned using the same settings used to align the unshuffled nucleotide sequences. The maximum and minimum bounds of these scans represent the degrees of sequence similarity expected following alignment amongst unrelated sequences with the same nucleotide composition as the real geminivirus sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Pairwise genome scans of local nucleotide sequence similarities (uncorrected by any evolutionary model – corresponding to p-distances in MEGA 4.0 with pairwise deletion of gaps) within a moving 100 nucleotide window between ECSV (isolate ECSV [Za-Gre3-g257-2007]), BCTIV and representatives of the four established geminivirus genera. Each coloured plot represents a different pairwise nucleotide sequence alignment (using CLUSTALW with a gap open penalty of 6 and gap extension penalty of 3) between a single representative of each of the six main geminivirus lineages and representatives of all the other lineages. The grey plots represent analogous scans between 20 geminivirus genome pairs in which the positions of nucleotides have been randomly reshuffled and aligned using the same settings used to align the unshuffled nucleotide sequences. The maximum and minimum bounds of these scans represent the degrees of sequence similarity expected following alignment amongst unrelated sequences with the same nucleotide composition as the real geminivirus sequences.
Mentions: While our analysis (Figure 4) supported the prevailing hypotheses that the curtoviruses and topocuviruses are inter-genus recombinants [27-29], it also indicated that BCTIV is probably not an inter-genus recombinant as suggested by Yazdi et al. [33]. BCTIV is instead identified as a close relative of the "mastrevirus-like" progenitor formerly proposed by Stanley et al. [28] and Rybicki [29] as the originator of the curtovirus coat protein gene. While our analysis also indicated that topocuviruses are the recombinant offspring of begomoviruses and curtoviruses, the identified recombination event in rep is within an extremely recombinogenic genome region such that it is very probable that either one or both of the identified parental sequences (i.e. the begomovirus CoGMV and the curtovirus Beet curly top virus [BCTV]) are also inter-species recombinants in this genome region [30-32]. The possibility of quite widespread ongoing rep sequence recombination amongst the begomoviruses, topocuviruses and begomoviruses is, for example, strongly supported by the fact that these lineages cannot be reliably resolved within the Rep amino acid sequence phylogeny (Figure 3b).

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