Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias
<p>Abstract</p> <p>Background</p> <p>Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families <it>Geminiviridae</it>, <it>Parvoviridae </it>and <it>Anellovirus </it>may be evolving at rates of ~...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-09-01
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| Series: | Virology Journal |
| Online Access: | http://www.virologyj.com/content/5/1/104 |
| _version_ | 1828411740156592128 |
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| author | Varsani Arvind Martin Darren P van der Walt Eric Polston Jane E Rybicki Edward P |
| author_facet | Varsani Arvind Martin Darren P van der Walt Eric Polston Jane E Rybicki Edward P |
| author_sort | Varsani Arvind |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families <it>Geminiviridae</it>, <it>Parvoviridae </it>and <it>Anellovirus </it>may be evolving at rates of ~10<sup>-4 </sup>substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered.</p> <p>Results</p> <p>We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained <it>in planta </it>for up to five years and displayed evolution rates of between 7.4 × 10<sup>-4 </sup>and 7.9 × 10<sup>-4 </sup>subs/site/year.</p> <p>Conclusion</p> <p>These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules.</p> |
| first_indexed | 2024-12-10T12:36:07Z |
| format | Article |
| id | doaj.art-18c7d61eda9a4ca18e44990eb4fad7cb |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-10T12:36:07Z |
| publishDate | 2008-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-18c7d61eda9a4ca18e44990eb4fad7cb2022-12-22T01:48:39ZengBMCVirology Journal1743-422X2008-09-015110410.1186/1743-422X-5-104Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution biasVarsani ArvindMartin Darren Pvan der Walt EricPolston Jane ERybicki Edward P<p>Abstract</p> <p>Background</p> <p>Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families <it>Geminiviridae</it>, <it>Parvoviridae </it>and <it>Anellovirus </it>may be evolving at rates of ~10<sup>-4 </sup>substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered.</p> <p>Results</p> <p>We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained <it>in planta </it>for up to five years and displayed evolution rates of between 7.4 × 10<sup>-4 </sup>and 7.9 × 10<sup>-4 </sup>subs/site/year.</p> <p>Conclusion</p> <p>These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules.</p>http://www.virologyj.com/content/5/1/104 |
| spellingShingle | Varsani Arvind Martin Darren P van der Walt Eric Polston Jane E Rybicki Edward P Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias Virology Journal |
| title | Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias |
| title_full | Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias |
| title_fullStr | Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias |
| title_full_unstemmed | Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias |
| title_short | Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias |
| title_sort | experimental observations of rapid maize streak virus evolution reveal a strand specific nucleotide substitution bias |
| url | http://www.virologyj.com/content/5/1/104 |
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