Sequence characteristics of PVY recombinants
Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the phy...
| Main Authors: | , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Microbiology Society
2009
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/90174 |
| _version_ | 1855515046321324032 |
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| author | Hu, X. Karasev, A.V. Brown, C.J. Lorenzen, J.H. |
| author_browse | Brown, C.J. Hu, X. Karasev, A.V. Lorenzen, J.H. |
| author_facet | Hu, X. Karasev, A.V. Brown, C.J. Lorenzen, J.H. |
| author_sort | Hu, X. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the physical and evolutionary mechanisms driving their emergence are not clear at the moment. The replicase-mediated template-switching model is considered the most likely mechanism for forming new RNA virus recombinants. Two factors, RNA secondary structure (especially stem-loop structures) and AU-rich regions, have been reported to affect recombination in this model. In this study, we investigated the influence of these two factors on PVY recombination from two perspectives: their distribution along the whole genome and differences between regions flanking the recombination junctions (RJs). Based on their distributions, only a few identified RJs in PVY genomes were located in lower negative FORS-D, i.e. having greater secondary-structure potential and higher AU-content regions, but most RJs had more negative FORS-D values upstream and/or higher AU content downstream. Our whole-genome analyses showed that RNA secondary structures and/or AU-rich regions at some sites may have affected PVY recombination, but in general they were not the main forces driving PVY recombination. |
| format | Journal Article |
| id | CGSpace90174 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2009 |
| publishDateRange | 2009 |
| publishDateSort | 2009 |
| publisher | Microbiology Society |
| publisherStr | Microbiology Society |
| record_format | dspace |
| spelling | CGSpace901742023-10-02T12:04:16Z Sequence characteristics of PVY recombinants Hu, X. Karasev, A.V. Brown, C.J. Lorenzen, J.H. potato virus y (pvy) genome potyvirus rna viruses virology Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the physical and evolutionary mechanisms driving their emergence are not clear at the moment. The replicase-mediated template-switching model is considered the most likely mechanism for forming new RNA virus recombinants. Two factors, RNA secondary structure (especially stem-loop structures) and AU-rich regions, have been reported to affect recombination in this model. In this study, we investigated the influence of these two factors on PVY recombination from two perspectives: their distribution along the whole genome and differences between regions flanking the recombination junctions (RJs). Based on their distributions, only a few identified RJs in PVY genomes were located in lower negative FORS-D, i.e. having greater secondary-structure potential and higher AU-content regions, but most RJs had more negative FORS-D values upstream and/or higher AU content downstream. Our whole-genome analyses showed that RNA secondary structures and/or AU-rich regions at some sites may have affected PVY recombination, but in general they were not the main forces driving PVY recombination. 2009-12-01 2018-01-15T10:50:43Z 2018-01-15T10:50:43Z Journal Article https://hdl.handle.net/10568/90174 en Limited Access Microbiology Society Hu, X., Karasev, A.V., Brown, C.J. & Lorenzen, J.H. (2009). Sequence characteristics of potato virus Y recombinants. Journal of General Virology, 90(12), 3033-3041. |
| spellingShingle | potato virus y (pvy) genome potyvirus rna viruses virology Hu, X. Karasev, A.V. Brown, C.J. Lorenzen, J.H. Sequence characteristics of PVY recombinants |
| title | Sequence characteristics of PVY recombinants |
| title_full | Sequence characteristics of PVY recombinants |
| title_fullStr | Sequence characteristics of PVY recombinants |
| title_full_unstemmed | Sequence characteristics of PVY recombinants |
| title_short | Sequence characteristics of PVY recombinants |
| title_sort | sequence characteristics of pvy recombinants |
| topic | potato virus y (pvy) genome potyvirus rna viruses virology |
| url | https://hdl.handle.net/10568/90174 |
| work_keys_str_mv | AT hux sequencecharacteristicsofpvyrecombinants AT karasevav sequencecharacteristicsofpvyrecombinants AT browncj sequencecharacteristicsofpvyrecombinants AT lorenzenjh sequencecharacteristicsofpvyrecombinants |