Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays
Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. How these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to host immune defenses is unknown. W...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2018-08-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/35453 |
| _version_ | 1811252967545765888 |
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| author | Thomas A Sasani Kelsey R Cone Aaron R Quinlan Nels C Elde |
| author_facet | Thomas A Sasani Kelsey R Cone Aaron R Quinlan Nels C Elde |
| author_sort | Thomas A Sasani |
| collection | DOAJ |
| description | Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. How these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to host immune defenses is unknown. We performed experimental evolution with vaccinia virus populations harboring a SNV in a gene actively undergoing copy number amplification. Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. Our analysis uncovered a mechanism of adaptive SNV homogenization reminiscent of gene conversion, which is actively driven by selection. This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. |
| first_indexed | 2024-04-12T16:43:43Z |
| format | Article |
| id | doaj.art-d8455d8b2f684fe0ae59e37a56e538b6 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:43:43Z |
| publishDate | 2018-08-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-d8455d8b2f684fe0ae59e37a56e538b62022-12-22T03:24:41ZengeLife Sciences Publications LtdeLife2050-084X2018-08-01710.7554/eLife.35453Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arraysThomas A Sasani0https://orcid.org/0000-0003-2317-1374Kelsey R Cone1https://orcid.org/0000-0002-4547-7174Aaron R Quinlan2https://orcid.org/0000-0003-1756-0859Nels C Elde3https://orcid.org/0000-0002-0426-1377Department of Human Genetics, University of Utah, Salt Lake, United StatesDepartment of Human Genetics, University of Utah, Salt Lake, United StatesDepartment of Human Genetics, University of Utah, Salt Lake, United StatesDepartment of Human Genetics, University of Utah, Salt Lake, United StatesPoxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. How these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to host immune defenses is unknown. We performed experimental evolution with vaccinia virus populations harboring a SNV in a gene actively undergoing copy number amplification. Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. Our analysis uncovered a mechanism of adaptive SNV homogenization reminiscent of gene conversion, which is actively driven by selection. This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems.https://elifesciences.org/articles/35453poxvirusexperimental evolutiongene conversionlong read sequencingcopy number variationvaccinia virus |
| spellingShingle | Thomas A Sasani Kelsey R Cone Aaron R Quinlan Nels C Elde Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays eLife poxvirus experimental evolution gene conversion long read sequencing copy number variation vaccinia virus |
| title | Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays |
| title_full | Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays |
| title_fullStr | Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays |
| title_full_unstemmed | Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays |
| title_short | Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays |
| title_sort | long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays |
| topic | poxvirus experimental evolution gene conversion long read sequencing copy number variation vaccinia virus |
| url | https://elifesciences.org/articles/35453 |
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