Drosophila duplication hotspots are associated with late-replicating regions of the genome.
Duplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects (e.g. duplications underlie a variety of diseases) but can also be highly advantageous. The phenotypic potential of newly arisen duplications has stim...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-11-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3207856?pdf=render |
| _version_ | 1811225943138631680 |
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| author | Margarida Cardoso-Moreira J J Emerson Andrew G Clark Manyuan Long |
| author_facet | Margarida Cardoso-Moreira J J Emerson Andrew G Clark Manyuan Long |
| author_sort | Margarida Cardoso-Moreira |
| collection | DOAJ |
| description | Duplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects (e.g. duplications underlie a variety of diseases) but can also be highly advantageous. The phenotypic potential of newly arisen duplications has stimulated wide interest in both the mutational and selective processes shaping these variants in the genome. Here we take advantage of the Drosophila simulans-Drosophila melanogaster genetic system to further our understanding of both processes. Regarding mutational processes, the study of two closely related species allows investigation of the potential existence of shared duplication hotspots, and the similarities and differences between the two genomes can be used to dissect its underlying causes. Regarding selection, the difference in the effective population size between the two species can be leveraged to ask questions about the strength of selection acting on different classes of duplications. In this study, we conducted a survey of duplication polymorphisms in 14 different lines of D. simulans using tiling microarrays and combined it with an analogous survey for the D. melanogaster genome. By integrating the two datasets, we identified duplication hotspots conserved between the two species. However, unlike the duplication hotspots identified in mammalian genomes, Drosophila duplication hotspots are not associated with sequences of high sequence identity capable of mediating non-allelic homologous recombination. Instead, Drosophila duplication hotspots are associated with late-replicating regions of the genome, suggesting a link between DNA replication and duplication rates. We also found evidence supporting a higher effectiveness of selection on duplications in D. simulans than in D. melanogaster. This is also true for duplications segregating at high frequency, where we find evidence in D. simulans that a sizeable fraction of these mutations is being driven to fixation by positive selection. |
| first_indexed | 2024-04-12T09:15:37Z |
| format | Article |
| id | doaj.art-09c0a0aef1e5478486dd255ae306c161 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-12T09:15:37Z |
| publishDate | 2011-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-09c0a0aef1e5478486dd255ae306c1612022-12-22T03:38:50ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042011-11-01711e100234010.1371/journal.pgen.1002340Drosophila duplication hotspots are associated with late-replicating regions of the genome.Margarida Cardoso-MoreiraJ J EmersonAndrew G ClarkManyuan LongDuplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects (e.g. duplications underlie a variety of diseases) but can also be highly advantageous. The phenotypic potential of newly arisen duplications has stimulated wide interest in both the mutational and selective processes shaping these variants in the genome. Here we take advantage of the Drosophila simulans-Drosophila melanogaster genetic system to further our understanding of both processes. Regarding mutational processes, the study of two closely related species allows investigation of the potential existence of shared duplication hotspots, and the similarities and differences between the two genomes can be used to dissect its underlying causes. Regarding selection, the difference in the effective population size between the two species can be leveraged to ask questions about the strength of selection acting on different classes of duplications. In this study, we conducted a survey of duplication polymorphisms in 14 different lines of D. simulans using tiling microarrays and combined it with an analogous survey for the D. melanogaster genome. By integrating the two datasets, we identified duplication hotspots conserved between the two species. However, unlike the duplication hotspots identified in mammalian genomes, Drosophila duplication hotspots are not associated with sequences of high sequence identity capable of mediating non-allelic homologous recombination. Instead, Drosophila duplication hotspots are associated with late-replicating regions of the genome, suggesting a link between DNA replication and duplication rates. We also found evidence supporting a higher effectiveness of selection on duplications in D. simulans than in D. melanogaster. This is also true for duplications segregating at high frequency, where we find evidence in D. simulans that a sizeable fraction of these mutations is being driven to fixation by positive selection.http://europepmc.org/articles/PMC3207856?pdf=render |
| spellingShingle | Margarida Cardoso-Moreira J J Emerson Andrew G Clark Manyuan Long Drosophila duplication hotspots are associated with late-replicating regions of the genome. PLoS Genetics |
| title | Drosophila duplication hotspots are associated with late-replicating regions of the genome. |
| title_full | Drosophila duplication hotspots are associated with late-replicating regions of the genome. |
| title_fullStr | Drosophila duplication hotspots are associated with late-replicating regions of the genome. |
| title_full_unstemmed | Drosophila duplication hotspots are associated with late-replicating regions of the genome. |
| title_short | Drosophila duplication hotspots are associated with late-replicating regions of the genome. |
| title_sort | drosophila duplication hotspots are associated with late replicating regions of the genome |
| url | http://europepmc.org/articles/PMC3207856?pdf=render |
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