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Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans
We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of Drosophila yakuba and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segre...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069613/ https://www.ncbi.nlm.nih.gov/pubmed/24710518 http://dx.doi.org/10.1093/molbev/msu124 |
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author | Rogers, Rebekah L. Cridland, Julie M. Shao, Ling Hu, Tina T. Andolfatto, Peter Thornton, Kevin R. |
author_facet | Rogers, Rebekah L. Cridland, Julie M. Shao, Ling Hu, Tina T. Andolfatto, Peter Thornton, Kevin R. |
author_sort | Rogers, Rebekah L. |
collection | PubMed |
description | We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of Drosophila yakuba and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting that deleterious impacts are common. Drosophila simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. Drosophila simulans displays an excess of high-frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited noncoding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change. |
format | Online Article Text |
id | pubmed-4069613 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-40696132014-06-25 Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans Rogers, Rebekah L. Cridland, Julie M. Shao, Ling Hu, Tina T. Andolfatto, Peter Thornton, Kevin R. Mol Biol Evol Discoveries We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of Drosophila yakuba and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting that deleterious impacts are common. Drosophila simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. Drosophila simulans displays an excess of high-frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited noncoding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change. Oxford University Press 2014-07 2014-04-07 /pmc/articles/PMC4069613/ /pubmed/24710518 http://dx.doi.org/10.1093/molbev/msu124 Text en © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Discoveries Rogers, Rebekah L. Cridland, Julie M. Shao, Ling Hu, Tina T. Andolfatto, Peter Thornton, Kevin R. Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans |
title | Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans |
title_full | Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans |
title_fullStr | Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans |
title_full_unstemmed | Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans |
title_short | Landscape of Standing Variation for Tandem Duplications in Drosophila yakuba and Drosophila simulans |
title_sort | landscape of standing variation for tandem duplications in drosophila yakuba and drosophila simulans |
topic | Discoveries |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069613/ https://www.ncbi.nlm.nih.gov/pubmed/24710518 http://dx.doi.org/10.1093/molbev/msu124 |
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