Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution
Abstract Background Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod an...
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | BMC Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12915-020-00789-1 |
| _version_ | 1818993943311810560 |
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| author | Dick Roelofs Arthur Zwaenepoel Tom Sistermans Joey Nap Andries A. Kampfraath Yves Van de Peer Jacintha Ellers Ken Kraaijeveld |
| author_facet | Dick Roelofs Arthur Zwaenepoel Tom Sistermans Joey Nap Andries A. Kampfraath Yves Van de Peer Jacintha Ellers Ken Kraaijeveld |
| author_sort | Dick Roelofs |
| collection | DOAJ |
| description | Abstract Background Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. Results Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (K S ), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in K S distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs. Conclusions Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods. |
| first_indexed | 2024-12-20T20:50:05Z |
| format | Article |
| id | doaj.art-283edb5182374ce9b5bb3ffa64a7f436 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-12-20T20:50:05Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-283edb5182374ce9b5bb3ffa64a7f4362022-12-21T19:26:56ZengBMCBMC Biology1741-70072020-05-0118111310.1186/s12915-020-00789-1Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolutionDick Roelofs0Arthur Zwaenepoel1Tom Sistermans2Joey Nap3Andries A. Kampfraath4Yves Van de Peer5Jacintha Ellers6Ken Kraaijeveld7Department of Ecological Science, Vrije UniversiteitCenter for Plant Systems Biology, VIBDepartment of Ecological Science, Vrije UniversiteitDepartment of Ecological Science, Vrije UniversiteitDepartment of Ecological Science, Vrije UniversiteitCenter for Plant Systems Biology, VIBDepartment of Ecological Science, Vrije UniversiteitOrigins CenterAbstract Background Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. Results Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (K S ), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in K S distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs. Conclusions Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.http://link.springer.com/article/10.1186/s12915-020-00789-1PolyploidyGene duplication and lossCo-linearityInsectaCollembolaGene tree reconciliation |
| spellingShingle | Dick Roelofs Arthur Zwaenepoel Tom Sistermans Joey Nap Andries A. Kampfraath Yves Van de Peer Jacintha Ellers Ken Kraaijeveld Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution BMC Biology Polyploidy Gene duplication and loss Co-linearity Insecta Collembola Gene tree reconciliation |
| title | Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution |
| title_full | Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution |
| title_fullStr | Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution |
| title_full_unstemmed | Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution |
| title_short | Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution |
| title_sort | multi faceted analysis provides little evidence for recurrent whole genome duplications during hexapod evolution |
| topic | Polyploidy Gene duplication and loss Co-linearity Insecta Collembola Gene tree reconciliation |
| url | http://link.springer.com/article/10.1186/s12915-020-00789-1 |
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