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Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution

(2020) BMC BIOLOGY. 18.
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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 (KS), 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 KS 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.
Keywords
Co-linearity, Collembola, Gene duplication and loss, Gene tree reconciliation, Insecta, Polyploidy, Synonymous distance

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MLA
Roelofs, Dick, et al. “Multi-Faceted Analysis Provides Little Evidence for Recurrent Whole-Genome Duplications during Hexapod Evolution.” BMC BIOLOGY, vol. 18, 2020, doi:10.1186/s12915-020-00789-1.
APA
Roelofs, D., Zwaenepoel, A., Sistermans, T., Nap, J., Kampfraath, A. A., Van de Peer, Y., … Kraaijeveld, K. (2020). Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution. BMC BIOLOGY, 18. https://doi.org/10.1186/s12915-020-00789-1
Chicago author-date
Roelofs, Dick, Arthur Zwaenepoel, Tom Sistermans, Joey Nap, Andries A. Kampfraath, Yves Van de Peer, Jacintha Ellers, and Ken Kraaijeveld. 2020. “Multi-Faceted Analysis Provides Little Evidence for Recurrent Whole-Genome Duplications during Hexapod Evolution.” BMC BIOLOGY 18. https://doi.org/10.1186/s12915-020-00789-1.
Chicago author-date (all authors)
Roelofs, Dick, Arthur Zwaenepoel, Tom Sistermans, Joey Nap, Andries A. Kampfraath, Yves Van de Peer, Jacintha Ellers, and Ken Kraaijeveld. 2020. “Multi-Faceted Analysis Provides Little Evidence for Recurrent Whole-Genome Duplications during Hexapod Evolution.” BMC BIOLOGY 18. doi:10.1186/s12915-020-00789-1.
Vancouver
1.
Roelofs D, Zwaenepoel A, Sistermans T, Nap J, Kampfraath AA, Van de Peer Y, et al. Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution. BMC BIOLOGY. 2020;18.
IEEE
[1]
D. Roelofs et al., “Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution,” BMC BIOLOGY, vol. 18, 2020.
@article{8663234,
  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 (KS), 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 KS 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.},
  articleno    = {57},
  author       = {Roelofs, Dick and Zwaenepoel, Arthur and Sistermans, Tom and Nap, Joey and Kampfraath, Andries A. and Van de Peer, Yves and Ellers, Jacintha and Kraaijeveld, Ken},
  issn         = {1741-7007},
  journal      = {BMC BIOLOGY},
  keywords     = {Co-linearity,Collembola,Gene duplication and loss,Gene tree reconciliation,Insecta,Polyploidy,Synonymous distance},
  language     = {eng},
  pages        = {13},
  title        = {Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution},
  url          = {http://dx.doi.org/10.1186/s12915-020-00789-1},
  volume       = {18},
  year         = {2020},
}

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