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Research article
Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: Evidence from the frequency of endosymbiotic DNA transfer
Deng-Ke Niu
Beijing Normal University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4503-2658
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT).
Results: We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae, the tardigrade Ramazzottius varieornatus, and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina. Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents.
Conclusions: Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.
Keywords
Horizontal gene transfer (HGT), Nuclear mitochondrial DNA (NUMT), Nuclear plastid DNA (NUPT), Double-strand breaks (DSBs), Non-homologous end joining (NHEJ), Bdelloid rotifers.
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CURRENT STATUS: Published
Version 2
Posted 15 Jun, 2020
Published
On 01 Jul, 2020
No community comments so far
Editorial decision: Minor revision
On 18 Jun, 2020
Reviewer #1 agreed
On 17 Jun, 2020
Review #1 received
Received 17 Jun, 2020
Reviewers invited
Invitations sent on 16 Jun, 2020
Editor assigned
On 15 Jun, 2020
Editor invited
On 14 Jun, 2020
Submission checks complete
On 13 Jun, 2020
No comments provided
Editorial decision: Major revision
On 08 Jun, 2020
Review #3 received
Received 29 Mar, 2020
Reviewer #3 agreed
On 14 Mar, 2020
Review #2 received
Received 07 Jan, 2020
Review #1 received
Received 21 Dec, 2019
Reviewer #2 agreed
On 25 Nov, 2019
Reviewer #1 agreed
On 23 Nov, 2019
Reviewers invited
Invitations sent on 20 Nov, 2019
Editor assigned
On 07 Nov, 2019
Submission checks complete
On 06 Nov, 2019
Editor invited
On 06 Nov, 2019
First submitted
On 05 Nov, 2019
Metrics
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: Evidence from the frequency of endosymbiotic DNA transfer
Deng-Ke Niu
Beijing Normal University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4503-2658
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 2
Posted 15 Jun, 2020
Published
On 01 Jul, 2020
No community comments so far
Editorial decision: Minor revision
On 18 Jun, 2020
Reviewer #1 agreed
On 17 Jun, 2020
Review #1 received
Received 17 Jun, 2020
Reviewers invited
Invitations sent on 16 Jun, 2020
Editor assigned
On 15 Jun, 2020
Editor invited
On 14 Jun, 2020
Submission checks complete
On 13 Jun, 2020
No comments provided
Editorial decision: Major revision
On 08 Jun, 2020
Review #3 received
Received 29 Mar, 2020
Reviewer #3 agreed
On 14 Mar, 2020
Review #2 received
Received 07 Jan, 2020
Review #1 received
Received 21 Dec, 2019
Reviewer #2 agreed
On 25 Nov, 2019
Reviewer #1 agreed
On 23 Nov, 2019
Reviewers invited
Invitations sent on 20 Nov, 2019
Editor assigned
On 07 Nov, 2019
Submission checks complete
On 06 Nov, 2019
Editor invited
On 06 Nov, 2019
First submitted
On 05 Nov, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
Background: Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT).
Results: We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae, the tardigrade Ramazzottius varieornatus, and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina. Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents.
Conclusions: Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.
Figure 1