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Research article
Renchao Zhou
School of Life Sciences, Sun Yat-sen University
Corresponding Author
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Background: With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with holoparasitic plants in Orobanchaceae, only Clade VI has no available plastid genome sequences for holoparasitic plants. In this study, we sequenced the plastome and transcriptome of Aeginetia indica , a holoparasitic plant in Clade VI of Orobanchaceae, to study its plastome evolution and the corresponding changes in the nuclear genome as a response of the loss of photosynthetic function.
Results: The plastome of A. indica is reduced to 86,212 bp in size, and almost all photosynthesis-related genes were lost. Massive fragments of the lost plastid genes were transferred into the mitochondrial and/or nuclear genomes. These fragments could not be detected in its transcriptomes, suggesting that they were non-functional. Most protein coding genes in the plastome showed the signal of relaxation of purifying selection. Plastome and transcriptome analyses indicated that the photosynthesis pathway is completely lost, and that the porphyrin and chlorophyll metabolism pathway is partially retained, although chlorophyll synthesis is not possible.
Conclusions: Our study suggests the loss of photosynthesis-related functions in A. indica in both the nuclear and plastid genomes. The lost plastid genes are transferred into its nuclear and/or mitochondrial genomes, and exist in very small fragments with no expression and are thus non-functional. The Aeginetia indica plastome also provides a resource for comparative studies on the repeated evolution of holoparasitism in Orobanchaceae.
Keywords
Aeginetia indica, plastid genome, transcriptome
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CURRENT STATUS: Published
View the published article at BMC Plant Biology.
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Posted 13 May, 2020
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Editorial decision: Accept
On 29 Apr, 2020
Submission checks complete
On 23 Nov, 2019
No comments provided
Editorial decision: Minor revision
On 17 Apr, 2020
Editor assigned
On 31 Mar, 2020
Submission checks complete
On 30 Mar, 2020
Editor invited
On 30 Mar, 2020
No comments provided
Editorial decision: Minor revision
On 29 Mar, 2020
Review #2 received
Received 28 Mar, 2020
Review #1 received
Received 28 Mar, 2020
Reviewer #2 agreed
On 15 Mar, 2020
Reviewers invited
Invitations sent on 12 Mar, 2020
Reviewer #1 agreed
On 12 Mar, 2020
Editor assigned
On 06 Mar, 2020
Submission checks complete
On 05 Mar, 2020
Editor invited
On 05 Mar, 2020
No comments provided
Editorial decision: Major revision
On 19 Dec, 2019
Review #3 received
Received 18 Dec, 2019
Reviewer #3 agreed
On 05 Dec, 2019
Review #1 received
Received 02 Dec, 2019
Review #2 received
Received 01 Dec, 2019
Reviewer #2 agreed
On 30 Nov, 2019
Reviewer #1 agreed
On 28 Nov, 2019
Reviewers invited
Invitations sent on 26 Nov, 2019
Editor assigned
On 21 Nov, 2019
Submission checks complete
On 20 Nov, 2019
Editor invited
On 20 Nov, 2019
First submitted
On 16 Nov, 2019
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Subject Areas
Plant Molecular Biology and Genetics
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See the published version of this preprint at BMC Plant Biology.
This is a preprint, 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
Renchao Zhou
School of Life Sciences, Sun Yat-sen University
Corresponding Author
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
View the published article at BMC Plant Biology.
Version 4
Posted 13 May, 2020
No community comments so far
Editorial decision: Accept
On 29 Apr, 2020
Submission checks complete
On 23 Nov, 2019
No comments provided
Editorial decision: Minor revision
On 17 Apr, 2020
Editor assigned
On 31 Mar, 2020
Submission checks complete
On 30 Mar, 2020
Editor invited
On 30 Mar, 2020
No comments provided
Editorial decision: Minor revision
On 29 Mar, 2020
Review #2 received
Received 28 Mar, 2020
Review #1 received
Received 28 Mar, 2020
Reviewer #2 agreed
On 15 Mar, 2020
Reviewers invited
Invitations sent on 12 Mar, 2020
Reviewer #1 agreed
On 12 Mar, 2020
Editor assigned
On 06 Mar, 2020
Submission checks complete
On 05 Mar, 2020
Editor invited
On 05 Mar, 2020
No comments provided
Editorial decision: Major revision
On 19 Dec, 2019
Review #3 received
Received 18 Dec, 2019
Reviewer #3 agreed
On 05 Dec, 2019
Review #1 received
Received 02 Dec, 2019
Review #2 received
Received 01 Dec, 2019
Reviewer #2 agreed
On 30 Nov, 2019
Reviewer #1 agreed
On 28 Nov, 2019
Reviewers invited
Invitations sent on 26 Nov, 2019
Editor assigned
On 21 Nov, 2019
Submission checks complete
On 20 Nov, 2019
Editor invited
On 20 Nov, 2019
First submitted
On 16 Nov, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Plant Biology.
Background: With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with holoparasitic plants in Orobanchaceae, only Clade VI has no available plastid genome sequences for holoparasitic plants. In this study, we sequenced the plastome and transcriptome of Aeginetia indica , a holoparasitic plant in Clade VI of Orobanchaceae, to study its plastome evolution and the corresponding changes in the nuclear genome as a response of the loss of photosynthetic function.
Results: The plastome of A. indica is reduced to 86,212 bp in size, and almost all photosynthesis-related genes were lost. Massive fragments of the lost plastid genes were transferred into the mitochondrial and/or nuclear genomes. These fragments could not be detected in its transcriptomes, suggesting that they were non-functional. Most protein coding genes in the plastome showed the signal of relaxation of purifying selection. Plastome and transcriptome analyses indicated that the photosynthesis pathway is completely lost, and that the porphyrin and chlorophyll metabolism pathway is partially retained, although chlorophyll synthesis is not possible.
Conclusions: Our study suggests the loss of photosynthesis-related functions in A. indica in both the nuclear and plastid genomes. The lost plastid genes are transferred into its nuclear and/or mitochondrial genomes, and exist in very small fragments with no expression and are thus non-functional. The Aeginetia indica plastome also provides a resource for comparative studies on the repeated evolution of holoparasitism in Orobanchaceae.
Figure 1
Figure 2
This is a list of supplementary files associated with this preprint. Click to download.
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