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Research article
Zhong-Hu Li
Northwest University
Corresponding Author
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Background: Transfer RNAs can participate in a variety of vital life activities. The gymnosperms with important ecological and economic values were the dominant and constructive species in the forest ecosystems in the North hemisphere. However, evolution and structural changes of chloroplast tRNA in gymnosperms remain largely unclear.
Results: In this study, the nucleotide evolution, phylogenetic relationships and structural variations of 1,779 chloroplast tRNAs in gymnosperms were determined. The number and types of tRNA genes contained in the chloroplast genome of different gymnosperms were not much different, the average amount of tRNA contained was 33, and the occurrence frequency of various types of tRNA in gymnosperms was generally consistent. Nearly half of the anti-codons were absent. Molecular sequence variation analysis revealed the conservative secondary structure of tRNA. About a quarter of the tRNA genes were found to contain precoded 3’ CCA tails. A few tRNAs underwent novel structural changes that were closely related to their minimum free energy, these structural changes affected the stability of tRNA. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors and tRNALeu was the most primitive type of tRNA. The transition rate of chloroplast tRNAs was higher than the transversion rate in gymnosperms. The tRNAs continuously have experienced more loss than duplication events during the evolutionary process.
Conclusions: These findings provided novel insights into the molecular evolution and biological characteristics of the chloroplast tRNA in gymnosperms.
Keywords
Chloroplast tRNA, Conservation, Evolution, Phylogenetic relationships, Minimum free energy
Figure 1
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Figure 3
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Figure 4
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This is a list of supplementary files associated with this preprint. Click to download.
- Tables.docx
- Tables.docx
- FigureS1.tif
Figure S1 Phylogenetic tree of gymnosperm chloroplast tRNAs. Phylogenetic tree was constructed using the Maximum likelihood method and 1000 bootstrap replicates using MEGA software.
- FigureS1.tif
Figure S1 Phylogenetic tree of gymnosperm chloroplast tRNAs. Phylogenetic tree was constructed using the Maximum likelihood method and 1000 bootstrap replicates using MEGA software.
- FigureS2.png
Figure S2 Duplication and loss events of gymnosperm chloroplast tRNAs. Duplication and loss analysis was conducted using Notung software.
- FigureS2.png
Figure S2 Duplication and loss events of gymnosperm chloroplast tRNAs. Duplication and loss analysis was conducted using Notung software.
- TableS1.docx
Table S1 54 gymnosperms and their NCBI ID Numbers.
- TableS1.docx
Table S1 54 gymnosperms and their NCBI ID Numbers.
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CURRENT STATUS: Under Review
Version 1
Posted 24 Nov, 2020
No community comments so far
Editorial decision: Major revision
On 27 Mar, 2021
Review #2 received
Received 25 Mar, 2021
Review #1 received
Received 05 Dec, 2020
Reviewer #2 agreed
On 03 Dec, 2020
Reviewer #1 agreed
On 20 Nov, 2020
Reviewers invited
Invitations sent on 15 Nov, 2020
Editor assigned
On 21 Oct, 2020
Submission checks complete
On 21 Oct, 2020
Editor invited
On 21 Oct, 2020
First submitted
On 19 Oct, 2020
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
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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
Zhong-Hu Li
Northwest 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: Under Review
Version 1
Posted 24 Nov, 2020
No community comments so far
Editorial decision: Major revision
On 27 Mar, 2021
Review #2 received
Received 25 Mar, 2021
Review #1 received
Received 05 Dec, 2020
Reviewer #2 agreed
On 03 Dec, 2020
Reviewer #1 agreed
On 20 Nov, 2020
Reviewers invited
Invitations sent on 15 Nov, 2020
Editor assigned
On 21 Oct, 2020
Submission checks complete
On 21 Oct, 2020
Editor invited
On 21 Oct, 2020
First submitted
On 19 Oct, 2020
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
Background: Transfer RNAs can participate in a variety of vital life activities. The gymnosperms with important ecological and economic values were the dominant and constructive species in the forest ecosystems in the North hemisphere. However, evolution and structural changes of chloroplast tRNA in gymnosperms remain largely unclear.
Results: In this study, the nucleotide evolution, phylogenetic relationships and structural variations of 1,779 chloroplast tRNAs in gymnosperms were determined. The number and types of tRNA genes contained in the chloroplast genome of different gymnosperms were not much different, the average amount of tRNA contained was 33, and the occurrence frequency of various types of tRNA in gymnosperms was generally consistent. Nearly half of the anti-codons were absent. Molecular sequence variation analysis revealed the conservative secondary structure of tRNA. About a quarter of the tRNA genes were found to contain precoded 3’ CCA tails. A few tRNAs underwent novel structural changes that were closely related to their minimum free energy, these structural changes affected the stability of tRNA. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors and tRNALeu was the most primitive type of tRNA. The transition rate of chloroplast tRNAs was higher than the transversion rate in gymnosperms. The tRNAs continuously have experienced more loss than duplication events during the evolutionary process.
Conclusions: These findings provided novel insights into the molecular evolution and biological characteristics of the chloroplast tRNA in gymnosperms.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
- Tables.docx
- Tables.docx
- FigureS1.tif
Figure S1 Phylogenetic tree of gymnosperm chloroplast tRNAs. Phylogenetic tree was constructed using the Maximum likelihood method and 1000 bootstrap replicates using MEGA software.
- FigureS1.tif
Figure S1 Phylogenetic tree of gymnosperm chloroplast tRNAs. Phylogenetic tree was constructed using the Maximum likelihood method and 1000 bootstrap replicates using MEGA software.
- FigureS2.png
Figure S2 Duplication and loss events of gymnosperm chloroplast tRNAs. Duplication and loss analysis was conducted using Notung software.
- FigureS2.png
Figure S2 Duplication and loss events of gymnosperm chloroplast tRNAs. Duplication and loss analysis was conducted using Notung software.
- TableS1.docx
Table S1 54 gymnosperms and their NCBI ID Numbers.
- TableS1.docx
Table S1 54 gymnosperms and their NCBI ID Numbers.
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