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Research article
xiujun zhang
Wuhan Botanical Garden
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
RNA editing is a post-transcriptional modification that complement variation at the DNA level. Until now, different RNA editing systems were found in the major eukaryotic lineages. However, the evolution trajectory in plant chloroplast remains unclear. To gain a better understanding of RNA editing in plant chloroplast, in this study, based on publicly available RNA-seq data across three clades (fern, gymnosperm, and angiosperm), we provided a detailed analysis of RNA editing events in plant chloroplasts and discussed the evolution of RNA editing in land plants.
Results
There were a total of 5,389 editing sites located in leaf chloroplast identified across 21 plants after rigorous screening. We found that the cluster of RNA editing sites across 21 plants complied with the phylogenetic tree based on linked protein sequences approximately, there is a common phenomenon that more editing sites occurred in ancient plants for all the three clades. Statistics results revealed that majority (~ 95%) of the editing events resulted in non-synonymous codon changes, RNA editing occurred in second codon position was mainly the largest, and RNA editing caused an overall increase in hydrophobicity of the resulting proteins. The analyses also revealed that there was an uneven distribution of editing sites among species, genes, and codon positions, the average RNA editing extent varied among different plants as well as genes, a lowest RNA editing extent (0.43) was detected in Selaginella moellendorffii. Finally, we found that the loss of editing sites along angiosperm evolution is mainly occurring by reduce of cytosines content, where fern plants has the highest cytosine content.
Conclusions
Many of the RNA sites identified in our study have not been previously reported and provide a valuable data set for future research community. Our findings also provide valuable information for evolution of RNA editing in plants.
Keywords
RNA editing, plant, RNA sequencing, cytosine, evolution
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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.
Research article
xiujun zhang
Wuhan Botanical Garden
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 07 Jul, 2020
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
RNA editing is a post-transcriptional modification that complement variation at the DNA level. Until now, different RNA editing systems were found in the major eukaryotic lineages. However, the evolution trajectory in plant chloroplast remains unclear. To gain a better understanding of RNA editing in plant chloroplast, in this study, based on publicly available RNA-seq data across three clades (fern, gymnosperm, and angiosperm), we provided a detailed analysis of RNA editing events in plant chloroplasts and discussed the evolution of RNA editing in land plants.
Results
There were a total of 5,389 editing sites located in leaf chloroplast identified across 21 plants after rigorous screening. We found that the cluster of RNA editing sites across 21 plants complied with the phylogenetic tree based on linked protein sequences approximately, there is a common phenomenon that more editing sites occurred in ancient plants for all the three clades. Statistics results revealed that majority (~ 95%) of the editing events resulted in non-synonymous codon changes, RNA editing occurred in second codon position was mainly the largest, and RNA editing caused an overall increase in hydrophobicity of the resulting proteins. The analyses also revealed that there was an uneven distribution of editing sites among species, genes, and codon positions, the average RNA editing extent varied among different plants as well as genes, a lowest RNA editing extent (0.43) was detected in Selaginella moellendorffii. Finally, we found that the loss of editing sites along angiosperm evolution is mainly occurring by reduce of cytosines content, where fern plants has the highest cytosine content.
Conclusions
Many of the RNA sites identified in our study have not been previously reported and provide a valuable data set for future research community. Our findings also provide valuable information for evolution of RNA editing in plants.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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