REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes

Giudice, Claudio Lo; Pesole, Graziano; Picardi, Ernesto

doi:10.3389/fpls.2018.00482

Cited by 31 publications

(33 citation statements)

References 26 publications

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“…With increasing numbers of editing sites identified in plants, database is needed to store the editing sites found by different studies. Up to now, REDIdb collected over 25,000 RNA editing sites among 281 species (Lo Giudice, Pesole, & Picardi, ), and database PED even contained the editing sites in 1,621 plant species (Li et al, ). All these tools and databases give convenience to people of the C‐to‐U RNA editing community.…”

Section: Introductionmentioning

confidence: 99%

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The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

Chu

Wei

2019

Plant Direct

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C‐to‐U RNA editing is the conversion from cytidine to uridine at RNA level. In plants, the genes undergo C‐to‐U RNA modification are mainly chloroplast and mitochondrial genes. Case studies have identified the roles of C‐to‐U editing in various biological processes, but the functional consequence of the majority of C‐to‐U editing events is still undiscovered. We retrieved the deep sequenced transcriptome data in roots and shoots of Arabidopsis thaliana and profiled their C‐to‐U RNA editomes and gene expression patterns. We investigated the editing level and conservation pattern of these C‐to‐U editing sites. The levels of nonsynonymous C‐to‐U editing events are higher than levels of synonymous events. The fraction of nonsynonymous editing sites is higher than neutral expectation. Highly edited cytidines are more conserved at DNA level, and the gene expression levels are correlated with C‐to‐U editing levels. Our results demonstrate that the global C‐to‐U editome is shaped by natural selection and that many nonsynonymous C‐to‐U editing events are adaptive. The editing mechanism might be positively selected and maintained and could have profound effects on the modified RNAs.

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Section: Introductionmentioning

confidence: 99%

“…Up to now, REDIdb collected over 25,000 RNA editing sites among 281 species (Lo Giudice, Pesole, & Picardi, 2018), and database PED even contained the editing sites in 1,621 plant species (Li et al, 2019). All these tools and databases give convenience to people of the C-to-U RNA editing community.…”

Section: Introductionmentioning

confidence: 99%

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

Chu

Wei

2019

Plant Direct

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“…This strategy allows a transcriptome-wide fast detection of editing sites and has enormous potential to deepen our knowledge of transcriptional processes in plant. Indeed, the number of complete plant organellar genomes and related transcriptome data have considerably grown in the last decade, and tens of thousands of editing sites have been identi ed in more and more plants [18,19]. However, this strategy is also a challenging task due to its accuracy of mapping the RNA-seq reads against genomic sequence, hence, so different bioinformatic strategies have been introduced to improve the detection of RNA editing sites [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

A comprehensive study on chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis

zhang

Fang

Jiang

et al. 2020

Preprint

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Abstract 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.

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“…These editing sites are not always correctly or completely annotated in primary database such as GenBank, where they are often indicated as misc_feature or as simple exception notes. To overcome these limitations, researchers have developed a series of specialized databases, among which REDIdb was the first specialized database to collect plant RNA editing events and annotate them in their biological context (Giudice et al, 2018). The latest version of REDIdb contains 26618 RNA editing sites distributed among 281 organisms, including those C-to-U RNA editing sites in rice mitochondria.…”

Section: Introductionmentioning

confidence: 99%

Site to site detection and analysis of C-to-U RNA editing in rice mitochondria-encoded ORFs

Zheng

Huang

Chen

et al. 2020

Preprint

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Background Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA editing. In plants, C-to-U modification is almost omnipresent in chloroplasts and mitochondria, where it mainly serves to restore evolutionarily conserved amino acids by changing the codon information. The important roles that C-to-U RNA editing plays in organelle biogenesis, adaptation to environmental changes, and signal transduction have been confirmed in different plant species. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alteration need to be investigated further. Results Here, we totally identified 539 C-to-U editing sites in rice mitochondria-encoded ORFs, 87.2% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, with the support of the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 539 C-to-U RNA editing sites in their biological context. Conclusions We detected 539 C-to-U editing sites in rice mitochondria-encoded ORFs and annotated them with more precise information, which will facilitate our investigation on the function of C-to-U editing events in rice.

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REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes

Cited by 31 publications

References 26 publications

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

A comprehensive study on chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis

Site to site detection and analysis of C-to-U RNA editing in rice mitochondria-encoded ORFs

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