Mapping of plastid RNA editing sites of Helianthus and identification of differential editing in fungal infected plants

Duruvasula, SreeLekha; Sujatha, M.; Ulaganathan, Kandasamy

doi:10.1016/j.cpb.2019.100109

Cited by 5 publications

(2 citation statements)

References 35 publications

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“…In plant organellar transcripts, it was previously thought to be an error-correcting process. On the other hand, the current sequence resources of genomes and transcriptome enabled researchers to better comprehend its importance in plants developments under the abiotic stress conditions [10]. The most common editing types in non-flowering land plants are adenosine (A) to inosine (I) in tRNA, cytidine (C) to uridine (U) in messenger tRNA and RNA, and urea to cytidine (C) in mRNA [11].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide investigation and functional analysis of RNA editing sites in wheat

Rasool

Ishtiaq²,

Uzair³

et al. 2022

PLoS ONE

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Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in controlling environmental stresses. The genome-wide identification and functional characterization of RESs in different types of wheat genotypes was done. We employed six wheat genotypes by RNA-seq analyses to achieve RESs. The findings revealed that RNA editing events occurred on all chromosomes equally. RNA editing sites were distributed randomly and 10–12 types of RESs were detected in wheat genotypes. Higher number of RESs were detected in drought-tolerant genotypes. A-to-I RNA editing (2952, 2977, 1916, 2576, 3422, and 3459) sites were also identified in six wheat genotypes. Most of the genes were found to be engaged in molecular processes after a Gene Ontology analysis. PPR (pentatricopeptide repeat), OZ1 (organelle zinc-finger), and MORF/RIP gene expression levels in wheat were also examined. Normal growth conditions diverge gene expression of these three different gene families, implying that normal growth conditions for various genotypes can modify RNA editing events and have an impact on gene expression levels. While the expression of PPR genes was not change. We used Variant Effect Predictor (VEP) to annotate RNA editing sites, and Local White had the highest RESs in the CDS region of the protein. These findings will be useful for prediction of RESs in other crops and will be helpful in drought tolerance development in wheat.

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Section: Introductionmentioning

confidence: 99%

Genome-wide investigation and functional analysis of RNA editing sites in wheat

Rasool

Ishtiaq²,

Uzair³

et al. 2022

PLoS ONE

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“…Previously, RES was thought to be a proofreading mechanism because it corrected the mitochondrial mRNA through deletion/addition of uridine ( Golden and Hajduk, 2006 ). With the passage of time and inventions of new sequencing techniques such as RNA sequencing (RNA-seq) enables the researcher to its importance in plants developments under the abiotic stress conditions ( Duruvasula et al, 2019 ). This type of RNA editing is dominant, occurred in nucleus, cytosol, plastids, and mitochondria.…”

Section: Introductionmentioning

confidence: 99%

Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress

Rehman

Uzair²,

Chao

et al. 2022

Front. Plant Sci.

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Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.

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