Exploring the RNA Editing Events and Their Potential Regulatory Roles in Tea Plant (Camellia sinensis L.)

Zhang, Mengyuan; Li, Zhuo; Wang, Zijian; Xiao, Yao; Liu, Bao; Wang, Min; An, Chuanjing; Gao, Yuefang

doi:10.3390/ijms232113640

Cited by 4 publications

(1 citation statement)

References 62 publications

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“…RNA editing events are highly frequent in plant mitochondrial genomes and are critical for gene expression [10,81]. RNA editing sites in different plant mitogenomes exhibit certain variations.…”

Section: Rna Editing In the R Chingii Mitogenomementioning

confidence: 99%

Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family

Han,

Feng,

Wang

et al. 2024

Genes

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Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding.

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Section: Rna Editing In the R Chingii Mitogenomementioning

confidence: 99%

Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family

Han,

Feng,

Wang

et al. 2024

Genes

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PlantC2U: deep learning of cross-species sequence landscapes predicts plastid C-to-U RNA editing in plants

Xu,

Li,

Song

et al. 2024

Journal of Experimental Botany

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In plants, C-to-U RNA editing is mainly occurred in the plastids and mitochondria transcripts, which contributes to complex transcriptional regulatory network. More evidences reveal that RNA editing plays critical roles in plant growth and development. However, RNA editing sites accurately detected by transcriptome sequencing data alone are still challenging. In the present study, we develop PlantC2U, which is a convolutional neural network to predict plastid C-to-U RNA editing based on the genomic sequence. PlantC2U achieves over 95% sensitivity and 99% specificity, which outperforms PREPACT tool, random forest, and support vector machine. PlantC2U not only further checks RNA editing sites from transcriptome data to reduce the possible false positives, but also assesses the effect of different mutations on C-to-U RNA editing based on the flanking sequences. Moreover, we found the patterns of tissue-specific RNA editing in mangrove plant Kandelia obovata, and observed reduced C-to-U RNA editing rates in cold stress response of K. obovata, suggesting their potential regulatory roles in the plants stress adaption. In addition, we present RNAeditDB, available online at https://jasonxu.shinyapps.io/RNAeditDB/. Together, PlantC2U and RNAeditDB would help researchers explore the RNA editing events in plants and thus would be of broad utility for the plant research community.

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Genome‐Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi‐Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves

Xu,

Wang,

Sun

et al. 2024

Plant Cell & Environment

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Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point, and so forth. Furthermore, we combined genome‐wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS‐type) and Maker00003187 (P‐type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1 and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1, and rpoC2 in our previous study and the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNA pull‐down assays revealed that Maker00002998 PPR protein might be involved in the post‐transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.

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Exploring the RNA Editing Events and Their Potential Regulatory Roles in Tea Plant (Camellia sinensis L.)

Cited by 4 publications

References 62 publications

Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family

Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family

PlantC2U: deep learning of cross-species sequence landscapes predicts plastid C-to-U RNA editing in plants

Genome‐Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi‐Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves

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