Dynamic response of RNA editing to temperature in grape by RNA deep sequencing DOI Creative Commons
Aidi Zhang, Xiaohan Jiang, Fuping Zhang

et al.

Functional & Integrative Genomics, Journal Year: 2019, Volume and Issue: 20(3), P. 421 - 432

Published: Nov. 19, 2019

Abstract RNA editing is a post-transcriptional process of modifying genetic information on molecules, which provides cells an additional level gene expression regulation. Unlike mammals, in land plants, converts C-to-U residues organelles. However, its potential roles response to different stressors (heat, salt, and so on) remains unclear. Grape one the most popular economically important fruits world, production, like other crops, must deal with abiotic biotic stresses, cause reductions yield fruit quality. In our study, we tested influence environmental factor temperature whole mRNA from grape organelle. total, identified 122 627 sites chloroplast mitochondria respectively average efficiency nearly ~ 60%. The analyses revealed that number non-synonymous were higher than synonymous sites, amino acid substitution type tends be hydrophobic. Additionally, overall decreased rises, especially for several transcripts ( matK , ndhB etc.). We also found PPR genes may contribute decline at high temperature. Our findings suggested events very sensitive heat stress; changes stress adaption grape.

Language: Английский

Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae DOI Creative Commons
Daliang Liu, Zhihan Zhang,

Yanlin Hao

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 25, 2024

Abstract Background Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin evolutionary history. Result We sequenced complete organelle genomes gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited quadripartite structure large single-copy region (LSC), small (SSC), pair inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, four rRNAs. mitochondrial (681,203 alternative conformations alongside monocyclic structure: 61 encoding 38 20 three rRNAs, RNA editing-impacting genes, ATP6 , RPL16 COX2 NAD4L NAD5 NAD7 RPS1 . Comparative analyses revealed frequent recombination events apparent rRNA gene gains losses Theaceae. In genomes, protein-coding strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic confirmed Stewartieae's early divergence within shedding light on characteristics evolution Conclusions studied detailed characterization structure, composition, repeated sequences, along with identification lateral transfer (LGT) complexities. discovery number repetitive sequences simple repeats (SSRs) has led new molecular phylogenetic markers. Decoding organellar provides valuable genomic resources for further studies plant phylogenomics biology.

Language: Английский

Citations

6
Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae DOI Creative Commons
Yuanyuan Li, Youyan Liu,

Xu Zeng

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: April 23, 2024

Angelica dahurica is a kind of Chinese traditional herbs with economic and ornament value, widely distributed in China. Despite its significance, there have been limited comprehensive investigations on the genome A. , particularly regarding mitochondrial genomes. To investigate conversion between chloroplast genome, complete circular was assembled using Oxford Nanopore Technologies (ONT) long reads. The had length 228,315 base pairs (bp) 45.06% GC content. encodes 56 genes, including 34 protein-coding 19 tRNA genes 3 rRNA genes. Moreover, we discovered that 9 homologous large fragments based sequence similarity. This first report for which could provide an insight communication plastid also give reference medicinal plants within family.

Language: Английский

Citations

6
RNA editing in plants: A comprehensive survey of bioinformatics tools and databases DOI
Claudio Lo Giudice, Irene Hernández, Luigi R. Ceci

et al.

Plant Physiology and Biochemistry, Journal Year: 2019, Volume and Issue: 137, P. 53 - 61

Published: Feb. 2, 2019

Language: Английский

Citations

42
The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation DOI Creative Commons

Duan Chu,

Lai Wei

Plant Direct, Journal Year: 2019, Volume and Issue: 3(9)

Published: Sept. 1, 2019

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

Language: Английский

Citations

41
Dynamic response of RNA editing to temperature in grape by RNA deep sequencing DOI Creative Commons
Aidi Zhang, Xiaohan Jiang, Fuping Zhang

et al.

Functional & Integrative Genomics, Journal Year: 2019, Volume and Issue: 20(3), P. 421 - 432

Published: Nov. 19, 2019

Abstract RNA editing is a post-transcriptional process of modifying genetic information on molecules, which provides cells an additional level gene expression regulation. Unlike mammals, in land plants, converts C-to-U residues organelles. However, its potential roles response to different stressors (heat, salt, and so on) remains unclear. Grape one the most popular economically important fruits world, production, like other crops, must deal with abiotic biotic stresses, cause reductions yield fruit quality. In our study, we tested influence environmental factor temperature whole mRNA from grape organelle. total, identified 122 627 sites chloroplast mitochondria respectively average efficiency nearly ~ 60%. The analyses revealed that number non-synonymous were higher than synonymous sites, amino acid substitution type tends be hydrophobic. Additionally, overall decreased rises, especially for several transcripts ( matK , ndhB etc.). We also found PPR genes may contribute decline at high temperature. Our findings suggested events very sensitive heat stress; changes stress adaption grape.

Language: Английский

Citations

40