Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing

doi:10.3390/ijms22189842

KIB OpenIR

	Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing
	He,Zheng-Shan ; Zhu,Andan ; Yang,Jun-Bo ; Fan,Weishu ; Li,De-Zhu
	2021
发表期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN	1422-0067
卷号	22 期号:18 页码:9842
摘要	Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based on the Illumina short reads which were unable to capture the full spectrum of transcript intermediates within an organelle. To fully investigate the intermediates during intron splicing and the underlying relationships with RNA editing, we used PacBio DNA-seq and Iso-seq, together with Illumina short reads genome and transcriptome sequencing data to assemble the chloroplast and mitochondrial genomes of Nymphaea 'Joey Tomocik' and analyze their posttranscriptional features. With the direct evidence from Iso-seq, multiple intermediates partially or fully intron-spliced were observed, and we also found that both cis- and trans-splicing introns were spliced randomly. Moreover, by using rRNA-depleted and non-Oligo(dT)-enrichment strand-specific RNA-seq data and combining direct SNP-calling and transcript-mapping methods, we identified 98 and 865 RNA-editing sites in the plastome and mitogenome of N. 'Joey Tomocik', respectively. The target codon preference, the tendency of increasing protein hydrophobicity, and the bias distribution of editing sites are similar in both organelles, suggesting their common evolutionary origin and shared editing machinery. The distribution of RNA editing sites also implies that the RNA editing sites in the intron and exon regions may splice synchronously, except those exonic sites adjacent to intron which could only be edited after being intron-spliced. Our study provides solid evidence for the multiple intermediates co-existing during intron-splicing and their interplay with RNA editing in organelle genomes of a basal angiosperm.
关键词	Nymphaea organelle genomes transcriptomes intron splicing RNA editing MESSENGER-RNA PLANT-MITOCHONDRIA WHEAT CHLOROPLASTS ACCURATE SITES EXPRESSION EVOLUTION ALIGNMENT PROTEINS
DOI	10.3390/ijms22189842
WOS记录号	WOS:000699622100001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73700
专题	中国科学院昆明植物研究所
作者单位	1.[He, Zheng-Shan 2.Zhu, Andan 3.Yang, Jun-Bo 4.Fan, Weishu 5.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 6.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	He,Zheng-Shan,Zhu,Andan,Yang,Jun-Bo,et al. Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2021,22(18):9842.
APA	He,Zheng-Shan,Zhu,Andan,Yang,Jun-Bo,Fan,Weishu,&Li,De-Zhu.(2021).Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,22(18),9842.
MLA	He,Zheng-Shan,et al."Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 22.18(2021):9842.