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PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

文献类型： 外文期刊

作者： Shi, Jinsong 1 ; Yan, Shuangyong 3 ; Li, Wenjing 2 ; Yang, Xiurong 5 ; Cui, Zhongqiu 3 ; Li, Junling 3 ; Li, Guangsheng 5 ; Li, Yuejiao 5 ; Hu, Yanping 4 ; Gao, Shan 1 ;

作者机构： 1.Nankai Univ, Coll Life Sci, Tianjin 300071, Peoples R China

2.Nanjing Univ Sch Med, Nanjing, Peoples R China

3.Tianjin Acad Agr Sci, Tianjin Inst Crop Res, Tianjin, Peoples R China

4.Chinese Acad Sci, Northwest Inst Plateau Biol, Qinghai Prov Key Lab Qinghai Tibet Plateau Biol Re, Xining 810008, Qinghai, Peoples R China

5.Northwest Inst Plateau Biol, Chinese Acad Sci, Key Lab Adaptat & Evolut Plateau Biota, Xining, Qinghai, Peoples R China

6.Tianjin Acad Agr Sci, Inst Plant Protect, Tianjin, Peoples R China

关键词： TIS; TTS; AT-rich region; polyA-like site; Arabidopsis thaliana

期刊名称：RNA BIOLOGY （ 影响因子：4.1； 五年影响因子：5.0 ）

ISSN： 1547-6286

年卷期： 2023 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.

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