Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis
Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis
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千岁兰质体基因组和最高表达的线粒体基因的 RNA 编辑完全丧失
DOI：
10.1007/s11427-018-9450-1
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发表时间：
2019-04-01
影响因子：
9.1
通讯作者：
Zhu, Andan
中科院分区：
文献类型：
--
作者：
Fan, Weishu;Guo, Wenhu;Zhu, Andan
裸子植物的比较基因组学分析表明，基于预测分析，威威schia mirabilis线粒体RNA编辑位点大量丢失。然而，缺乏证实这一大规模丢失事件的经验或转录组数据，并且RNA位点丢失的潜在机制尚不清楚。通过将基因组序列与转录组和反转录PCR测序数据进行比较，我们全面分析了W. mirabilis和第二种裸子植物银杏（Ginkgo biloba）线粒体和质体基因组（分别为有丝分裂基因组和质体基因组）中的RNA编辑模式。对于W. mirabilis，我们在有丝分裂基因组的13个蛋白质编码基因中发现了99个编辑位点，并且在质体中完全丢失了RNA编辑。威氏裂丝基因组中少数编辑频率较高的基因与基因表达水平呈较强的负相关。与含有1405个线粒体编辑位点和345个质体编辑位点的双叶棘猴（G. biloba）的比较分析显示，mirabilis的编辑损失主要是由于基因组水平上可编辑的胞嘧啶被胸腺嘧啶取代，这可能是由后处理引起的。我们的研究结果是首次发现单个属中有丝分裂基因组和质体的大量编辑缺失。此外，我们的研究结果表明，基因表达水平和后加工都促进了植物细胞器基因组中RNA编辑的进化。
Comparative genomics among gymnosperms suggested extensive loss of mitochondrial RNA editing sites from Welwitschia mirabilis based on predictive analysis. However, empirical or transcriptome data to confirm this massive loss event are lacking, and the potential mechanisms of RNA site loss are unclear. By comparing genomic sequences with transcriptomic and reverse-transcription PCR sequencing data, we performed a comprehensive analysis of the pattern of RNA editing in the mitochondrial and plastid genomes (mitogenome and plastome, respectively) of W. mirabilis and a second gymnosperm, Ginkgo biloba. For W. mirabilis, we found only 99 editing sites located in 13 protein-coding genes in the mitogenome and a complete loss of RNA editing from the plastome. The few genes having high editing frequency in the Welwitschia mitogenome showed a strong negative correlation with gene expression level. Comparative analyses with G. biloba, containing 1,405 mitochondrial and 345 plastid editing sites, revealed that the editing loss from W. mirabilis is mainly due to the substitution of editable cytidines to thymidines at the genomic level, which could be caused by retroprocessing. Our result is the first study to uncover massive editing loss from both the mitogenome and plastome in a single genus. Furthermore, our results suggest that gene expression level and retroprocessing both contributed to the evolution of RNA editing in plant organellar genomes.