Zhu Yingjie, Luo Hongmei, Zhang Xin, Song Jingyuan, Sun Chao, Ji Aijia, Xu Jiang, Chen Shilin
The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
Genetics. 2014 Apr;196(4):1047-57. doi: 10.1534/genetics.114.161414. Epub 2014 Feb 4.
RNA editing is a widespread, post-transcriptional molecular phenomenon that diversifies hereditary information across various organisms. However, little is known about genome-scale RNA editing in fungi. In this study, we screened for fungal RNA editing sites at the genomic level in Ganoderma lucidum, a valuable medicinal fungus. On the basis of our pipeline that predicted the editing sites from genomic and transcriptomic data, a total of 8906 possible RNA-editing sites were identified within the G. lucidum genome, including the exon and intron sequences and the 5'-/3'-untranslated regions of 2991 genes and the intergenic regions. The major editing types included C-to-U, A-to-G, G-to-A, and U-to-C conversions. Four putative RNA-editing enzymes were identified, including three adenosine deaminases acting on transfer RNA and a deoxycytidylate deaminase. The genes containing RNA-editing sites were functionally classified by the Kyoto Encyclopedia of Genes and Genomes enrichment and gene ontology analysis. The key functional groupings enriched for RNA-editing sites included laccase genes involved in lignin degradation, key enzymes involved in triterpenoid biosynthesis, and transcription factors. A total of 97 putative editing sites were randomly selected and validated by using PCR and Sanger sequencing. We presented an accurate and large-scale identification of RNA-editing events in G. lucidum, providing global and quantitative cataloging of RNA editing in the fungal genome. This study will shed light on the role of transcriptional plasticity in the growth and development of G. lucidum, as well as its adaptation to the environment and the regulation of valuable secondary metabolite pathways.
RNA编辑是一种广泛存在的转录后分子现象，它使各种生物体中的遗传信息多样化。然而，对于真菌中基因组规模的RNA编辑知之甚少。在本研究中，我们在珍贵的药用真菌灵芝中，从基因组水平筛选真菌RNA编辑位点。基于我们从基因组和转录组数据预测编辑位点的流程，在灵芝基因组中总共鉴定出8906个可能的RNA编辑位点，包括2991个基因的外显子和内含子序列以及5'-/3'-非翻译区和基因间区域。主要的编辑类型包括C到U、A到G、G到A和U到C的转换。鉴定出四种推定的RNA编辑酶，包括三种作用于转运RNA的腺苷脱氨酶和一种脱氧胞苷酸脱氨酶。通过京都基因与基因组百科全书富集和基因本体分析对含有RNA编辑位点的基因进行功能分类。富含RNA编辑位点的关键功能分组包括参与木质素降解的漆酶基因、参与三萜生物合成的关键酶和转录因子。总共随机选择了97个推定的编辑位点，并通过PCR和桑格测序进行验证。我们对灵芝中的RNA编辑事件进行了准确且大规模的鉴定，提供了真菌基因组中RNA编辑的全局和定量编目。这项研究将阐明转录可塑性在灵芝生长发育中的作用，以及其对环境的适应性和对有价值的次生代谢途径的调控。
