Department of Biology, University of Western Ontario, London, Ontario, Canada.
Genome Biol Evol. 2017 Oct 1;9(10):2650-2657. doi: 10.1093/gbe/evx207.
Organelle genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both organelle- and nuclear-encoded machinery. Next generation sequencing (NGS) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate organelle genome transcription. However, most of the available eukaryotic RNA-sequencing (RNA-seq) data are used to study nuclear transcription only, even though large numbers of organelle-derived reads can typically be mined from these experiments. Here, we use publicly available RNA-seq data to assess organelle genome transcription in 59 diverse plastid-bearing species. Our RNA mapping analyses unraveled pervasive (full or near-full) transcription of mitochondrial, plastid, and nucleomorph genomes. In all cases, 85% or more of the organelle genome was recovered from the RNA data, including noncoding (intergenic and intronic) regions. These results reinforce the idea that organelles transcribe all or nearly all of their genomic material and are dependent on post-transcriptional processing of polycistronic transcripts. We explore the possibility that transcribed intergenic regions are producing functional noncoding RNAs, and that organelle genome noncoding content might provide raw material for generating regulatory RNAs.
细胞器基因组在内容、结构和大小方面表现出显著的多样性，并且在其基因表达模式方面也存在多样性，这些都受到细胞器和核编码机制的控制。下一代测序（NGS）技术产生了前所未有的基因组和转录组数据，可用于研究细胞器基因组转录。然而，大多数可用的真核生物 RNA 测序（RNA-seq）数据仅用于研究核转录，尽管这些实验通常可以从大量细胞器衍生的读段中进行挖掘。在这里，我们使用公开可用的 RNA-seq 数据来评估 59 种具有不同质体的物种中的细胞器基因组转录。我们的 RNA 映射分析揭示了线粒体、质体和核质体基因组的普遍（完全或几乎完全）转录。在所有情况下，从 RNA 数据中回收了 85%或更多的细胞器基因组，包括非编码（基因间和内含子）区域。这些结果强化了这样一种观点，即细胞器转录其全部或几乎全部基因组物质，并依赖于多顺反子转录本的转录后加工。我们探讨了转录的基因间区域是否产生功能性非编码 RNA，以及细胞器基因组的非编码含量是否可能为生成调节性 RNA 提供原料。
