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首页> 外文期刊>Journal of King Saud University >Metatranscriptomic analysis reveals co-expression pattern of mitochondrial oxidative phosphorylation (OXPHOS) genes among different species of bony fishes in muscle tissue
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Metatranscriptomic analysis reveals co-expression pattern of mitochondrial oxidative phosphorylation (OXPHOS) genes among different species of bony fishes in muscle tissue

机译：MetaTranscriptomic分析揭示了在肌肉组织中不同物种中的线粒体氧化磷酸化（汤膦）基因的共表达模式

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Mitochondrion is an organelle responding to providing cell energy by oxidative phosphorylation (OXPHOS) reaction. In the mitochondrial genome of animals, 13 important protein-coding genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, CTYB, COX1, COX2, COX3 ATP6, ATP8) play important roles on mediating the OXPHOS reaction. The study is to compare the expressional level of 13 mitochondrial PCGs among muscle of diverse fish species to ask whether the 13 PCGs expressional level is correlated to fish living habitat or phylogenetic position. We used a metatranscriptomic approach to explore the expression level of 13 PCGs among diverse fish species (24 bony fish and one cartilaginous fish) by downloading the raw next-generation data from the NCBI SRA database and using two commercial software of Geneious and CLCBio to perform gene mapping and gene expression profiling. Principal component analysis (PCA) and hierarchy clustering were utilized to study the gene or species relationship based on 13 PCGs’ expression pattern. Based on the results, we discovered the expression pattern of PCG genes derived from the same OXPHOS complex is closer to each other showing co-expression or co-regulation relationship. The 13 PCGs expression profile was not co-related to fish living habitats but instead, well correlated to their phylogenetic position. The clustering results for 13 PCGs’ expressional patterns showed bony fish and cartilaginous fish were grouped into two distinct clades. For bony fish clades, all COX genes displayed high expression patterns while for the cartilaginous clade, the CYTB gene was highly expressed with the low expression level of COX3. In conclusion, by using the metatranscriptomic approach, we were able to explore and compare the gene expression profiles of 13 PCGs from diverse fish species for the first time. The co-expression pattern of 13 PCGs discovered in fish was well consistent with previous observations done in plants or mammals. However, one has to keep in mind that the current finding results were based only on one example of a cartilaginous fish that was accessible in the SRA database. Thus, future studies are needed by constructing more additional cartilaginous fish muscle transcriptomes.
机译：线粒体是通过氧化磷酸化（汤膦）反应提供细胞能量的细胞器。在动物的线粒体基因组中，13个重要的蛋白质编码基因（ND1，ND2，ND3，ND4，ND4L，ND5，ND6，CTYB，COX1，COX2，COX3 ATP6，ATP8）在介导氧噬反应中起重要作用。该研究是比较多种鱼类肌肉中13个线粒体PCG的表达水平，以询问13个PCG表达水平是否与鱼类生活栖息地或系统发育位置相关。我们使用了MetaTranscriptomic方法来探讨通过从NCBI SRA数据库下载RAW的下一代数据并使用两种疯狂和CLCBIO的商业软件来探讨各种鱼类（24个骨鱼和一个软骨鱼）中的13个PCG的表达水平。基因映射和基因表达分析。主要成分分析（PCA）和层次聚类基于13 PCGS表达模式研究基因或物种关系。基于结果，我们发现了衍生自相同毒物复合物的PCG基因的表达模式更接近彼此显示共表达或共调节关系。 13个PCGS表达配置文件与鱼类生活栖息地没有与鱼类生活栖息地共同相关，而是与其系统发育位置良好相关。 13个PCG的表达模式的聚类结果显示骨鱼和软骨鱼被分成两种不同的枝条。对于骨鱼曲面，所有COX基因显示出高表达模式，而对于软骨型疏水，CytB基因高度表达，具有COX3的低表达水平。总之，通过使用MetaTransfriptomic方法，我们能够首次探索和比较13个PCG的基因表达谱。在鱼类中发现的13个PCG的共表达模式与在植物或哺乳动物中进行的先前观察结果很好。然而，必须记住，目前的发现结果仅基于在SRA数据库中可访问的软骨鱼的一个例子。因此，通过构建更多额外的软骨鱼肌肉转录om需要未来的研究。

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