Metatranscriptomic analysis reveals co-expression pattern of mitochondrial oxidative phosphorylation (OXPHOS) genes among different species of bony fishes in muscle tissue

Abstract

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.

Keywords

• Metagenomics
• Muscle
• Transcriptome
• Protein-coding gene
• Mitogenome