The complete mitochondrial genome of the Cyathochromis obliquidens

Abstract

The Cyathochromis obliquidens, the only member of Cyathochromis genus, is widely spread in Africa. In this study, we firstly reported the complete mitochondrial genome of C. obliquidens. The whole mitochondrial genome is 16,581 bp in length, including 2 ribosomal RNA genes, 22 transfer RNA genes and 13 protein-coding genes. Its GC content is 45.94%, similar to the other species from the same family, like Alticorpus geoffreyi (45.82%). We also analyzed the complete mitochondrial genome of C. obliquidens and its phylogenic relationship with other 14 related species, which would help our better understanding of the evolution of Cichlidae mitochondrial genome.

Keywords:

• Mitochondrial genome
• Cyathochromis obliquidens
• phylogenic relationship

As a member of Cichlidae family, the Cyathochromis obliquidens is widely spread in Africa (Meyer et al. 2015). Here, we firstly reported the complete mitochondrial genome of C. obliquidens, which would facilitate our understanding of the mitochondrial genome and the phylogenic relationship of the Cichlidae family.

In this study, we assembled the complete mitochondrial genome of C. obliquidens (Genbank accession: MF033354) based on the raw data of the whole genome of a C. obliquidens (SRA: ERP002088). The C. obliquidens sample (Sample ID: SAMEA2661259) was collected from a trawler catch in the Southeast Arm of Lake Malawi and sequenced by the Wellcome Trust Sanger Institute (SC) in their Cichlid diversity sequencing WTMGM student project.

By using SOAPaligner/soap2 (V2.21) (Li et al. 2009), we mapped all the raw reads to the reference genome, complete mitochondrial genome of Alticorpus geoffreyi (Genbank accession: NC_028033) (Qi et al. 2016). We assembled these reads which could map to the reference genome by SPAdes3 (V3.1.0) (Bankevich et al. 2012), and got the complete circular mitochondrial genome of C. obliquidens. Also, we used DOGMA(Wyman et al. 2004) and tRNAscan-SE 2.0 (Lowe & Eddy 1997) to annotate the complete mitochondrial genome.

The mitochondrial genome of C. obliquidens is 16,581 bp in length, contains 37 genes, including 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA) and 13 protein-coding genes (PCGs). The lengths of 22 tRNA genes range from 67 bp (tRNA^Cys and tRNA^Ser) to 74 bp (tRNA^Leu and tRNA^Lys), whereas 16S rRNA is 1676 bp and 12S rRNA is 941 bp. Twenty-eight genes contain 2 rRNA, 14 tRNA and 12 PCGs are H-strand, while the remaining 9 genes including 1 PCGs (ND6) and 8 tRNA are L-strand. All PCGs in C. obliquidens are started with ATG and stopped with TAN or AGA, except for COX1 started with GTG. The GC content of this mitochondrial genome is 45.94% (27.43% A, 26.63%T, 30.08% C, 15.86% G), similar to A. geoffreyi (45.82%) from the same family, Cichlidae.

Furthermore, we used MEGA7 (V7.0.25) (Kumar et al. 2016) to construct the phylogenetic tree on the complete mitochondrial genomes of C. obliquidens, 2 species with the same phylum, 2 species from the same class and other 10 closely related species by Maximum likelihood method (Figure 1). Those results would facilitate our understanding of the mitochondrial evolution of Cichlidae family.

Figure 1. Maximum likelihood tree of complete mitochondrial genome of C. obliquidens and 14 other closely species, which have the Genbank accession numbers of their complete mitochondrial genome sequences in front.

Acknowledgements

The authors would like to thank Wellcome Trust Sanger Institute (SC) for generating and uploading the raw data of the C. obliquidens used in this study. This work was sponsored by Qing Lan project in Jiangsu Province.

Disclosure statement

The authors declare no conflict of interest.

Additional information

Funding

This work was sponsored by Qing Lan project in Jiangsu Province.