Abstract
The present study reported the complete mitochondrial genome of Alticorpus geoffreyi for the first time. The mitochondrial genome of A. geoffreyi possesses 16,578 bp in length, involving 22 transfer RNA genes, 2 ribosomal RNA, 13 protein-coding genes and one control region. In addition, its GC content is 45.82% that is similar to that of Astatotilapia calliptera (the GC content of 45.90%). Based on the complete mitochondrial genomes of 14 closely related species, the phylogenetic tree was further made to show their phylogenic relationship. The results will serve as a useful dataset for studying the evolution of Cichlidae mitochondrial genome.
The Alticorpus geoffreyi is a member of Cichlidae native to the Southeast Arm of Lake Malawi. Our present study reported the complete mitochondrial genome of A. geoffreyi for the first time, which would facilitate our understanding of the genetics, systematics and phylogenetic relationships of the many species of Cichlidae family.
The complete mitochondrial genome of A. geoffreyi (GenBank accession NC_028033) was assembled based on its raw sequences of whole genome (GenBank accession ERP002088) (Tan et al. Citation2015). The whole genome of this species was sequenced by the Wellcome Trust Sanger Institute (SC) in the project PRJEB1254 (NCBI accession number), and the accession number of the sample on NCBI is SAMEA1904331. Additionally, its complete mitochondrial genome sequence was also annotated by using DOGMA (Alverson et al. Citation2010).
The entire mitochondrial genome of A. geoffreyi possesses 16,578 bp, involving 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs) and one control region. 28 genes including 12 PCGs, 14 tRNA and 2 rRNA are H-strand, whereas 9 genes including 1 PCG and 8 tRNA are L-strand. 11 PCGs had ATG start codon except for cox1 with GTG and nd6 with TTA. Three complete stop codons (TAA, TAG and CAT) and one incomplete stop codon (T– –) were found in the PCGs in A. geoffreyi. The 22 tRNA genes begin from 67 bp (tRNASer, tRNACys) to 74bp (tRNALeu), while 16S rRNA possesses 1675 bp and 12S rRNA possesses 941 bp in length. In addition, its GC content is 45.82% (27.58% A, 26.60% T, 30.15% C and 15.67% G) that is similar to that of Astatotilapia calliptera (the GC content of 45.90%). Based on the complete mitochondrial genomes of the A. geoffreyi, A. calliptera (GenBank accession no. NC_018560), and other 12 closely related species, we also used MEGA6.06 to construct the phylogenetic tree by Maximum likelihood method (; Stamatakis et al. Citation2002; Tamura et al. Citation2013; Qi et al. Citation2015). Those results would facilitate our understanding of the evolution of Cichlidae mitochondrial genome.
Figure 1. Maximum likelihood tree of complete mitochondrial genome of A. geoffreyi and 13 other closely species, which have complete mitochondrial genome sequences in NCBI. The numbers in front of the species are GenBank accession numbers.
Acknowledgements
The authors would like to thank Wellcome Trust Sanger Institute (SC) for generating the raw sequencing data of the Alticorpus geoffreyi used in this study.
Disclosure statement
The authors declare no conflict of interest. This work was sponsored the National Natural Science Foundation of China (81500977), by the Education Departmental Natural Science Research Funds of Jiangsu Provincial Higher School of China (14KJB180022).
References
- Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol. 27:1436–1448.
- Qi DS, Zhang SC, Jiang J, Zhang LQ, Fu YY, Du ZM, Wang M, Huang XJ, Wang YL, Song YJ, et al. 2015. The complete mitochondrial genome of the Fossorochromis rostratus. Mitochondrial DNA. [Epub ahead of print].
- Stamatakis AP, Ludwig T, Meier H, Wolf MJ. 2002. AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method. Proc IEEE Comput Soc Bioinform Conf. 1:21–28.
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30:2725–2729.
- Tan M, Zhang R, Hardman C, Zhou X. 2015. Mitochondrial genome of Hylaeus dilatatus (Hymenoptera: Colletidae). Mitochondrial DNA. [Epub ahead of print].