Mitochondrial DNA Part B Resources
ISSN: (Print) 2380-2359 (Online) Journal homepage: http://www.tandfonline.com/loi/tmdn20
The complete mitochondrial genome of the Copadichromis mloto Da-Shi Qi, Jie Jiang, Mei Wang, Lian-Qin Zhang & Xiao-Jing Huang To cite this article: Da-Shi Qi, Jie Jiang, Mei Wang, Lian-Qin Zhang & Xiao-Jing Huang (2016) The complete mitochondrial genome of the Copadichromis mloto, Mitochondrial DNA Part B, 1:1, 809-810, DOI: 10.1080/23802359.2016.1222253 To link to this article: http://dx.doi.org/10.1080/23802359.2016.1222253
© 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Published online: 22 Nov 2016.
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Date: 23 November 2016, At: 06:21
MITOCHONDRIAL DNA PART B: RESOURCES, 2016 VOL. 1, NO. 1, 809–810 http://dx.doi.org/10.1080/23802359.2016.1222253
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Copadichromis mloto Da-Shi Qi, Jie Jiang, Mei Wang, Lian-Qin Zhang and Xiao-Jing Huang Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
ABSTRACT
ARTICLE HISTORY
The present study reported the complete mitochondrial genome of Copadichromis mloto for the first time. The mitochondrial genome of C. mloto possesses 16,583bp in length, involving 22 transfer RNA genes, 2 ribosomal RNA, 13 protein-coding genes and a control region. In addition, its GC content is 45.94% that is similar to that of C. virginalis (the GC content of 45.74%). Based on the complete mitochondrial genomes of 13 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.
Received 29 July 2016 Accepted 5 August 2016
The Copadichromis mloto is a member of Cichlidae native to the Southeast Arm of Lake Malawi (14 06'46.9”S 35 07'05.6”E). Our present study reported the complete mitochondrial genome of C. mloto 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 C. mloto (Genbank accession KX196155) was assembled based on its raw sequences of whole genome (Genbank accession ERP002088). 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 SAMEA1877497. All the reads were mapped to a full mitochondrial genome reference sequences of C. virginalis (Genbank accession: NC_029761) by using SOAPaligner/soap2 (V2.21). Then we assembled the reads which could map to the reference genome by SPAdes3 (V3.1.0), and get the circular mitochondrial genome. Additionally, its complete mitochondrial genome sequence was also annotated by using DOGMA (Alverson et al. 2010).
CONTACT Da-Shi Qi
[email protected]
KEYWORDS
Copadichromis mloto; genome; phylogenic relationship
The entire mitochondrial genome of C. mloto possesses 16,583 bp, involving 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs) and a 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. All PCGs in C. mloto stopped with TAG or TAA except for cox2 and nd4 with AGA and nd6 with CAT. The 22 tRNA genes begin from 67 bp (tRNASer, tRNACys) to 74bp (tRNALeu), while 16S rRNA possesses 1676 bp and 12S rRNA possesses 941 bp in length. In addition, its GC content is 45.94% (27.49% A, 26.58% T, 30.12% C, and 15.82% G) that is similar to that of C. virginalis (the GC content of 45.74%). Based on the complete mitochondrial genomes of the C. mloto and other 12 closely related species, we also used MEGA6.06 to construct the phylogenetic tree by Maximum likelihood method (Figure 1) (Stamatakis et al. 2002; Tamura et al. 2013; Qi et al. 2015). Those results would facilitate our understanding of the evolution of Cichlidae mitochondrial genome.
Department of Genetics, Xuzhou Medical University, Xuzhou, PR China
ß 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Figure 1. Maximum likelihood tree of complete mitochondrial genome of C. mloto and 12 other closely species, which have complete mitochondrial genome sequences in NCBI. The numbers in front of the species are genbank accession numbers.
Acknowledgements
References
The authors would like to thank Wellcome Trust Sanger Institute (SC) for generating the raw sequencing data of the C. mloto used in this study.
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. doi: 10.3109/19401736.2015.1082097. 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.
Disclosure statement The authors declare no conflict of interest.
Funding This work was sponsored by the Education Departmental Natural Science Research Funds of Jiangsu Provincial Higher School of China [14KJB180022] ; National Natural Science Foundation of China, 10.13039/ 501100001809 [81500977].
