Abstract
In the present study, for the first time, we reported the complete mitochondrial genome of Lethrinops lethrinus, which is 16,582 bp in length, including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes and a control zone. Moreover, its GC content is 45.99% (27.42% A, 26.59% T, 30.10% C, and 15.88% G), similar to that of Alticorpus geoffreyi (GC content of 45.82%). We further made the phylogenetic tree on the complete mitochondrial genomes of the above two species and other 12 closely related species to show their phylogenic relationship. The above results would facilitate our understanding of the evolution of Cichlidae mitochondrial genome.
Keywords: Lethrinops lethrinus, genome, phylogenic relationship
The Lethrinops lethrinus is a member of Cichlidae native to the Southeast Arm of Lake Malawi. The present study reported the complete mitochondrial genome of Lethrinops lethrinus for the first time, which would facilitate our understanding of the genetics, systematics and phylogenetic relationships of the many species of Cichlidae family.
All the reads were mapped to a full mitochondrial genome reference sequences of Alticorpus geoffreyi (Genbank accession:NC_028033) 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, we annotated the complete mitochondrial genome sequence using DOGMA. 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 SAMEA1920094.
The entire mitochondrial genome of Lethrinops lethrinus possesses 16,582 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. All PCGs in Lethrinops lethrinus started with ATG except for cox1 with GTG and nd6 with AAT and stopped with TAA or TAG except for nd6 with CAT and cox2 and nd4 with AGA. The 22 tRNA genes begin from 67 bp (tRNASer, tRNACys) to 74bp (tRNALeu), while 16S rRNA possesses 1676 bp and 12S rRNA possesses 943 bp in length. In addition, its GC content is 45.99% (27.42% A, 26.59% T, 30.10% C, and 15.88% G) that is similar to that of Alticorpus geoffreyi (the GC content of 45.82%). Based on the complete mitochondrial genomes of the Lethrinops lethrinus, Alticorpus geoffreyi (Genbank accession NC_028033), 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.
Figure 1.
Maximum likelihood tree of complete mitochondrial genome of L. lethrinus 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 Lethrinops lethrinus used in this study.
Disclosure statement
The authors declare no conflict of interest.
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