The complete mitochondrial genome of the Rana sangzhiensis Shen and its phylogenetic analyses

Abstract

The mitochondrial genome of one Rana pseudo-rana species Rana sangzhiensis Shen was sequenced and annotated. The mitogenome is 19,207 bp in length, containing 37 typical genes. The A + T content of the whole mitogenome is 56.6%. All of the protein-condoning genes (PCGs) started with ATG and stopped with TGA. The tRNA-Pro, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu, andND5 are located in the circular mitochondrial L chain. The phylogeny tree is monophyletic among 14 related Rana species. The R. sangzhiensis Shen cluster was more closely related to R. amurensis Boulenger and R. kunyuensis Lu, Y.-Y., and P.-P. Li. This mitochondrial genome can be used for further analyses of Ranidae mitochondrial comparative genomics to improve the understanding of diverse Ranidae species.

Keywords:

• Mitochondrial DNA
• Rana sangzhiensis Shen
• phylogenetic analysis

The Rana sangzhiensis as a kind of small and medium-sized frog belonging to Rana pseudo-rana, Ranidae. The R. sangzhiensis Shen is distributed in Chenzhou, Yongzhou, Hengyang, Loudi, Huaihua and Xiangxi City, Hunan province, China. The R. sangzhiensis Shen generally lives in stream migration water and the surrounding grass with the mountain altitude of 800–1000 meters above sea level, and comes out to hunt for food in the day, and in the night only to mate in the breeding season (Xiang-Rong et al. 2008).

A male adult of R. sangzhiensis Shen was collected from Xingning Town (Zixing, Chenzhou City, Hunan Province, China) (113°43.0′E, 27°99.9′N), in October 2019. The specimens (No. Zg-zx) were stored at −80 °C in our laboratory (College of Animal Science and Technology, Hunan Agriculture University). Total genomic DNA of the R. sangzhiensis Shen was extracted from fertilized eggs using the Column Animal DNA out (Beijing Tiandz, Beijin, China) following the kit’s instructions. Then, the mitochondrial genome (mitogenome) of R. sangzhiensis Shen was sequenced by Illumina sequencing platform (Wuhan Biowefind biotechnology Co., Ltd, Wuhan, China). The reads were assembled and annotated using Generous Prime (v2019.1.3.). All tRNA genes were identified by ARWEN v1.2 (Laslett and Canbäck 2008). The annotated sequences of mitogenome were submitted to GenBank with the accession number MT782121. All protein-condoning genes (PCGs) were aligned using MAFFT algorithm in the TranslatorX (Katoh et al. 2019), and then poorly aligned results were removed by Gblocks 9.1 b (Castresana 2000; Abascal et al. 2010).

Mitogenome of R. sangzhiensis Shen has 19,207 bp in length, including 37 typical genes (13 PCGs, 22 tRNA genes and 2 rRNA genes). The overall nucleotide composition of the mitogenome is 27.3% for A, 28.5% for C, 14.7% for G and 29.3% for T. The A + T content of genes is 56.6%. All of PCGs started with ATG and stopped with TGA. The tRNA-Pro, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu and ND5 are located in the circular mitochondrial L chain. The length of 22 tRNA is range from 67 bp (tRNA-Ser) to 74 bp (tRNA-Asn). Genes of 16S rRNA and 12S rRNA are 1576 bp and 930 bp, respectively. To validate the phylogenetic position of R. sangzhiensis Shen, we perform multiple sequence alignment by MEGA 6.0 (Tamura et al. 2013) and construct a maximum likelihood tree based on the complete mitochondrial genome sequences of 16 species in Ranidae. The phylogenetic tree (Figure 1) revealed that 14 Rana species constituted five subclades, the R. sangzhiensis Shen clustered in one clade, the R. sangzhiensis Shen cluster was more closely related to R. amurensis Boulenger and R. kunyuensis Lu, Y.-Y. and P.-P. Li.

Figure 1. Phylogenetic analysis infers the evolutionary relationship of R. sangzhiensis Shen. The tree was constructed based on maximum likelihood (ML) tree method using Mega 6.0. The GenBank accession number for each species is indicated after the scientific name.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MT782121. The associated BioProject, SRA, and Bio-Sample numbers are 20TD07, PRJNA678467, and Zg-zx respectively.

Additional information

Funding

This research was supported by the Science Foundation of Hunan Biological and Electromechanical Polytechnic [20TD07], the National Natural Science Foundation of China [31672640], Blue Granary [2018YFD0900200], and Healthy Pond Technology System of Aquaculture Industry in Hunan province.