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Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae)

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Abstract

The soft-shell turtles Apalone spinifera (AS) and Apalone ferox (AF) are two important economic species. AF is found in the Yellow River of China, and is a confirmed member of the Trionychidae family. However, the classification of AS was in dispute. Mitochondrial genomes (mitogenomes) have been widely used for species identification, as well as population and phylogenetic analysis. In order to understand the phylogenetic and mitogenomic features of AS and AF, the complete mitogenomes were sequenced, annotated and analyzed in this study. The complete mitogenomes of AS and AF are 16,817 bp and 16,756 bp in length, respectively. Both mitogenomes contain 37 genes, seven short intergenic spacers and two long intergenic spacers. Comparative analysis showed that there are 1,137 variation sites (6.79%) between the two mitogenomes. AS and AF mitogenomes both show a usage preference in terms of nucleotides, codons and amino acids. In addition, the non-synonymous substitution rate/synonymous substitution rate indicates that all protein-coding genes (PCGs) have undergone a strong purifying selection. Phylogenetic trees constructed by 13 PCGs show a clear phylogenetic relationship of the soft-shell turtles and suggest that AS is a sister species to AF of the genus Apalone. The data could be useful for further research of species identification, population analysis and the mitogenomic features of soft-shell turtles.

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Abbreviations

COXI:

Cytochrome oxidase subunit I

COX II:

Cytochrome oxidase subunit II

COX III:

Cytochrome oxidase subunit III

ATP8:

ATPase subunit 8

ATP6:

ATPase subunit 6

ND1:

NADH dehydrogenase subunit 1

ND2:

NADH dehydrogenase subunit 2

ND3:

NADH dehydrogenase subunit 3

ND4:

NADH dehydrogenase subunit 4

ND4L:

NADH dehydrogenase subunit 4L

ND5:

NADH dehydrogenase subunit 5

ND6:

NADH dehydrogenase subunit 6

Cytb:

Cytochrome b

CSB:

Conserved sequence block

bp:

Base pair

PCR:

Polymerase chain reaction

Ka/Ks:

Non-synonymous substitution rate/synonymous substitution rate

AF:

Apalone ferox

AS:

Apalone spinifera

ML:

Maximum Likelihood

BI:

Bayesian

PCGs:

Protein coding genes

mt:

Mitochondrial

mtDNA:

Mitochondrial DNA

tRNA:

Transfer ribonucleic acid

rRNA:

Ribosome ribonucleic acid

OL :

L-strand replication origin

CR:

Control region

RSCU:

Relative synonymous codon usage

BP:

Bootstrap support

PP:

Posterior probability

IGS:

Intergenic spacers

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Acknowledgements

This work was supported by the Anhui Natural Science Foundation of the Colleges and Universities (KJ2016A241), the Open Project of National Key Laboratory of the Ecological and Biological Technology for Institute of Hydrobiology of Chinese Academy of Sciences (2016FB16), the National Natural Science Foundation of China (31802273), and the Key Youth Fund of Anhui Agricultural University (2015ZD05).

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Authors and Affiliations

  1. College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China

    Peng Yu, Xiaoli Yang, Weishang Zhou, Xuan Liu, Quan Wan & Jun Zhang

  2. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China

    Peng Yu, Wentao Yang & Li Zhou

  3. University of Chinese Academy of Sciences, Beijing, 100049, China

    Peng Yu & Wentao Yang

  4. Mingguang Modern Agricultural Science and Technology Cooperation Promotion Service Center, Mingguang, 239400, China

    Jun Zhang

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  1. Peng Yu
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Correspondence to Jun Zhang.

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Yu, P., Yang, X., Zhou, W. et al. Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae). Genetica 147, 165–176 (2019). https://doi.org/10.1007/s10709-019-00059-1

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