The complete mitochondrial genome of the Madagascan plowshare tortoise Astrochelys yniphora (Testudines, Testudinidae)

Abstract

We sequenced and characterized the complete mitochondrial genome of the Madagascan plowshare tortoise Astrochelys yniphora (Testudines, Testudinidae). This genome was 16,527 bp and consisted of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a noncoding control region. The genome organization, gene order, and base composition were identical to the typical vertebrate. There was no an additional C in arm of tRNA^Lys gene secondary structure. Astrochelys yniphora 945 bp control region concluded the variable number of tandem repeats (VNTRs). The complete mitogenome of A. yniphora provides the basic data to molecular systematics research of Testudinidae.

Keywords:

• Astrochelys yniphora
• mitochondrial genome
• phylogeny

The critically endangered plowshare tortoise (Astrochelys yniphora) is endemic to Madagascar and is one of the rarest tortoises (Morgan and Chng 2018). Astrochelys yniphora belongs to the genus Astrochelys within the family Testudinidae. At present, only partial mitochondrial genome of A. yniphora has been published on NCBI (Reid et al. 2011), the complete mitochondrial genome sequence has not been reported.

The specimen of A. yniphora (Code No. 26080218) was collected from Shanghai Zoo of China (CN) (32°42′N, 122°52′E) and stored in Conservation and Exploitation Research of Biological Resources Lab of Anhui Normal University. Total genomic DNA was extracted from the muscle tissues by the phenol/chloroform method (Zhou et al. 2015). The mitochondrial sequence was amplified by PCR using sixteen pairs of primers and recovered by Gel Extract Purification Kit (TaKaRa, Dalian). Purified PCR products were cloned and sequenced with ABI3730 automated sequencer (Invitrogen Co., Ltd, USA). BioEdit v7.2.3 was used to sequence assembly after sequencing (Xiong et al. 2010). Protein-coding genes were then aligned using TranslatorX (Abascal et al. 2010). The tRNA gene was localized with tRNAscan-SE v2.0, the rRNA gene and control region were aligned with other turtles (Li et al. 2017). The complete mitochondrial genome sequence of A. yniphora was submitted to GenBank (accession number JX317746.1).

The A. yniphora complete mitochondrial genome was a circular molecule of 16,527 bp. The arrangement of mitogenes was in agreement with the general features of vertebrates and consists of two rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and one control region (Liu et al. 2018). Total contents of T, C, A, and G were 25.8%, 26.6%, 35.1%, and 12.6%, respectively. The results showed that the anti-G bias of mtDNA based on low content of G which conserved with other vertebrates. The lengths of 16S rRNA and 12S rRNA genes were 1607 bp and 973 bp, respectively. There was no an additional C in arm of tRNA^Lys gene secondary structure, this feature as an identification feature of the mitochondrial genome of Testudinidae, which consistent with previous reports. The length of control region was 945 bp, the variable number of tandem repeats (VNTRs) concluded motifs CAATA and CAATT were identified in this region.

Phylogenetic trees obtained using the Bayesian and maximum-likelihood (ML) methods were depicted in Figure 1, based on 13 PCGs datasets of 17 Testudinidae species and two Geoemydidea species with RAxML v8.2.12 (Stamatakis 2014) and MrBayes v3.2.7 (Huelsenbeck and Ronquist 2001), two Geoemydidea species as outgroups. The result indicated a sister relationship between A. yniphora and A. radiata, A. yniphora lies within the genus Astrochelys and has a sister group relationship with Aldabrachelys, combined with the genus Centrochelys forming a monophyletic clade, and establishing a sister group relationship with the genus Stigmochelys. The evolutionary relationships of these species were consistent with the previously reports (Fritz and Bininda-Emonds 2007; Reid et al. 2011; Lourenco et al. 2012), but the phylogenetic positions of these remains to be further studied.

Figure 1. Phylogenetic trees for A. yniphora and the other 16 Testudinidae species reconstructed based on 13 PCGs datasets, Mauremys reevesii and Cuora flavomarginata as outgroups. Number above each node indicates the BI/ML bootstrap support values.

Acknowledgements

The authors are grateful for the comments provided by the reviewers and editors regarding the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was supported by the National Natural Science Foundation of China [NSFC, No. 31372198], the Research Fund of the Key Laboratory of Biotic Environment and Ecological Safety of Anhui province, the Natural Science Research Project in Colleges and Universities of Anhui province [No. KJ2017A254].