The complete mitochondrial genome of the Yarkand

Mitochondrial DNA, 2012; Early Online: 1–3

MITOGENOME ANNOUNCEMENT

The complete mitochondrial genome of the Yarkand toad-headed agama, Phrynocephalus axillaris (Reptilia, Squamata, Agamidae) JUN LI1,2, XIANGUANG GUO1, DALI CHEN3, & YUEZHAO WANG1

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Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China, 2University of Chinese Academy of Sciences, Beijing 100039, People’s Republic of China, and 3Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, People’s Republic of China (Received 8 November 2012; accepted 12 November 2012)

Abstract The complete mitochondrial genome of the Yarkand toad-headed agama Phrynocephalus axillaris, the first complete mitogenome from the genus Phrynocephalus, was determined. The total length of this complete mitogenome is 17,937 bp, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions (CRs). The overall base composition of the H-strand is 36.4% A, 26.0% T, 25.4% C, and 12.3% G. The gene arrangement and composition of the mitogenome are similar to those of other Agaminae lizards, albeit with one CR existing between the tRNA Thr gene and tRNA Pro gene and another CR containing 17 copies of 77-bp tandem repeats inserting between the tRNA Phe and 12S rRNA. The complete mitogenome sequence of P. axillaris provided fundamental data for resolving phylogenetic and genetic problems related to this species and genus Phrynocephalus.

Keywords: Agamidae, mitogenome, Phrynocephalus axillaris

In this study, we determined the complete mitochondrial genome of the Yarkand toad-headed agama, Phrynocephalus axillaris, with the GenBank accession number KC119493. The mtDNA sequence was annotated with the aid of a web-based tool MITOS (Bernt et al. 2012). The specimen of P. axillaris used in this study was sampled from Ruoqiang County, China. Published sequences of Xenagama taylori, Takydromus tachydromoides, Calotes versicolor, and Chlamydosaurus kingii (Macey et al. 2006; Amer and Kumazawa 2007; Kumazawa 2007; Ujvari and Madsen 2008; GenBank accession numbers DQ008215, AB080237, AB183287, and EF090421, respectively) were used to design 12 pairs of specific primers. The organization of mitochondrial genome is shown in Table I. The complete mtDNA of P. axillaris is 17,937 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 2

control regions (CRs). Most mitochondrial genes are encoded on the H-strand with the exception of one protein-coding gene (ND6) and eight tRNA genes (tRNA Gln, tRNA Ala, tRNA Asn, tRNA Cys, tRNA Tyr, tRNA Ser, tRNA Glu, and tRNA Pro). The overall base composition of the H-strand is 36.4% A, 26.0% T, 12.3% G, and 25.4% C. COI, ATP6, COIII, ND4L, and ND5 begin with ATG as start codon. ND1, ND2, ND3, and ND4 begin with ATT; COII, ATP8, and ND6 begin with GTG; and cyt b begins with ATA. ATP8, ND4L, ND4, ND5, and cyt b genes are terminated with TAA as stop codon; ND2, COI, and ND6 end with AGA; ND1 ends with TAG, and the other four protein-coding genes end with an incomplete stop codon (a single stop nucleotide T). Most genes are the same order and orientation as found in other Agaminae lizards, albeit with one CR existing between the tRNA Thr gene and the tRNA Pro gene and

Correspondence: X. Guo and Y. Wang, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China. Tel: þ 86 28 82890779. Fax: þ 86 28 82890288. E-mail: [email protected]; E-mail: [email protected] ISSN 1940-1736 print/ISSN 1940-1744 online q 2012 Informa UK, Ltd. DOI: 10.3109/19401736.2012.752477

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J. Li et al. Table I. Characteristics of the mitochondrial genome of the Yarkand toad-headed agama, P. axillaris.


Codon Gene/element

From

tRNA Phe CR 12S rRNA tRNA Val 16S rRNA tRNA Leu( UAA) ND1 tRNA Gln tRNA Ile tRNA Met ND2 tRNA Trp tRNA Ala tRNA Asn tRNA Cys tRNA Tyr COI tRNA Ser(UGA) tRNA Asp COII tRNA Lys ATP8 ATP6 COIII tRNA Gly ND3 tRNA Arg ND4L ND4 tRNA His tRNA Ser(GCU) tRNA Leu(UAG) ND5 ND6 tRNA Glu Cyt b tRNA Thr CR tRNA Pro

1 71 2234 3103 3168 4650 4721 5686 5766 5833 5897 6931 7001 7069 7155 7210 7276 8815 8888 8957 9642 9705 9857 10,539 11,323 11,388 11,725 11,793 12,077 13,443 13,506 13,564 13,636 15,393 15,876 15,944 17,091 17,157 17,808

To 70 2233 3105 3167 4646 4723 5689 5757 5832 5895 6931 7000 7069 7140 7209 7275 8823 8884 8956 9641 9704 9863 10,538 11,322 11,387 11,724 11,792 12,083 13,441 13,505 13,563 13,634 15,405 15,875 15,943 17,113 17,156 17,807 17,877

Length (bp) 70 2163 872 65 1479 74 969 72 67 63 1035 70 69 72 55 66 1548 70 69 685 63 159 682 784 65 337 68 291 1365 63 58 71 1770 483 68 1170 66 651 70

Start

Stop

ATT

TAG

ATT

AGA

ATG

AGA

GTG

T–

GTG ATG ATG

TAA T– T–

ATT

T–

ATG ATT

TAA TAA

ATG GTG

TAA AGA

ATA

TAA

Intergenic nucleotides* 60 0 0 23 0 3 23 24 8 0 1 21 0 21 14 0 0 29 3 0 0 0 27 0 0 0 0 0 27 1 0 0 1 213 0 0 223 0 0

Strand† H – H H H H H L H H H H L L L L H L H H H H H H H H H H H H H H H L L H H – L

* Numbers correspond to the nucleotides separating different genes. Negative numbers indicate overlapping nucleotides between adjacent genes; † H and L denote heavy and light strands, respectively.

another CR containing 17 copies of 77-bp tandem repeats inserting between the tRNA Phe and 12S rRNA. The agamid lizard Phrynocephalus comprises approximately 37 distinct species (Barabanov and Ananjeva 2007). Highly adapted to sand dunes and desert environments, they are one of the major components of the central Asian desert fauna (Zhao and Alder 1993). Despite the progress that has been made in recent years for the systematics and diversification of certain Phrynocephalus groups, the large-scale pattern of their evolution in time and space remains open (Guo and Wang 2007; Melville et al. 2009). In addition, none of these species has the complete mitochondrial genome reported. P. axillaris is endemic to Tarim Basin and its adjacent regions (Turpan-Hami Basin and Dunhuang Basin) in China. As an effort to fill this gap, we determined the complete

mitochondrial genome of P. axillaris. The result will facilitate the exploration of the genetic and evolutionary characteristics of mitogenomes related to this species and help to elucidate the phylogeny and biogeography of the genus Phrynocephalus. Acknowledgements We thank Yun Xia and Yonghui Ye for their assistance in the laboratory work. Declaration of interest: This study was supported by the National Natural Science Foundation of China (31272281) and the Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2EW-Q-6, KSCX2-EW-J-22). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

The mitogenome of Phrynocephalus axillaris


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