The complete mitochondrial genome of the Tamarisk gerbil, Meriones tamariscinus (Rodentia: Muridae)

Abstract

The complete mitochondrial genome of the Tamarisk jird, Meriones tamariscinus, was sequenced. The 16,389bp genome contains 37 genes, typical for rodent mitogenomes, including 22 tRNA genes, 2 rRNA genes, and 13 protein-coding genes. The total GC content of the mitochondrial genome is 36.8%, with a base composition of 34.0% A, 24.5% C, 12.3% G, and 29.2% T. The phylogenetic analysis showed that M. tamariscinus was classified in the genus Meriones, Muridae.

Keywords:

• Phylogenetic analysis
• Tamarisk jird
• mitogenome

The Tamarisk jird (Meriones tamariscinus) is a rodent that inhabits desert and semi-desert areas. The animal was collected from Khorgos (44°7′39″N, 80°24′13E), China, and was identified by morphology and DNA sequence (Gu et al. 2011). The complete mitochondrial genome of M. tamariscinus (GenBank accession no. KX688104) was sequenced by using long PCR and Sanger sequencing. The circular mitochondrial genome was 13,689 bp long and contained 37 genes (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) that are typically found in rodent mitochondrial genomes (Table 1) (Jiang et al. 2012). The base composition was 29.2% T, 24.5% C, 34.9% A and 12.3% G. The overall disproportional A + T content was 63.2%, which was higher than any of the three previously studied Meriones species (M. unguiculatus, 63%; M. libycus, 61.6%; and M. meridianus, 62.7%)(Luo & Liao 2016a, 2016b). ATG was used as the start codon of eight protein-coding genes, while ATA was used by ND1, GTG was used by ND4L, and ATT was used by ND2, ND3, and ND5. The unusual start codons ATA and ATT have also been observed in other mammals (Jiang et al. 2012). The coding regions of the genes Cox1, Cox2, ATPase8, ATPase6, ND3, ND4L, and ND5 were terminated by TAA, while ND6 was terminated by TAG. Five incomplete stop codons T(––) were found in the ND1, ND2, Cox3, ND4, and cytb genes. Incomplete stop codons have been observed in many other mammals (Peng et al. 2007). Several pairs of genes overlapped: ATPase8 and ATPase6, ATPase6 and Cox3, and ND4L and ND4 (Table 1). Two rRNA genes (12S rRNA and 16S rRNA) were identified via DOGMA with default settings and refined through alignment to homologous genes in other mitochondrial genomes. The 12S rRNA gene was 951 bp in length, and the 16S rRNA gene was 1572 bp in length. These genes had 61.5% and 63.8% A + T content, respectively. They were flanked by tRNA^Phe and tRNA^Leu and separated by tRNA^Val. The length of M. tamariscinus tRNA genes ranged from 59 to 75 bp. Of the 22 tRNA genes, 21 could fold into a cloverleaf secondary structure. The tRNA^ser(AGN) was only 59 bp in length and was missing the dihydrouridine stem and loop. This loss is common among vertebrates (Zhong et al. 2010). The putative origin of replication for the light strand (O_L) is located in the WANCY cluster between tRNA^Asn and tRNA^Cys. The concatenated nucleotide sequence of the 12 protein-coding genes encoded on the H-strand from 26 available mitochondrial genomes and M. tamariscinus mitogenome were used to reconstruct the phylogenetic relationships using neighbour-joining (NJ), maximum-likelihood (ML), and minimum evolution(ME) methods (Ito et al. 2010). The phylogenetic methods produced the same tree topology in the branching patterns. The monophyly of the Meriones clade received relatively strong support (Figure 1; BP = 100%). The phylogenetic analysis showed Rattus forming a clade with Mus, and this clade was closer to the Meriones clade than was the other clade. This finding demonstrates that Meriones, including M. libycus and M. meridianus, should be placed in Muridae.

Figure 1. A maximum-likelihood tree of M. tamariscinus and 26 rodents inferred from 12 mitochondrial genes in H-strand. Percentage bootstrap values are shown on interior branches with 1000 replicates for the ML method. GenBank accession numbers are indicated in brackets.

Table 1. Elements and base composition of M. tamariscinus mitochondrial genome.

					Base composition (%)
Gene	Position	Size (bp)	Start	Stop	T	C	A	G	Strand
tRNA^Phe	1–69	69			23.2	21.7	39.1	15.9	H
12S RNA	70–1020	951			25.1	21.1	36.4	17.1	H
tRNA^Val	1021–1087	67			22.4	22.4	40.3	14.9	H
16S RNA	1086–2657	1572			25.5	19.5	38.3	16.7	H
tRNA^Leu1	2660–2734	75			26.7	17.3	34.7	17.3	H
NADH1	2735–3689	955	ATA	T––	31.6	27.2	29.4	11.7	H
tRNA^Ile	3690–3757	68			32.4	16.2	39.7	16.2	H
tRNA^Gln	3826–3755	72			26.4	29.2	30.6	13.9	L
tRNA^Met	3838–3906	69			18.8	31.9	30.4	18.8	H
NADH2	3910–4948	1039	ATT	T––	30.8	25.5	36.1	7.6	H
tRNA^Trp	4947–5011	65			24.6	20.0	35.4	11.6	H
tRNA^Ala	5082–5014	69			30.4	23.2	34.8	30.4	L
tRNA^Asn	5158–5088	71			28.2	26.8	29.6	28.2	L
tRNA^Cys	5255–5189	67			35.8	19.4	31.3	13.4	L
tRNA^Tyr	5343–5276	68			30.9	23.5	30.9	22.7	L
Cox1	5345–6889	1545	ATG	TAA	30.1	24.6	30.2	15.1	H
tRNA^Ser1	6955–6887	69			26.1	27.5	31.9	14.5	L
tRNA^Asp	6959–7027	69			36.2	8.7	44.9	10.1	H
Cox2	7029–7715	687	ATG	TAA	27.4	25.3	34.2	13.1	H
tRNA^Lys	7716–7780	65			30.8	16.9	36.9	15.4	H
ATPase 8	7782–7985	204	ATG	TAA	27.5	24	42.2	6.4	H
ATPase 6	7944–8624	681	ATG	TAA	28.9	28.3	32.9	9.8	H
Cox3	8624–9407	784	ATG	T––	29.5	26.1	30.9	13.5	H
tRNA^Gly	9408–9475	68			32.4	14.7	38.2	14.7	H
NADH3	9476–9823	348	ATT	TAA	35.3	24.4	29.6	10.6	H
tRNA^Arg	9828–9895	68			39.7	13.2	36.8	10.3	H
NADH4L	9897–10,193	297	GTG	TAA	31.6	24.9	31	12.5	H
NADH4	10,187–11,564	1378	ATG	T––	29.8	26.5	34.5	9.3	H
tRNA^His	11,565–11,633	69			34.8	13	39.1	13	H
tRNA^Ser2	11,634–11,692	59			25.4	22	35.6	16.9	H
tRNA^Leu	11,693–11,761	68			30.4	17.4	37.7	14.5	H
NADH5	11,762–13,573	1812	ATT	TAA	30.5	26.4	33.7	9.4	H
NADH6	13,575–14,093	519	ATG	TAG	21.4	27.7	43.4	7.5	L
tRNA^Glu	14,162–14,094	69			31.6	25.2	30.6	12.6	L
Cyt b	14,167–15,310	1144	ATG	T––	31.6	25.2	30.6	12.6	H
tRNA^Thr	15,311–15,377	67			31.3	14.9	35.8	17.9	H
tRNA^Pro	15,378–15,445	68			19.1	27.9	36.8	16.2	L
CR	15,446–16,389	944			30.9	23.8	34.2	11	H

Disclosure statement

The authors declare that there are no conflicts of interest.

Additional information

Funding

This study was supported by the National Science Foundation of China [grant number 31572348 and 31272393], Key Projects in the National Science & Technology Pillar Program [grant number 2015BAI09B01] and Beijing Natural Science Foundation [grant number 7141002].