Phylogenetic analyses of the harvest mouse, Micromys minutus (Rodentia: Muridae) based on the complete mitogenome sequences
Introduction
The harvest mouse, Micromys minutus, which is the smallest rodent of the Muridae, is widely distributed in the Old World (Corbet, 1978). The geographical range of the harvest mouse is relatively wide, extending from northwest Spain through central Europe to Siberia, Tibet, Assam, Taiwan, and Japan (Trout, 1978). The basic high-level taxonomy of Micromys has remained the sole member of the Muridae until a distinct species Micromys erythrotis (Blyth, 1856) was proposed for the subpopulations in Northern Vietnam and South China. This hypothesis has been confirmed by Abramov et al. (2009) based on sequences from the mitochondrial cytochrome b gene, control region and morphological data. The M. minutus is unusual among murines in its habitat preference which includes various open communities such as grassy Lang, salt marshes, sedgelands and agricultural fields (Churchfield et al., 1997). An adult harvest mouse is 50–80 mm long from nose to base of tail, with a length further 50–70 mm for the tail, the robust prehensile tail and rather broad feet are adapted specifically for climbing (Forder, 2006). Harvest mouse has a unique nesting behavior: they build non-breeding shelter nests closer to the ground, and build breeding shelter nests in the stems of plants high above the ground. Non-breeding nests are often smaller, not designed to last as long as breeding nests (Forder, 2006).
As yet, in such a widely distributed and special species, the phylogenetic relationships of Micromys to other murine genera remain a subject to debate. The classification and evolution of the Micromys have been studied by a variety of methods. Morphological, karyotypical, and molecular data have all been used, so far there has been no resolution regarding this matter (Martin et al., 2000, DeBry and Sagel, 2001, Michaux et al., 2002, Lecompte et al., 2008, Lin et al., 2013). However, short DNA sequences had been used in these phylogenetic analysis, which may give rise to misleading conclusions among distantly related taxa (Cummings et al., 1995). The complete mitochondrial genome has been widely and successfully used in phylogenetic studies because of its small size, high substitution, unisexual mode of inheritance, and rich information of evolutionary (Wilson et al., 1985). Here, we reported the complete mitochondrial genome of M. minutus and its organization and structure, also re-examined it phylogenetic relationships within Muridae based on complete mitochondrial sequences from more species.
Section snippets
Samples and DNA extraction
Muscle of M. minutus was collected from Dujiangyan, Sichuan Province, China. The sample was preserved in 95% ethanol. Total genomic DNA was extracted using standard phenol/chloroform methods (Sambrook and Russell, 2001).
PCR amplification and sequencing
The primer pairs were designed based on the alignments of the relatively conserved regions of Muridae sets to amplify the complete mitochondrial gene of M. minutus. PCR (polymerase chain reaction) cycling was carried out on a PTC-100 thermal cycler (BioRad, Hercules, CA, USA).
Mitochondrial genome organization
The complete mitochondrial genome sequence of M. minutus was 16,232 bp in length and it was deposited in GenBank under accession number KP399599. The gene arrangement was similar to other rodent mitochondrial genomes (Table 2). Most mitochondrial genes were encoded on the H-strand, except for the ND6 gene and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser (UCN), tRNA-Pro, tRNA-Glu). Several overlaps were detected between protein-coding genes as shown in ATP8-ATP6,
A new initiation codon
The mitogenome of M. minutus exhibited a canonical genetic code, which is similar to other vertebrates. However, According to the careful inspection of the alignment for M. minutus at the 5′ region with those of other vertebrate animal's ND5, we supposed that the ND5 of M. minutus initiate with the AGT codon. This was confirmed by repeated sequencing to different individual's mtDNA of Micromys. This initiation codon has never been reported in the vertebrate mitochondrial genome before. In mouse
Acknowledgments
This work was supported by Chengdu Panda Breeding Research Foundation. We are grateful to appreciate Liang Dou at Sichuan University for the sample collection and identification, and Jie Huang for help with English editing.
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Authors contributed equally.