The Complete Mitochondrial Genome Structure Of The Moutain Hare(Lepus Timidus) And Its Genetic Diversity And Phylogenetic Evolution

The moutain hare (Lepus timidus) is one of the Class Ⅱ national protected species, and its genetic differentiation, system classification and evolution has been controversial.In this study we discussed about genetic diversity and system evolution of moutain hare based on the sequ-ences of its mitochondrial genome and D-loop region.The size of the complete mitochondrial genome of the moutain hare is about 17750 bp, which included 13 protein coding genes (PCGs),22 tRNA genes, two rRNA genes and 2 control regions. It is the same to the mitochondrial genome organization of other species in Lepus.9 of 37 coding genes are encoded by light chain, which included eight tRNA genes and ND6 gene. The other 28 coding genes are encoded by heavy chain. The base content of AT is more than that of CG, and the C is significantly more than G on heavy chain. There are 9 spacer regions and 14 overlay regions between each gene on mitochondrial genome of the moutain hare.13 protein-coding genes have a length of 11393bp, which regard ATG as initiation codon, excepting for ATT in 3 genes. Most of termination codons are ATT, and the other are mostly incomplete termination codons. CGA has the highest frequency in codon use, and CGG has the minimum. Amino acids of the highest frequency are Ala, Ile, Leu, Ser and Thr. The secondary structure predictions show that the tRNA have a typical structure of clover except tRNA-Ser(AGY), which has a missing of D arm. In addition, there are 29 pairs base mismatch. The origin of replication of L-strand is 43 bp in size, and the D-loop region has a length of 2299 bp, which located between 15448～18755bp. The TRS on D-loop region composed of 31 copies of repeat sequence which include 10 bases of ACCCACGTAC and GCGCACGTAC.There are differences between the mitochondrial genome sequences of the mountain hares which collected from different geographical locations, especially No.228 sample. In PCGs and 2 rRNA genes of Lepus in this study,12S rRNA gene had the slowest evolution rate, and ND4L gene won the fastest evolution rate. However, the ND3 gene had the fastest rate in the mountain hares.The haplotype diversity of D-loop region sequences in the mountain hare is 1, and has no a shared haplotype. The nucleotide diversity (π) is 0.043, and the nucleotide differences mean (k) is 47.366. There are frequent gene flow in different areas. The results show that the mountain hare has been dynamic equilibrium in history.The topological structures of phylogenetic tree constructed by different methods are basically the same, and the mountain hare belongs to the Arctic lineage. The seven mitochondrial genomes of the mountain hare cannot clustered into the same clade, which in No 12, No.004 and Finland(KJ397605) mountain hare individuals are relatively conservative and clustered into the same clade, but the other four individuals clustered into the other hares clades, which could due to genetic introgression.