The complete mitochondrial genome analysis of <i>Haemaphysalis hystricis</i> Supino, 1897 (Ixodida: Ixodidae) and its phylogenetic implications

In order to study the sequence characteristics, gene order, and codon usage of the mitochondrial genome of <i>Haemaphysalis hystricis</i>, and to explore its phylogenetic relationship, a total of 36 <i>H. hystricis</i> isolated from dogs were used as sample in this study. The mitochondrial genome of a <i>H. hystricis</i> was amplified with several pairs of specific primers by PCR, and was sequenced by first generation sequencing. The mitochondrial genome of <i>H. hystricis</i> was 14,719 bp in size, and it contained 37 genes including 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and AT-rich region. Each PCG sequence had different lengths, the sequence longest and shortest gene were <i>nad</i>5 (1,652 bp) and <i>atp</i>8 (155 bp), respectively, among the 13 PCGs. All PCGs used ATN as their initiation codon, 10 of 13 PCGs used TAN as their termination codon, and 3 of which had incomplete termination codon (TA/T). Most of the 22 tRNAs with different sizes could form the classical cloverleaf structures expect for <i>tRNA</i>-<i>Ala</i>, <i>tRNA</i>-<i>Ser1</i>, <i>tRNA</i>-<i>Ser2</i>, and <i>tRNA</i>-<i>Glu</i>, and there were base mismatch (U-U and U-G) in all the 22 tRNAs sequences. Two rRNAs, namely <i>rrnL</i> and <i>rrnS</i>, had different lengths, <i>rrnL</i> located between <i>tRNA</i>-<i>Leu1</i> and <i>tRNA</i>-<i>Val</i>, and <i>rrnS</i> located between <i>tRNA</i>-<i>Val</i> and <i>tRNA</i>-<i>Ile</i>, respectively. Two AT (D-loop) control areas with different lengths were in the mitochondrial genome, the NCRL was located between <i>tRNA</i>-<i>Leu2</i> and <i>tRNA</i>-<i>Cys</i>, and the NCRS was located between <i>rrnS</i> and <i>tRNA</i>-<i>Ile</i>. The complete mitochondrial genome sequence of <i>H. hystricis</i> was AT preferences, and the gene order is the same as that of other <i>Haemaphysalis</i> family ticks. However, phylogenetic analysis showed that <i>H. hystricis</i> was most closely related to <i>Haemaphysalis longicornis</i> among the selected ticks. The mitochondrial genome not only enriches the genome database, provides more novel genetic markers for identifying tick species, and studying its molecular epidemiology, population genetics, systematics, but also have implications for the diagnosis, prevention, and control of ticks and tick-borne diseases in animals and humans.