The leishmaniases are a group of vector borne diseases that are caused by flagellate of the genus Leishmania, which is transmitted by the bite of the sandfly, and affect as many as 12 million people worldwide with 1.5–2 million new cases each year in 88 countries . The genus Leishmania consists of nearly 30 species of morphologically similar kinetoplastid protozoa, and approximately 20 of these species are responsible for a spectrum of human diseases that ranges from mild to fatal infections [2, 3].
It is well accepted now that the genus Leishmania forms a monophyletic group with three distinct subgenera Leishmania (Leishmania), Leishmania (Viannia), and Leishmania (Sauroleishmania) . Once, the Leishmania-like parasites of reptiles were recognized as a separate genus L. (Sauroleishmania) [5, 6]. But the classification of lizard Leishmania as subgenus L. (Sauroleishmania) was proposed by Saf’janova , Croan et al., Orlando et al., Zelazny et al. and Fraga et al. on the basis of biological criteria and analysis of different Leishmania gene. According to the absolute chromosomal size difference index (aCSDI) analysis of as many as 31 “conserved” chromosomes, subgenera L. (Leishmania) is divided into clusters: (1) Old world representatives of subgenus Leishmania (OWL), and (2) New world representatives of subgenus Leishmania (NWL) and subgenus Viannia (NWV) .
The complexity of the taxonomy and phylogenetic relationships of the Chinese Leishmania was due to the extensive geographic area and complex ecological environment. Identification of species responsible for different leishmaniasis and clinical manifestation remains uncertain. The strains from cutaneous leishmaniasis (CL) in Xinjiang Uygur Autonomous Region (Xinjiang) especially in Karamay is closely related to L. tropica with analysis of SSU rDNA gene[11, 12], whereas the pathogen identified as Leishmania infantum[13, 14] or Leishmania turanica from the same geographic region Karamay also could cause CL. However, L. turanica is nonpathogenic to humans, according to Strelkova et al.. The parasites of some visceral leishmaniasis (VL) cases in Sichuan and Gansu provinces were L. donovani or undescribed species Leishmania sp. [17–19]. VL and CL have been reported in China to date the species of Leishmania comprises much more than that. The isolates in China were more heterogeneous than previously thought, requiring the reassignment of some isolates into different groups as described by Lu et al..
Over the past few decades, DNA markers including coding and non-coding genes have become additional information for advancing our understanding of evolutionary and phylogenetic relationships and species differentiation. Data pertaining to the ribosomal RNA (rRNA) gene sequences–in particular, the two non-coding, highly variable internal transcribed spacer regions (ITS1 and ITS2) are considered to be acceptable molecular criteria for resolving taxonomic questions and determining the phylogenetic affinities among closely related Leishmania species [17, 21–25]. While coding genes are also wildly used for taxonomic studies, such as metabolic enzymes (ICD, ME, MPI, G6PDH, ASAT, GPI, NH1, NH2, PGD and FH) [26, 27], heat-shock protein 70 gene (hsp70) , cytochrome oxidase II (CO II) , the gene encoding the largest subunit of RNA polymerase II (rpoIILS) [6, 8], the glycoprotein 63 gene (gp 63) , cysteine protease B genes (cpb)  and cytochrome b (cyt b) [31–35].
In previous ITS1 and CO II study [17, 19], we summarized the four endemic Leishmania species in China: L. donovani, L. infantum, Leishmania gerbilli, and L. turanica. We also noted that there might be an undescribed Leishmania species endemic in China and highlighted that the isolate IPHL/CN/77/XJ771 from Bachu County, Xinjiang, is L. donovani instead of L. infantum. To elucidate the phylogeny, evolution and epidemiology of interesting group of strains in China, further studies of more genes are required.
Cyt b is one of the cytochromes involved in the electron transport process of the mitochondrial respiratory chain is considered one of the most useful genes for phylogenetic work . Marco et al. proved that the cyt b gene sequencing can precisely identify the Leishmania spp. for all of the local stocks that are well characterized by multi-locus enzyme electrophoresis (MLEE), the current gold standard . Phylogeny and sequence variation of the genus Leishmania has also been discussed successfully with cyt b sequencing [34, 35]. In this paper, the cyt b gene of Leishmania from China was sequenced and analyzed using bioinformatics methods. Moreover, the phylogenetic relationships were reconstructed using cyt b sequences obtained by this study and download from the GenBank database. We then discuss in detail the implications of relationships between strains in China and other locations.