Fig 1.
The sampling areas in the Xinjiang Autonomous Region.
Leishmania samples were collected from oases (grey area) or desert (spotted area) (Upper Panel). SF, Shufu county; JS, eastern Jiashi county; BC, Bachu county; MF, Minfeng county. Black square: Patient, Black circle: Tarim hare, Black triangles: P.wui (vector). The Tarim basin is surrounded by the Tianshan mountains and Kunlun mountains which forms a barrier separating it from surrounding areas. https://usgs.maps.arcgis.com/apps/webappviewer/index.html?id=2b7d5dbc0be340b9b17f6d94aac5b713 (42.8–35.0°N, 71.4–87.6°E).
Table 1.
Leishmania isolates from Xinjiang.
Table 2.
List of reference strains used in this study.
Fig 2.
Phylogenetic tree based on the alignment of amplified section of the nagt sequences.
The phylogenetic tree was constructed using the Neighbor-Joining (NJ), Maximum likelihood (ML) and Minimum Evolution (ME) methods, bootstrap values were provided next to nodes (NJ/ML/ME), a value lower than 50 was indicated as (--). Information on the origins and hosts of isolates are provided. The terrain where isolates were collected in this study is indicated with triangle (▲, DT-ZVL foci) or square (■, AVL foci). don, L. donovani; inf, L. infantum; maj, L. major; aet, L. aethiopia; tro, L. tropica; tur, L. turanica; ger, L. gerbilli; mex, L. mexicana; bra, L. braziliensis; *, the species is suggested to be L. donovani.
Fig 3.
Multiple sequence alignment of the ITS1 sequences from different haplotypes of Xinjiang Leishmania isolates.
The detailed information for each haplotype (I1 to I6) are provided in Tables 1 and 2. The first nucleotide of the ITS1 region that follows the end of the 18s rRNA (NC_007268.2 of the L. major strain Friedlin complete genome) was designated as the starting site. Haplotype I6 was chosen as a reference (GenbankAccession: AM901452) and the aligned fragments between position 3 and 121 are shown. Areas shaded in grey show identical sequences while the variable sites were marked with the location of the nucleotide shown above. I1, indicates isolates of AVL foci and L. infantum strains. I2, indicates isolates from DT-ZVL foci and L. donovani.
Fig 4.
Statistical parsimony haplotype network and phylogenetic tree based on the ITS1 sequence of the L. donovani complex.
The network is generated with TCS software (version 1.21). The haplotypes, I1 to I6, as given in Fig 2, Tables 1 and 2, are represented by an oval circle. Small hollow circles represent unsampled haplotypes and each line represents one mutational step. The phylogenetic tree was constructed using the Neighbor-Joining (NJ), Maximum likelihood (ML) and Minimum Evolution (ME) methods, bootstrap values were provided next to nodes (NJ/ML/ME). The origins and hosts of the isolates are provided. Terrains where isolates were collected in this study are indicated with a triangle (▲, DT-ZVL foci) or a square (■, AVL foci). don, L. donovani; inf, L. infantum; maj, L. major; *, the species is suggested to be L. donovani.
Fig 5.
Haplotype network and phylogenetic tree based on the hsp70 sequences of the L. donovani complex.
A haplotype network constructed using Median Joining and post processing with an MP calculation. The haplotypes of H1 to H11, as given in Fig 2, Tables 1 and 2, are represented by yellow circles. Small red solid circles represent median joining points, and mutational sites between two circles are shown next to the connecting line. The subgenera Leishmania and Viannia are separated by a thick black line. The phylogenetic tree was constructed using the Neighbor-Joining (NJ), Maximum likelihood (ML) and Minimum Evolution (ME) methods, bootstrap values were provided next to nodes (NJ/ML/ME), values lower than 50 were indicated as (--). The origins and hosts of isolates are provided. The terrains where isolates were collected in this study are indicated with triangle (▲, DT-ZVL foci) or square (■, AVL foci). don, L. donovani; inf, L. infantum; maj, L. major; aet, L. aethiopia; tro, L. tropica; ama, L. amazonensis; mex, L. mexicana; bra, L. braziliensis; guy, L. guyanensis; *, the species is suggested to be L. donovani. (A total of 1047 NT between sites 590–1636 were analyzed in the final data set and are numbered from the start codon of the hsp70 gene). Note: MHOM/CN/00/Wangjie1 and IWUI/CN/77/771 are heterozygous and only H2 was analyzed. H1: Leishmania infantum and isolates from AVL; H2: isolates from DT-ZVL. Other details of each haplotype are provided in Tables 1 and 2.