Figure legends
Figure 1. Heat map and genomic landscape of theS. scabiei var. cuniculi genome. (a) Heat map of theS. scabiei var. cuniculi genome. (b) Genomic landscape of the S. scabiei var. cuniculi assembly over 100-kb chromosomal intervals. Tracks from outside to inside: 1. Positions of the nine chromosomes of S. scabiei ; 2. Gene density; 3. Repeat sequences across the genome; 4. GC content.
Figure 2. Evolution of the scabies mite genome. (a) Phylogenetic tree of S. scabiei var. cuniculi constructed using 1,338 shared single-copy orthologous genes and estimation of divergence time and expansion and contraction in gene families. (b) Genetic relationship of S. scabiei mite derived from four human, pig, dog and rabbit. (c) Principal component analysis (PCA) plot ofS. scabiei populations using autosomal single nucleotide polymorphisms (SNPs). The fraction of the variance explained is 47.44% for eigenvector 1 and 12.97% for eigenvector 2. (d) Demographic history of S. scabiei variants. Ancestral population size was inferred using pairwise sequentially Markovian coalescence (PSMC). Data are shown individually for 20 mite populations. Generation time (g ) = 0.0575 years, mutation rate (µ) = 5.8 × 10−9 mutations per bp per generation. Cartoon humans and animals in black represent the hosts of corresponding mite populations. Marked year on the top indicated the emerging of Archaic hunans and modern humans, as well as the domestication time of dogs, pigs and rabbits from currently available literatures.
Figure 3. Morphology of representative mites in the Acari and organization of Hox genes . (a) Schematic diagram of mammal skin. (b) Life cycle of sarcoptic mites. (c) Morphology of six species of female mites. (d) Organization of Hox genes of S. scabieiand other chelicerate species. Left panel, phylogenetic relationship adapted from Figure 2a; central panel, Hox genes and transcript directions; right panel, traditional taxonomy.
Figure 4. GO and KEGG enrichment of S. scabiei specific genes identified by orthoMCL. (a) GO. (b) KEGG.
Figure 5. Distribution of θπ ratios and FST values, which are calculated in 10-kb windows sliding in 5-kb steps. (a) Genomic regions with strong selective sweep signals between human mites and pig mites. Data points located to the left and right of the left and right vertical dashed lines, respectively (corresponding to the 5% left and right tails of the empirical θπ ratio distribution, where the θπ ratios are -0.7 and 1.4, respectively), and above the horizontal dashed line (the 5% right tail of the empirical FST distribution, where FST is 1.91) were identified as selected regions for human mites (blue points) and pig mites (red points), respectively. (b) Genomic regions with strong selective sweep signals between human mites and dog mites. Data points located to the left and right of the left and right vertical dashed lines, respectively (corresponding to the 5% left and right tails of the empirical θπ ratio distribution, where the θπ ratios are -0.7 and 1.4, respectively), and above the horizontal dashed line (the 5% right tail of the empirical FST distribution, where FST is 1.91) were identified as selected regions for human mites (blue points) and dog mites (red points), respectively.