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.