3.5 Strong selective sweep signals provided clues to the genetic
basis of variant divergence and cross-infestivity
Scanning electron microscopy and light microscopy showed that S.
scabiei lives in the skin stratum corneum reside at the interface of
stratum lucidum and stratum granulosum
(Estes et al. , 1983;
Neste & Lachapelle, 1981;
Van Neste, 1984). As shown inTable S20 , the epidermis of humans, pigs, dogs and rabbits are
46.9 ± 2.3 μm, 65.8 ± 1.8 μm, 18.94 ± 2.29 μm, and 17.0 ± 1.2 μm thick,
respectively (Bhandal et al. ,
2012; Bronaugh et al. , 1982;
Nicoli et al. , 2008), while the
stratum corneum of them are 16.8±0.7 μm, 26.4±0.4 μm, NA and 11.7±0.5
μm. According to the results of PSMC, humans, pigs, dogs and rabbits get
infected with scabies mites for more than 30 kyr ago, to reveal the
potential genome footprint that may left by a couple of hundred thousand
years co-evolution of the scabies mites and the hosts, we used FST & θπ
to find possible selection sweeping signal between any of the two hosts.
As shown in Figure 5, strong selective signals were observed
between pig mites and human mites: about 10 times as many genomic
regions with strong selective sweep signals in pig mites (3.84% of the
genome, containing 358 genes) as there are in human mites (0.40% of the
genome, containing 37 genes), with significant enrichment in
“cysteine-type peptidase activity (10 genes), Neuroactive
ligand-receptor interaction (18 genes), and Apoptosis (11 genes)
(Table S21 ).There are three times as many genomic regions with
strong selective sweep signals in dog mites (0.81% of the genome,
containing 77 genes) as there are in human mites (0.27% of the genome,
containing 25 genes), with high enrichment in “cysteine-type peptidase
activity (five genes) and apoptosis (five genes)(Table S21 ). As
shown in Table S22-24 , the involved genes mainly including Sar
s 1 allergen SMIPP-C (Peptidase C1A, papain C-terminal) and group 3
allergen SMIPP-S (Peptidase S1). However, as a recently emerging mite
variant, rabbit scabies mites showed very limited selective sweeping
signals compared with mites from any of the other three hosts
(Table S21 ), especially with human mites and dog mites, which
might be the explanation of cross-infestivity between rabbits and the
other three hosts.
Discussion
Genome assembly and evolution
Scabies mites represent a highly contagious ectoparasite that can affect
more than 100 mammal species (Escobaret al. , 2021). In this study, we presented the chromosome-scale
genome assembly for ectoparasite S. scabiei . To the best of our
knowledge, this is the first chromosome-level genome of all mite species
to be determined to date (Table 1 ), providing a reference
genome for comparative genomics of mite biology and further study of
scabies mite.
Genome evolution results showed that scabies mites from four hosts
clustering together, and rabbit mite is closer to human mites followed
by pig mites and dog mites. However, the population genetics results
indicated the clear cluster was defined by hosts, and rabbit mites seems
distantly related with other mites, providing evidence supporting the
hypothesis that S. scabiei is not a single panmictic population
and genetic subdivisions occurs according to the hosts
(Alasaad et al. , 2011;
Walton et al. , 2004). It thus can
be concluded that S. scabiei from various hosts are genetically
similar to each other and are likely variants of one species that mainly
clustered by host species.
If the variants classified by hosts is the case, is there any order of
infection time for mites from these hosts? Surprisingly, the origin time
of human mites support the current scientific consensus that humans are
the principal host for Sarcoptes mites. Domestication of dogs can be
traced back to at least around 15,000 years, and possibly earlier, being
domesticated from the gray wolf in East Asia around 100,000 years ago
(Bardeleben et al. , 2005;
Currier et al. , 2011;
Savolainen et al. , 2002;
Wayne et al. , 1997); moreover,
recent studies have shown that, in southern East Asia, the groups of
dogs and wolves began to diverge about 33,000 years ago
(Skoglund et al. , 2015;
Wang et al. , 2016;
Wang et al. , 2013). The estimated
origin time of dogs (about 37 kyr - 61 kyr) all fall within the time
frame of human domestication of domestic dogs (15,000 years to 100,000
years ago), indicating that the canine-derived scabies mites may have
come from human-derived scabies mites. However, the results showed that
pigs and rabbits get infected with scabies mites long before they were
domesticated by humans, contradicting the hypothesis that humans
transmitted scabies mites to animals through domestication activity
(Currier et al. , 2011a;
Friedman, 1936). The possible transfer of
human-derived mites to dogs probably reflected the intimate relationship
of humans and dogs.