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Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis.
[scrub typhus]
Leptotrombidium
pallidum
and
Leptotrombidium
scutellare
are
the
major
vector
mites
for
Orientia
tsutsugamushi
,
the
causative
agent
of
scrub
typhus
.
Before
these
organisms
can
be
subjected
to
whole-genome
sequencing
,
it
is
necessary
to
estimate
their
genome
sizes
to
obtain
basic
information
for
establishing
the
strategies
that
should
be
used
for
genome
sequencing
and
assembly
.
The
genome
sizes
of
L
.
pallidum
and
L
.
scutellare
were
estimated
by
a
method
based
on
quantitative
real-time
PCR
.
In
addition
,
a
k-mer
analysis
of
the
whole-genome
sequences
obtained
through
Illumina
sequencing
was
conducted
to
verify
the
mutual
compatibility
and
reliability
of
the
results
.
The
genome
sizes
estimated
using
qPCR
were
191
±
7
Mb
for
L
.
pallidum
and
262
±
13
Mb
for
L
.
scutellare
.
The
k-mer
analysis-based
genome
lengths
were
estimated
to
be
175
Mb
for
L
.
pallidum
and
286
Mb
for
L
.
scutellare
.
The
estimates
from
these
two
independent
methods
were
mutually
complementary
and
within
a
similar
range
to
those
of
other
Acariform
mites
.
The
estimation
method
based
on
qPCR
appears
to
be
a
useful
alternative
when
the
standard
methods
,
such
as
flow
cytometry
,
are
impractical
.
The
relatively
small
estimated
genome
sizes
should
facilitate
whole-genome
analysis
,
which
could
contribute
to
our
understanding
of
Arachnida
genome
evolution
and
provide
key
information
for
scrub
typhus
prevention
and
mite
vector
competence
.