Molecular Ecology Resources,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 20, 2025
ABSTRACT
Pardosa
spiders,
belonging
to
the
wolf
spider
family
Lycosidae,
play
a
vital
role
in
maintaining
health
of
forest
and
agricultural
ecosystems
due
their
function
pest
control.
This
study
presents
chromosome‐level
genome
assemblies
for
two
allied
species,
P.
laura
agraria
.
Both
species'
genomes
show
notable
expansion
helitron
transposable
elements,
which
contributes
large
sizes.
Methylome
analysis
indicates
that
has
higher
overall
DNA
methylation
levels
compared
may
not
only
aids
element‐driven
but
also
positively
affects
three‐dimensional
organisation
after
transposon
amplification,
thereby
potentially
enhancing
stability.
Genes
associated
with
hyper‐differentially
methylated
regions
(compared
)
are
enriched
functions
related
mRNA
processing
energy
production.
Furthermore,
combined
transcriptome
methylome
profiling
uncovered
complex
regulatory
interplay
between
gene
expression,
emphasising
important
body
regulation
expression.
Comparative
genomic
shows
significant
cuticle
protein
detoxification‐related
families
,
improve
its
adaptability
various
habitats.
provides
essential
methylomic
insights,
offering
deeper
understanding
relationship
elements
stability,
illuminating
adaptive
evolution
species
differentiation
among
spiders.
Plants,
Год журнала:
2024,
Номер
13(17), С. 2462 - 2462
Опубликована: Сен. 3, 2024
Transposable
elements
(TEs)
significantly
contribute
to
the
evolution
and
diversity
of
plant
genomes.
In
this
study,
we
explored
roles
TEs
in
genomes
Citrus
Citrus-related
genera
by
constructing
a
pan-genome
TE
library
from
20
published
accessions.
Our
results
revealed
an
increase
content
number
types
compared
original
annotations,
as
well
decrease
unclassified
TEs.
The
average
length
per
assembly
was
approximately
194.23
Mb,
representing
41.76%
(Murraya
paniculata)
64.76%
(Citrus
gilletiana)
genomes,
with
mean
value
56.95%.
A
significant
positive
correlation
found
between
genome
size
both
content.
Consistent
difference
whole-genome
(39.83
Mb)
genera,
contained
34.36
Mb
more
sequences
than
Analysis
estimated
insertion
time
half-life
long
terminal
repeat
retrotransposons
(LTR-RTs)
suggested
that
removal
not
primary
factor
contributing
differences
among
These
findings
collectively
indicate
are
determinants
play
major
role
shaping
structures.
Principal
coordinate
analysis
(PCoA)
Gene
Ontology
(GO)
Kyoto
Encyclopedia
Genes
Genomes
(KEGG)
identifiers
fragmented
were
predominantly
derived
ancestral
while
intact
crucial
recent
evolutionary
diversification
Citrus.
Moreover,
presence
or
absence
near
AdhE
superfamily
closely
associated
bitterness
trait
species.
Overall,
study
enhances
annotation
provides
valuable
data
for
future
genetic
breeding
agronomic
research
Molecular Ecology,
Год журнала:
2021,
Номер
30(23), С. 6211 - 6228
Опубликована: Июль 29, 2021
Abstract
Introduced
populations
of
invasive
organisms
have
to
cope
with
novel
environmental
challenges,
while
having
reduced
genetic
variation
caused
by
founder
effects.
The
mechanisms
associated
this
“genetic
paradox
species”
has
received
considerable
attention,
yet
few
studies
examined
the
genomic
architecture
species.
Populations
heart
node
ant
Cardiocondyla
obscurior
belong
two
distinct
lineages,
a
New
World
lineage
so
far
only
found
in
Latin
America
and
more
globally
distributed
Old
lineage.
In
present
study,
we
use
population
approaches
compare
lineages
apparent
divergent
potential.
We
find
that
strong
differentiation
began
at
least
40,000
generations
ago
activity
transposable
elements
(TEs)
contributed
significantly
divergence
both
possibly
linked
very
unusual
distribution
TEs
Furthermore,
show
introgression
from
is
dominant
source
diversity
lineage,
despite
lineages'
differentiation.
Our
study
uncovers
underlying
introduced
C
.
could
contribute
species'
adaptive
Briefings in Bioinformatics,
Год журнала:
2022,
Номер
24(1)
Опубликована: Ноя. 3, 2022
Abstract
LTR-retrotransposons
are
the
most
abundant
repeat
sequences
in
plant
genomes
and
play
an
important
role
evolution
biodiversity.
Their
characterization
is
of
great
importance
to
understand
their
dynamics.
However,
identification
classification
these
elements
remains
a
challenge
today.
Moreover,
current
software
can
be
relatively
slow
(from
hours
days),
sometimes
involve
lot
manual
work
do
not
reach
satisfactory
levels
terms
precision
sensitivity.
Here
we
present
Inpactor2,
accurate
fast
application
that
creates
LTR-retrotransposon
reference
libraries
very
short
time.
Inpactor2
takes
assembled
genome
as
input
follows
hybrid
approach
(deep
learning
structure-based)
detect
elements,
filter
partial
finally
classify
intact
into
superfamilies
and,
few
tools
do,
lineages.
This
tool
advantage
multi-core
GPU
architectures
decrease
execution
times.
Using
rice
genome,
showed
run
time
5
minutes
(faster
than
other
tools)
has
best
accuracy
F1-Score
tested
here,
also
having
second
specificity
only
surpassed
by
EDTA,
but
achieving
28%
higher
For
large
genomes,
up
seven
times
faster
available
bioinformatics
tools.
Molecular Ecology Resources,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 20, 2025
ABSTRACT
Pardosa
spiders,
belonging
to
the
wolf
spider
family
Lycosidae,
play
a
vital
role
in
maintaining
health
of
forest
and
agricultural
ecosystems
due
their
function
pest
control.
This
study
presents
chromosome‐level
genome
assemblies
for
two
allied
species,
P.
laura
agraria
.
Both
species'
genomes
show
notable
expansion
helitron
transposable
elements,
which
contributes
large
sizes.
Methylome
analysis
indicates
that
has
higher
overall
DNA
methylation
levels
compared
may
not
only
aids
element‐driven
but
also
positively
affects
three‐dimensional
organisation
after
transposon
amplification,
thereby
potentially
enhancing
stability.
Genes
associated
with
hyper‐differentially
methylated
regions
(compared
)
are
enriched
functions
related
mRNA
processing
energy
production.
Furthermore,
combined
transcriptome
methylome
profiling
uncovered
complex
regulatory
interplay
between
gene
expression,
emphasising
important
body
regulation
expression.
Comparative
genomic
shows
significant
cuticle
protein
detoxification‐related
families
,
improve
its
adaptability
various
habitats.
provides
essential
methylomic
insights,
offering
deeper
understanding
relationship
elements
stability,
illuminating
adaptive
evolution
species
differentiation
among
spiders.
