Royal Society Open Science,
Год журнала:
2024,
Номер
11(12)
Опубликована: Дек. 1, 2024
also
known
as
southern
pine
beetle
(SPB),
is
the
most
damaging
insect
forest
pest
in
southeastern
United
States.
Genomic
data
are
important
to
provide
information
on
biology
and
identify
molecular
targets
develop
improved
management
approaches.
Here,
we
produced
a
chromosome-level
genome
assembly
of
SPB
using
long-read
sequencing
data.
Synteny
analyses
confirmed
conservation
core
Coleopteran
Stevens
elements
validated
Museum
collections
harbor
millions
of
samples,
largely
unutilized
for
long-read
sequencing.
Here,
we
use
ethanol-preserved
samples
containing
kilobase-sized
DNA
to
show
that
amplification-free
protocols
can
yield
contiguous
genome
assemblies.
Additionally,
using
a
modified
amplification-based
protocol,
employing
an
alternative
polymerase
overcome
PCR
bias,
assemble
the
3.1
Gb
maned
sloth
genome,
surpassing
previous
500
Mb
protocol
size
limit.
Our
also
improves
assemblies
other
difficult-to-sequence
molluscs
and
arthropods,
including
millimeter-sized
organisms.
By
highlighting
as
valuable
sample
resources
facilitating
assembly
tiny
challenging
organisms,
our
study
advances
efforts
obtain
reference
genomes
all
eukaryotes.
Cell Genomics,
Год журнала:
2024,
Номер
4(4), С. 100527 - 100527
Опубликована: Март 26, 2024
The
seventh
iteration
of
the
reference
genome
assembly
for
Rattus
norvegicus-mRatBN7.2-corrects
numerous
misplaced
segments
and
reduces
base-level
errors
by
approximately
9-fold
increases
contiguity
290-fold
compared
with
its
predecessor.
Gene
annotations
are
now
more
complete,
improving
mapping
precision
genomic,
transcriptomic,
proteomics
datasets.
We
jointly
analyzed
163
short-read
whole-genome
sequencing
datasets
representing
120
laboratory
rat
strains
substrains
using
mRatBN7.2.
defined
∼20.0
million
sequence
variations,
which
18,700
predicted
to
potentially
impact
function
6,677
genes.
also
generated
a
new
genetic
map
from
1,893
heterogeneous
stock
rats
annotated
transcription
start
sites
alternative
polyadenylation
sites.
mRatBN7.2
assembly,
along
extensive
analysis
genomic
variations
among
strains,
enhances
our
understanding
genome,
providing
researchers
an
expanded
resource
studies
involving
rats.
Proceedings of the National Academy of Sciences,
Год журнала:
2024,
Номер
121(21)
Опубликована: Май 13, 2024
The
ecoevolutionary
drivers
of
species
niche
expansion
or
contraction
are
critical
for
biodiversity
but
challenging
to
infer.
Niche
may
be
promoted
by
local
adaptation
constrained
physiological
performance
trade-offs.
For
birds,
evolutionary
shifts
in
migratory
behavior
permit
the
broadening
climatic
into
varied,
seasonal
environments.
Broader
niches
can
short-lived
if
diversifying
selection
and
geography
promote
speciation
subdivision
across
gradients.
To
illuminate
breadth
dynamics,
we
ask
how
“outlier”
defy
constraints.
Of
363
hummingbird
species,
giant
(
Patagona
gigas
)
has
broadest
a
large
margin.
test
roles
behavior,
trade-offs,
genetic
structure
maintaining
its
exceptional
breadth,
studied
movements,
respiratory
traits,
population
genomics.
Satellite
light-level
geolocator
tracks
revealed
an
>8,300-km
loop
migration
over
Central
Andean
Plateau.
This
included
3-wk,
~4,100-m
ascent
punctuated
upward
bursts
pauses,
resembling
acclimatization
routines
human
mountain
climbers,
accompanied
surging
blood-hemoglobin
concentrations.
Extreme
was
deep
genomic
divergence
from
high-elevation
resident
populations,
with
decisive
postzygotic
barriers
gene
flow.
two
forms
occur
side-by-side
differ
almost
imperceptibly
size,
plumage,
traits.
taxon
is
world’s
largest
hummingbird,
previously
undiscovered
that
describe
name
here.
hummingbirds
demonstrate
limits
on
breadth:
when
ancestral
expanded
due
evolution
(or
loss)
extreme
followed.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 23, 2023
Abstract
The
planarian
Schmidtea
mediterranea
can
regenerate
its
entire
body
from
small
tissue
fragments
and
is
studied
as
regeneration
model
species.
assembly
functional
analysis
of
genomes
has
proven
challenging
due
high
A/T
content
(70%
A/T),
repetitive
nature,
limited
transferability
routine
laboratory
protocols
to
their
divergent
biochemistry.
Only
few
often
fragmented
genome
assemblies
are
currently
available,
open
challenges
include
the
provision
well-annotated
chromosome-scale
reference
species
other
planarians
for
a
comparative
evolution
perspective.
Here
we
report
haplotype-phased,
high-quality
gene
annotations
sexual
S2
strain
S.
provide
putative
regulatory
region
via
optimized
ATAC-seq
ChIP-seq
protocols.
To
additionally
leverage
sequence
conservation
element
annotations,
generated
chromatin
accessibility
data
three
closest
relatives
:
polychroa
,
nova
lugubris
.
We
find
substantial
divergence
in
protein-coding
sequences
regions,
yet
reveal
remarkable
ChIP-mark
bearing
regions
identified
promoters
enhancers
resulting
high-confidence
set
evolutionary
conserved
provides
valuable
resource
circuits
within
taxon.
In
addition,
our
four
first
perspective
on
evolution.
Our
analyses
frequent
retrotransposon-associated
chromosomal
inversions
inter-chromosomal
translocations
that
lead
degradation
synteny
across
genus.
Interestingly,
further
independent
near-complete
losses
ancestral
metazoan
two
flatworm
groups,
indicating
platyhelminth
largely
evolve
without
syntenic
constraints.
work
resources
research
community
sets
foundation
genomics
planarians.
contrast
between
fast
structural
elements,
suggesting
unique
flatworms
where
positioning
may
not
be
essential.
Genes,
Год журнала:
2023,
Номер
14(5), С. 1050 - 1050
Опубликована: Май 8, 2023
The
growth
and
development
of
the
Longissimus
Dorsi
muscle
are
complex,
playing
an
important
role
in
determination
pork
quality.
study
at
mRNA
level
is
particularly
crucial
for
finding
molecular
approaches
to
improving
meat
quality
pig
breeding.
current
utilized
transcriptome
technology
explore
regulatory
mechanisms
intramuscular
fat
(IMF)
deposition
three
core
developmental
stages
(natal
stage
on
day
1,
growing
60,
finishing
210)
Ningxiang
pigs.
Our
results
revealed
441
differentially
expressed
genes
(DEGs)
common
1
vs.
60
210,
GO
(Gene
Ontology)
analysis
showed
that
candidate
RIPOR2,
MEGF10,
KLHL40,
PLEC,
TBX3,
FBP2,
HOMER1
may
be
closely
related
development,
while
KEGG
(Kyoto
Encyclopedia
Genes
Genomes)
DEGs
(UBC,
SLC27A5,
RXRG,
PRKCQ,
PRKAG2,
PPARGC1A,
PLIN5,
PLIN4,
IRS2,
CPT1B)
involved
PPAR
(Peroxisome
Proliferator-Activated
Receptor)
signaling
pathway
adipocytokine
pathway,
which
might
play
a
pivotal
regulation
IMF
deposition.
PPI
(Protein-Protein
Interaction
Networks)
found
STAT1
gene
was
top
hub
gene.
Taken
together,
our
provide
evidence
optimize
carcass
mass.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Март 7, 2024
Museum
collections
harbor
millions
of
samples,
largely
unutilized
for
long-read
sequencing.
Here,
we
use
ethanol-preserved
samples
containing
kilobase-sized
DNA
to
show
that
amplification-free
protocols
can
yield
contiguous
genome
assemblies.
Additionally,
using
a
modified
amplification-based
protocol,
employing
an
alternative
polymerase
overcome
PCR
bias,
assembled
the
3.1
Gb
maned
sloth
genome,
surpassing
previous
500
Mb
protocol
size
limit.
Our
also
improves
assemblies
other
difficult-to-sequence
molluscs
and
arthropods,
including
millimeter-sized
organisms.
By
highlighting
as
valuable
sample
resources
facilitating
assembly
tiny
challenging
organisms,
our
study
advances
efforts
obtain
reference
genomes
all
eukaryotes.
iScience,
Год журнала:
2025,
Номер
28(5), С. 112477 - 112477
Опубликована: Апрель 18, 2025
Old
World
camels
exhibit
many
unique
traits
for
adaptations
to
desert
environments,
distinct
from
New
within
the
same
family.
Here,
we
conducted
a
comparative
genomic
analysis
of
three
camel
species
relative
four
species,
as
well
cattle,
pigs,
mice,
and
humans
search
genes
showing
positive
selection
specific
variations
in
camels.
We
identified
under
selection,
with
small
indels,
inactivated
associated
lipid
metabolism
skin
characteristics
Especially,
through
experimental
validation,
confirmed
inactivation
TAS2R16,
gene
encoding
prominent
bitter
taste
receptor,
which
could
enable
consume
certain
toxic
plants
other
mammals.
These
findings
provide
insights
into
genetic
basis
underlying
distinctive
energy
metabolism,
water-salt
homeostasis,
dietary
Molecular Ecology Resources,
Год журнала:
2025,
Номер
unknown
Опубликована: Май 5, 2025
ABSTRACT
Optimal
preservation
of
tissues
from
the
field
to
long‐term
cryo‐storage
is
paramount
securing
genetic
resources
for
research
needs.
DNA
techniques
vary,
with
flash
freezing
currently
considered
gold
standard
in
tissue
preservation.
However,
samples
presents
challenges,
necessitating
a
more
comprehensive
understanding
quantity
and
quality
preserved
different
archival
collections.
We
compared
metrics
extractions
field‐collected
amphibian,
squamate
bird
collections
that
were
flash‐frozen
liquid
nitrogen
or
fixed
either
ethanol
lysis
buffer
prior
cryopreservation.
also
included
extracted
known
tank
failures
provide
baseline
degradation
under
very
worst‐case
scenario.
Flash‐frozen
often
higher
yields
DNA,
but
peak
fragment
size,
percentage
fragments
larger
than
10
kb
integrity
numbers
all
significantly
reduced
first
fixative
buffers.
This
pattern
was
observed
across
independent
between
buffer‐preserved
pair
replicates.
Degradation
seen
distinct
failures.
suggest
occurred
during
shipping,
sample
sorting/accession
subsequent
subsampling
when
may
partially
fully
thaw,
exposing
damaging
freeze–thaw
processes.
By
contrast,
buffers
likely
protected
damage.
study
highlights
using
multiple
methods
minimising
cycles
most
robust
protection
against
sources
encountered
by