G3 Genes Genomes Genetics,
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 19, 2024
Abstract
Peppermint,
Mentha
×
piperita
L.,
is
a
hexaploid
(2n
=
6x
72)
and
the
predominant
cultivar
of
commercial
mint
oil
production
in
US.
This
threatened
because
high
susceptibility
to
fungal
disease
verticillium
wilt,
caused
by
Verticillium
dahliae.
report
details
first
draft
polyploid
chromosome-level
genome
assembly
for
this
species.
The
“Mitcham”
resource
will
broaden
comparative
studies
resistance,
essential
biosynthesis,
hybridization
events
within
genus
Mentha.
It
also
be
valuable
contribution
body
phylogenetic
involving
other
genera
that
contain
species
with
varying
ploidy
levels.
Journal of Experimental Botany,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 10, 2025
Abstract
Plants
host
a
range
of
DNA
elements
capable
self-replication.
These
molecules,
usually
associated
to
the
activity
transposable
or
viruses,
are
found
integrated
in
genome
form
extrachromosomal
DNA.
The
these
can
impact
plasticity
by
variety
mechanisms,
including
generation
structural
variants,
shuffling
regulatory
coding
sequences
across
genome,
and
endoduplication.
This
dynamically
alter
gene
expression
stability,
ultimately
affecting
plant
development
response
environmental
changes.
While
activation
is
often
considered
deleterious
their
role
creating
variation
important
adaptation
evolution.
Moreover,
mechanisms
which
mobile
proliferate
have
been
exploited
for
engineering,
contributed
understand
how
desirable
traits
be
generated
crops.
In
this
review,
we
discuss
origins
roles
element
on
biology,
as
well
potential
function
current
application
biotechnology.
Science,
Год журнала:
2025,
Номер
388(6743), С. 191 - 198
Опубликована: Апрель 10, 2025
Huanglongbing
(HLB)
is
a
devastating
citrus
disease.
In
this
work,
we
report
an
HLB
resistance
regulatory
circuit
in
Citrus
composed
of
E3
ubiquitin
ligase,
PUB21,
and
its
substrate,
the
MYC2
transcription
factor,
which
regulates
jasmonate-mediated
defense
responses.
A
helitron
insertion
PUB21
promoter
introduced
multiple
MYC2-binding
cis-elements
to
create
linking
activity
with
degradation.
Ectopic
expression
natural
dominant-negative
paralog
discovered
distant
relatives
stabilized
conferred
HLB.
Antiproteolysis
peptides
(APPs),
identified
by
artificial
intelligence,
binding
inhibiting
activity.
14–amino
acid
peptide,
APP3-14,
molecularly
controlled
greenhouse
field
trials.
This
approach
represents
strategy
combat
uncultivable
pathogens
through
targeted
disease
protein
stabilization.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 2, 2024
ABSTRACT
Transposable
elements
(TEs)
are
DNA
sequences
with
the
ability
to
propagate
themselves
within
genomes.
Their
mobilization
is
catalyzed
by
self-encoded
factors,
yet
these
factors
have
been
poorly
investigated.
Here,
we
leveraged
extensive
long-and
short-read
transcriptome
data,
structural
predictions,
and
regulatory
networks
analyses,
construct
a
comprehensive
atlas
of
TE
transcripts
their
encoded
products
in
model
organism
Arabidopsis
thaliana
.
We
uncovered
hundreds
transcriptionally
competent
TEs,
each
potentially
encoding
multiple
proteins
either
through
distinct
genes,
alternative
splicing,
or
post-translational
processing.
Structural-based
protein
analyses
revealed
hitherto
unidentified
domains,
uncovering
multimerization
binding
domains
forming
macromolecular
complexes.
Furthermore,
demonstrate
that
expression
highly
intertwined
transcriptional
network
cellular
identified
transcription
cis-regulatory
associated
coordinated
during
development
response
environmental
cues.
This
functional
provides
valuable
resource
for
studying
mechanisms
involved
transposition
consequences
genome
organismal
function.
The
WD40
repeat
proteins
are
crucial
components
of
eukaryotic
genomes
and
contribute
to
a
wide
array
plant
developmental
processes
environmental
interactions.
However,
the
true
extent
intraspecific
diversity
in
plants
is
unclear.
We
defined
nearly
complete
species-wide
pan-WD40ome
maize
based
on
published
genome
sequences
26
nested
association
mapping
(NAM)
population
founders.
largely
saturated
with
inclusion
approximately
20
inbred
lines,
about
95%
being
present
at
least
two
architectural
domains,
additional
consequent
spatial
protein
structures
suggested
functional
pan-WD40ome.
This
finding
was
supported
by
significant
associations
between
87
genes
19
agronomic,
3
kernel-quality,
biotic-stress
traits,
as
well
multiple
molecular
pathways
through
which
trait-associated
were
predicted
function.
In
addition,
exhibited
abundant
genomic
variations
among
NAM
Sequence
analysis
indicated
that
gene
duplications
translocations
caused
Helitron
transposons
may
play
important
roles
amplification
during
evolution
family.
summary,
this
study
provides
comprehensive
framework
for
understanding
structural
other
agronomically
species
complex
genomes,
excellent
candidate
genes/alleles
genetic
improvement.
Despite
the
striking
conservation
of
animal
chromosomes,
their
repetitive
element
complements
are
vastly
diverse.
Only
recently,
high
quality
chromosome-level
genome
assemblies
enabled
identification
repeat
compositions
along
a
broad
range
chromosomes.
Here,
utilizing
assembly
Hydractinia
symbiolongicarpus,
colonial
hydrozoan
cnidarian,
we
describe
an
accumulation
single
372
bp
unit
in
subtelomeric
regions.
Based
on
sequence
divergence,
its
partial
affinity
with
Helitron
group
can
be
detected.
This
is
associated
repeated
minisatellite
about
150
bp.
Together,
they
account
for
26.1%
(126
Mb
483
Mb).
could
explain
size
increase
observed
H.
symbiolongicarpus
compared
other
cnidarians,
yet
distinguishes
this
expansion
from
large
cnidarian
genomes,
such
as
Hydra
vulgaris,
where
localized
propagation
absent.
Additionally,
identify
derivative
IS3EU-like
DNA
accumulated
at
putative
centromeric
Our
analysis
further
reveals
that
Helitrons
generally
comprise
proportion
(11.8%).
We
investigated
presence
and
distributions
across
several
genomes.
find
Nematostella
vectensis,
anthozoan
Helitron-like
sequences
were
similarly
All
these
findings
suggest
derivatives
prone
to
forming
chromosomal
extensions
cnidarians
through
local
amplification
regions,
driving
variable
expansions
within
clade.
Genes,
Год журнала:
2025,
Номер
16(5), С. 528 - 528
Опубликована: Апрель 29, 2025
Background:
Understanding
the
role
of
repetitive
elements
(REs)
in
cancer
development
is
crucial
for
identifying
novel
biomarkers
and
therapeutic
targets.
Methods:
This
study
investigated
locus-specific
dysregulation
REs,
including
differential
expression
methylation
across
12
TCGA
types
stratified
by
their
genomic
context
(i.e.,
genic
intergenic
REs).
Results:
We
found
uniquely
dysregulated
REs
co-regulated
with
corresponding
transcripts
associated
distinct
biological
functions
different
types.
Uniquely
were
identified
each
type
used
to
cluster
sample
Recurrently
several
types,
genes
up-regulated
involved
cell
cycle
processes
those
down-regulated
extracellular
matrix.
Interestingly,
four
out
five
consistently
all
located
intronic
region
TMEM252,
a
recently
discovered
tumor
suppressor
gene.
TMEM252
was
also
10
suggesting
its
potential
importance
wide
range
With
DNA
array
data,
we
higher
prevalence
hypo-methylated
most
(10
12).
Despite
slight
overlaps
between
differentially
expressed
methylated
showed
that
negatively
correlates
some
these
Conclusions:
Our
findings
highlight
cancer-specific
recurrent
deregulation
functional
associations,
as
pan-cancer
suppressor,
providing
new
insights
into
biomarker
discovery
development.
