Persicaria
tinctoria
(2n
=
40)
is
an
important
traditional
medicinal
plant
and
natural
dye
source
within
the
genus
Persicaria.
P.
has
been
utilized
for
its
antibacterial,
antiviral,
anti-inflammatory,
tumor
treatment
properties.
Additionally,
it
served
as
a
blue
thousands
of
years
worldwide,
continues
to
be
used
in
countries
such
China
Japan.
Here,
we
assembled
tetraploid
chromosome-scale
genome
tinctoria,
organized
into
two
subgenomes:
subgenome
A,
which
contains
10
pseudochromosomes
with
size
888.67
Mb
scaffold
N50
90.56
Mb,
B,
also
comprises
771.58
76.84
Mb.
Repeat
sequences
constitute
77.9%
genome.
A
total
76,742
high-confidence
protein-coding
genes
were
annotated,
94.28%
these
assigned
functional
annotations.
This
high-quality
assembly
will
provide
valuable
genomic
resources
studying
biosynthesis
evolution
indigoids
indigo
plants,
well
further
research
on
Polygonaceae
family.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Янв. 2, 2025
Plant
roots
perceive
heat
stress
(HS)
and
adapt
their
architecture
accordingly,
which
in
turn
influence
the
yield
crops.
Investigating
heterogeneity
cell
type-specific
response
to
HS
is
essential
for
improving
crop
resilience.
Here,
we
generate
single-cell
transcriptional
landscape
of
maize
(Zea
mays)
HS.
We
characterize
15
clusters
corresponding
9
major
types
identify
cortex
as
main
root
type
responsive
with
most
differentially
expressed
genes
its
trajectory
being
preferentially
affected
upon
find
that
size
strongly
correlated
tolerance
experimentally
validated
by
using
inbred
lines
genetic
mutation
analysis
one
candidate
gene
maize,
providing
potential
indicator
targets
improvement.
Moreover,
interspecies
comparison
reveals
conserved
core
markers
plants,
are
validated.
These
results
provide
a
universal
atlas
unraveling
programs
specify
maintain
identity
at
level.
authors
reveal
relationship
between
tolerance.
Journal of Cotton Research,
Год журнала:
2024,
Номер
7(1)
Опубликована: Июнь 4, 2024
Abstract
Single-cell
RNA
sequencing
(scRNA-seq)
is
one
of
the
most
advanced
technologies
for
studying
transcriptome
landscape
at
single-cell
revolution.
It
provides
numerous
advantages
over
traditional
RNA-seq.
Since
it
was
first
used
to
profile
in
plants
2019,
has
been
extensively
employed
perform
different
research
plants.
Recently,
scRNA-seq
also
quickly
adopted
by
cotton
community
solve
lots
scientific
questions
which
have
never
solved.
In
this
comment,
we
highlighted
significant
progress
employing
genetic
and
genomic
study
its
future
potential
applications.
International Journal of Molecular Sciences,
Год журнала:
2025,
Номер
26(1), С. 329 - 329
Опубликована: Янв. 2, 2025
Salt
stress
is
an
environmental
factor
that
limits
plant
seed
germination,
growth,
and
survival.
We
performed
a
comparative
RNA
sequencing
transcriptome
analysis
during
germination
of
the
seeds
from
two
cultivars
with
contrasting
salt
tolerance
responses.
A
transcriptomic
comparison
between
salt-tolerant
cotton
cv
Jin-mian
25
salt-sensitive
Su-mian
3
revealed
both
similar
differential
expression
patterns
genotypes
stress.
The
genes
related
to
aquaporins,
kinases,
reactive
oxygen
species
(ROS)
scavenging,
trehalose
biosynthesis,
phytohormone
biosynthesis
signaling
include
ethylene
(ET),
gibberellin
(GA),
abscisic
acid
(ABA),
jasmonic
(JA),
brassinosteroid
(BR)
were
systematically
investigated
cultivars.
Despite
involvement
these
in
cotton’s
response
positive
or
negative
ways,
their
levels
mostly
genotypes.
Interestingly,
PXC2
gene
(Ghir_D08G025150)
was
identified,
which
encodes
leucine-rich
repeat
receptor-like
protein
kinase
(LRR-RLK).
This
showed
induced
pattern
after
treatment
but
not
3.
Our
multifaceted
approach
illustrated
cotton.
Cold
stress
significantly
challenges
cotton
growth
and
productivity,
yet
the
genetic
molecular
mechanisms
underlying
cold
tolerance
remain
poorly
understood.
We
employed
RNA-seq
iterative
weighted
gene
co-expression
network
analysis
(WGCNA)
to
investigate
transposable
element
(TE)
expression
changes
at
six
time
points
(0
h,
2
4
6
12
24
h).
Thousands
of
differentially
expressed
genes
(DEGs)
were
identified,
exhibiting
time-specific
patterns
that
highlight
a
phase-dependent
transcriptional
response.
While
A
D
subgenomes
contributed
comparably
DEG
numbers,
numerous
homeologous
pairs
showed
differential
expression,
indicating
regulatory
divergence.
Iterative
WGCNA
uncovered
125
modules,
with
some
enriched
in
specific
chromosomes
or
chromosomal
regions,
suggesting
localized
hotspots
for
Notably,
transcription
factors,
including
MYB73,
ERF017,
MYB30,
OBP1,
emerged
as
central
regulators
within
these
modules.
Analysis
11
plant
hormone-related
revealed
dynamic
ethylene
(ETH)
cytokinins
(CK)
playing
significant
roles
stress-responsive
pathways.
Furthermore,
we
documented
over
15,000
TEs,
TEs
forming
five
distinct
clusters.
TE
families,
such
LTR/Copia,
demonstrated
enrichment
clusters,
their
potential
role
modulators
under
stress.
These
findings
provide
valuable
insights
into
complex
networks
response
cotton,
highlighting
key
components
involved
regulation.
This
study
provides
targets
breeding
strategies
aimed
enhancing
cotton.
Crop Design,
Год журнала:
2024,
Номер
3(2), С. 100057 - 100057
Опубликована: Фев. 24, 2024
Over
the
past
decade,
bulk
RNA
sequencing
(RNA-seq)
has
become
an
indispensable
tool
in
molecular
biology,
and
have
made
novel
development,
with
two
innovative
methodologies
being
developed,
single-cell
(scRNA-seq)
technology
spatial
transcriptome
(ST)
technology.
The
scRNA-seq
allows
researchers
to
analyze
gene
expression
individual
cells,
providing
more
detailed
information
relative
technologies.
Meanwhile,
ST
overcomes
limitations
of
terms
loss
information,
enabling
scientists
better
understand
distribution
within
tissues.
These
advancements
transcriptomics
technologies
revolutionize
field
genomics
been
widely
used
disease
diagnosis
medicine.
However,
they
are
less
utilized
plant
research.
This
review
describes
advantage
three
technologies,
presents
their
applications
sciences.
Frontiers in Plant Science,
Год журнала:
2025,
Номер
16
Опубликована: Фев. 25, 2025
Maize
ranks
among
the
most
essential
crops
globally,
yet
its
growth
and
yield
are
significantly
hindered
by
salt
stress,
posing
challenges
to
agricultural
productivity.
To
utilize
saline-alkali
soils
more
effectively
enrich
maize
germplasm
resources,
identifying
salt-tolerant
genes
in
is
essential.
In
this
study,
we
used
a
inbred
line,
SPL02,
salt-sensitive
Mo17.
We
treated
both
lines
with
180
mmol/L
sodium
chloride
(NaCl)
for
0
days,
3
6
9
days
at
three-leaf
stage
(V3).
Through
comprehensive
morphological,
physiological,
transcriptomic
analyses,
assessed
stress
effects
identified
hub
pathways
associated
tolerance.
Our
analysis
25,383
expressed
genes,
substantial
differences
gene
expression
patterns
across
treatment
stages.
found
8,971
differentially
(DEGs)-7,111
unique
SPL02
4,791
Mo17-indicating
dynamic
changes
under
stress.
DEGs
primarily
MAPK
signaling
pathway,
phenylpropanoid
biosynthesis,
hormone
conditions.
Mo17,
responses
mediated
through
abscisic
acid-activated
pathway
response.
Additionally,
our
weighted
co-expression
network
(WGCNA)
pinpointed
five
that
likely
play
central
roles
mediating
These
functions
including
phosphate
import
ATP-binding
protein,
glycosyltransferase,
WRKY
transcription
factors.
This
study
offers
valuable
insights
into
complex
regulatory
networks
governing
response
identifies
further
investigation.
findings
contribute
knowledge
enhancing
resilience
sustainability
saline-affected
environments.
