Development,
Journal Year:
2022,
Volume and Issue:
149(6)
Published: March 14, 2022
ABSTRACT
Understanding
the
development
of
tissues,
organs
and
entire
organisms
through
lens
single-cell
genomics
has
revolutionized
developmental
biology.
Although
transcriptomics
been
pioneered
in
animal
systems,
from
an
experimental
perspective,
plant
holds
some
distinct
advantages:
cells
do
not
migrate
relation
to
one
another,
new
organ
formation
(of
leaves,
roots,
flowers,
etc.)
continues
post-embryonically
persistent
stem
cell
populations
known
as
meristems.
For
a
time,
studies
lagged
behind
or
culture-based,
approaches,
largely
owing
difficulty
dissociating
their
rigid
walls.
Recent
intensive
single-nucleus
isolation
techniques
across
species
opened
up
wide
range
approaches.
This
produced
rapidly
expanding
diversity
information
tissue
types
species,
concomitant
with
creative
methods.
In
this
brief
Spotlight,
we
highlight
technical
developments
how
they
have
led
profiling
various
organs.
We
also
emphasize
contribution
revealing
trajectories
among
different
within
Furthermore,
present
efforts
toward
comparative
analysis
tissues
at
level.
Single-cell
is
beginning
generate
comprehensive
relating
emerge
populations.
The Plant Cell,
Journal Year:
2024,
Volume and Issue:
36(4), P. 812 - 828
Published: Jan. 17, 2024
Abstract
Single-cell
and
single-nucleus
RNA-sequencing
technologies
capture
the
expression
of
plant
genes
at
an
unprecedented
resolution.
Therefore,
these
are
gaining
traction
in
molecular
developmental
biology
for
elucidating
transcriptional
changes
across
cell
types
a
specific
tissue
or
organ,
upon
treatments,
response
to
biotic
abiotic
stresses,
between
genotypes.
Despite
rapidly
accelerating
use
technologies,
collective
standardized
experimental
analytical
procedures
support
acquisition
high-quality
data
sets
still
missing.
In
this
commentary,
we
discuss
common
challenges
associated
with
single-cell
transcriptomics
plants
propose
general
guidelines
improve
reproducibility,
quality,
comparability,
interpretation
make
readily
available
community
fast-developing
field
research.
Plant Biotechnology Journal,
Journal Year:
2021,
Volume and Issue:
19(11), P. 2261 - 2276
Published: June 26, 2021
Summary
Single‐cell
RNA‐seq
(scRNA‐seq)
has
been
highlighted
as
a
powerful
tool
for
the
description
of
human
cell
transcriptome,
but
technology
not
broadly
applied
in
plant
cells.
Herein,
we
describe
successful
development
robust
protoplast
isolation
system
peanut
leaf.
A
total
6,815
single
cells
were
divided
into
eight
clusters
based
on
reported
marker
genes
by
applying
scRNA‐seq.
Further,
pseudo‐time
analysis
was
used
to
developmental
trajectory
and
interaction
network
transcription
factors
(TFs)
distinct
types
during
leaf
growth.
The
enabled
re‐investigation
primordium‐driven
processes
mesophyll
epidermis.
These
results
suggest
that
palisade
likely
differentiate
spongy
cells,
while
epidermal
originated
earlier
than
primordium.
Subsequently,
developed
method
integrated
multiple
technologies
efficiently
validate
scRNA‐seq
result
homogenous
population.
expression
levels
several
TFs
strongly
correlated
with
ontogeny
accordance
obtained
values.
Additionally,
AHL23
(
AT‐HOOK
MOTIF
NUCLEAR
LOCALIZED
PROTEIN
23
),
which
is
localized
nucleus,
promoted
growth
when
ectopically
expressed
Arabidopsis
modulating
phytohormone
pathway.
Together,
our
study
displays
application
can
provide
new
hypotheses
regarding
differentiation
blade
Arachis
hypogaea
.
We
believe
this
approach
will
enable
significant
advances
functional
allotetraploid
other
species.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: March 24, 2023
SUMMARY
Extensive
studies
of
the
reference
plant
Arabidopsis
have
enabled
a
deep
understanding
tissues
throughout
development,
yet
census
cell
types
and
states
development
is
lacking.
Here,
we
present
single-nucleus
transcriptome
atlas
seed-to-seed
employing
over
800,000
nuclei,
encompassing
diverse
set
across
ten
developmental
stages,
with
spatial
transcriptomic
validation
dynamic
seed
silique.
Cross-organ
analyses
revealed
transcriptional
conservation
heterogeneity
within
individual
influenced
by
organ-of-origin
timing,
including
groups
transcription
factors,
suggesting
gatekeeping
factor
activation.
This
provides
resource
for
study
type
specification
continuum
stimulus-response
genetic
perturbations
at
single-cell
resolution.
Annual Review of Plant Biology,
Journal Year:
2023,
Volume and Issue:
74(1), P. 87 - 109
Published: March 1, 2023
The
establishment,
maintenance,
and
removal
of
epigenetic
modifications
provide
an
additional
layer
regulation,
beyond
genetically
encoded
factors,
by
which
plants
can
control
developmental
processes
adapt
to
the
environment.
Epigenetic
inheritance,
while
historically
referring
information
not
in
DNA
sequence
that
is
inherited
between
generations,
also
refer
are
maintained
within
individual
but
reset
generations.
Both
types
inheritance
occur
plants,
functions
mechanisms
distinguishing
two
great
interest
field.
Here,
we
discuss
examples
dynamics
maintenance
during
selected
stages
growth
development
their
functional
consequences.
states
dynamic
response
stress,
with
consequences
for
transposable
element
regulation.
How
resetting
generations
occurs
normal
stress
emerging
area
research.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Jan. 2, 2024
The
persistent
cereal
endosperm
constitutes
the
majority
of
grain
volume.
Dissecting
gene
regulatory
network
underlying
development
will
facilitate
yield
and
quality
improvement
crops.
Here,
we
use
single-cell
transcriptomics
to
analyze
developing
maize
(Zea
mays)
during
cell
differentiation.
After
obtaining
transcriptomic
data
from
17,022
single
cells,
identify
12
clusters
corresponding
five
types
revealing
complex
transcriptional
heterogeneity.
We
delineate
temporal
gene-expression
pattern
6
7
days
after
pollination.
profile
genomic
DNA-binding
sites
161
transcription
factors
differentially
expressed
between
constructed
a
by
combining
with
direct
profiles,
identifying
181
regulons
containing
genes
encoding
along
their
high-confidence
targets,
Furthermore,
map
clusters,
cell-cluster-specific
essential
regulators,
experimentally
validated
three
predicted
key
regulators.
This
study
provides
framework
for
understanding
function
at
resolution.
Crop Design,
Journal Year:
2023,
Volume and Issue:
2(2), P. 100041 - 100041
Published: Aug. 1, 2023
High-throughput
sequencing
technologies
at
single-cell
resolution
have
great
potential
to
reveal
a
new
landscape
of
plant
cells.
Single-cell/nucleus
RNA
(scRNA/snRNA),
single-cell/nucleus
assay
for
transposase
accessible
chromatin
(scATAC/snATAC)
and
spatial
transcriptome
been
applied
in
multiple
tissues.
Consequently,
significant
increase
publications
on
transcriptomics
was
seen
the
recent
two
years.
In
this
review,
we
will
summarize
advantages
weaknesses
these
approaches,
offer
glimpse
their
developments
cell
biology,
bioinformatic
tools
databases
latest
Crop Design,
Journal Year:
2024,
Volume and Issue:
3(2), P. 100057 - 100057
Published: Feb. 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.
Nature Plants,
Journal Year:
2024,
Volume and Issue:
10(6), P. 1018 - 1026
Published: May 28, 2024
Abstract
The
endosperm
is
a
reproductive
tissue
supporting
embryo
development.
In
most
flowering
plants,
the
initial
divisions
of
nuclei
are
not
succeeded
by
cellularization;
this
process
occurs
only
after
specific
number
mitotic
cycles
have
taken
place.
timing
cellularization
significantly
influences
seed
viability
and
size.
Previous
research
implicated
auxin
as
key
factor
in
initiating
nuclear
determining
cellularization.
Here
we
uncover
involvement
family
clustered
response
factors
(cARFs)
dosage-sensitive
regulators
cARFs
,
maternally
expressed
paternally
silenced,
shown
to
induce
cellularization,
thereby
restricting
growth.
Our
findings
align
with
predictions
parental
conflict
theory,
suggesting
that
represent
major
molecular
targets
conflict.
We
further
demonstrate
recurring
amplification
Brassicaceae,
an
evolutionary
reinforcing
maternal
control
over
study
highlights
antagonistic
on
converges
biosynthesis
signalling.