A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Март 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.
Язык: Английский
Auxin as an architect of the pectin matrix
Journal of Experimental Botany,
Год журнала:
2023,
Номер
74(22), С. 6933 - 6949
Опубликована: Май 11, 2023
Abstract
Auxin
is
a
versatile
plant
growth
regulator
that
triggers
multiple
signalling
pathways
at
different
spatial
and
temporal
resolutions.
A
cell
surrounded
by
the
wall,
complex
dynamic
network
of
polysaccharides.
The
wall
needs
to
be
rigid
provide
mechanical
support
protection
highly
flexible
allow
shape
acquisition.
modification
pectin
components,
among
other
processes,
mechanism
which
auxin
activity
alters
properties
wall.
precisely
controls
transcriptional
output
several
genes
encoding
remodelling
enzymes,
their
local
activity,
deposition,
modulation
in
developmental
contexts.
This
review
examines
regulating
chemistry
organ,
cellular,
subcellular
levels
across
diverse
species.
Moreover,
we
ask
questions
remain
addressed
fully
understand
interplay
between
development.
Язык: Английский
Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 17, 2024
Abstract
Single-cell
RNA
sequencing
(scRNA-seq)
technology
is
a
powerful
tool
for
exploring
cell
heterogeneity
and
lineage
dynamics,
revealing
complex
mechanisms
driving
tissue
function
development.
However,
plant
cell’s
rigid
walls
require
protoplasing
step,
an
enzymatic
process
that
can
introduce
biases.
The
impact
of
protoplasting
on
scRNA-seq
data
remains
poorly
understood.
In
this
study,
we
analyzed
gene
expression
patterns
from
bulk
RNA-seq
various
tissues
before
after
protoplasting.
Cell-type
specific
effects
were
discovered
in
different
tissues.
Protoplasting-related
biases
found
to
distort
clustering,
marker
identification,
multi-omics
integration.
By
calculating
protoplasted
scores
based
expression,
identified
mitigated
effects,
enabling
the
accurate
clustering
annotation
tobacco
BY-2
cells
identification
cell-cycle-related
genes.
Our
findings
underscore
importance
assessing
correcting
analysis,
offering
new
insights
more
interpretation
biological
discovery.
Язык: Английский