Genome biology,
Journal Year:
2023,
Volume and Issue:
24(1)
Published: April 4, 2023
Homoeologs
are
defined
as
homologous
genes
resulting
from
allopolyploidy.
Bread
wheat,
Triticum
aestivum,
is
an
allohexaploid
species
with
many
homoeologs.
Homoeolog
expression
bias,
referring
to
the
relative
contribution
of
homoeologs
transcriptome,
critical
for
determining
traits
that
influence
wheat
growth
and
development.
Asymmetric
transcription
has
been
so
far
investigated
in
a
tissue
or
organ-specific
manner,
which
could
be
misleading
due
mixture
cell
types.
Science,
Journal Year:
2020,
Volume and Issue:
370(6518)
Published: Sept. 17, 2020
Roots
primed
for
better
phosphate
uptake
Phosphate
is
a
key
resource
plants,
and
remediating
deficiency
drives
considerable
fertilizer
use.
In
low-phosphate
conditions,
roots
make
more
root
hairs,
which
makes
them
able
to
take
up
what
little
can
be
found.
Wendrich
et
al.
performed
single-cell
transcriptomics
on
the
developing
Arabidopsis
queried
resulting
gene-expression
atlas
responses
related
vascular
development.
The
authors
found
that
signals
regulating
hair
development
began
in
inner
vasculature
of
with
transcription
factors
drove
production
hormone
cytokinin.
Response
cascades
identified
through
transcriptome
database
pointed
genes
epidermal
cells
regulate
Science
,
this
issue
p.
eaay4970
The Plant Cell,
Journal Year:
2021,
Volume and Issue:
33(3), P. 511 - 530
Published: Jan. 1, 2021
The
leaf
vasculature
plays
a
key
role
in
solute
translocation.
Veins
consist
of
at
least
seven
distinct
cell
types,
with
specific
roles
transport,
metabolism,
and
signaling.
Little
is
known
about
vascular
cells,
particular
the
phloem
parenchyma
(PP).
PP
effluxes
sucrose
into
apoplasm
as
basis
for
loading,
yet
has
been
characterized
only
microscopically.
Here,
we
enriched
cells
from
Arabidopsis
leaves
to
generate
single-cell
transcriptome
atlas
vasculature.
We
identified
19
clusters,
encompassing
epidermis,
guard
hydathodes,
mesophyll,
all
used
metabolic
pathway
analysis
define
their
roles.
Clusters
comprising
were
transporters,
including
SWEET11
SWEET12
UmamiT
amino
acid
efflux
carriers.
provide
evidence
that
development
occurs
independently
ALTERED
PHLOEM
DEVELOPMENT,
transcription
factor
required
differentiation.
have
unique
pattern
metabolism
activity
companion
(CCs),
explaining
differential
distribution/metabolism
acids
veins.
kinship
relation
clusters
strikingly
similar
vein
morphology,
except
clear
separation
CC
other
PP.
In
summary,
our
RNA-sequencing
provides
wide
range
information
relationship
types.
Developmental Cell,
Journal Year:
2022,
Volume and Issue:
57(4), P. 543 - 560.e9
Published: Feb. 1, 2022
In
all
multicellular
organisms,
transcriptional
networks
orchestrate
organ
development.
The
Arabidopsis
root,
with
its
simple
structure
and
indeterminate
growth,
is
an
ideal
model
for
investigating
the
spatiotemporal
signatures
underlying
developmental
trajectories.
To
map
gene
expression
dynamics
across
root
cell
types
time,
we
built
a
comprehensive,
organ-scale
atlas
at
single-cell
resolution.
addition
to
estimating
progressions
in
pseudotime,
employed
mathematical
concept
of
optimal
transport
infer
trajectories
identify
their
regulators.
demonstrate
utility
interpret
new
datasets,
profiled
mutants
two
key
regulators
resolution,
shortroot
scarecrow.
We
report
transcriptomic
vivo
evidence
tissue
trans-differentiation
mixed
identity
phenotype
Our
results
support
as
rich
community
resource
unraveling
programs
that
specify
maintain
regulate
Molecular Plant,
Journal Year:
2021,
Volume and Issue:
14(3), P. 372 - 383
Published: Jan. 10, 2021
Similar
to
other
complex
organisms,
plants
consist
of
diverse
and
specialized
cell
types.
The
gain
unique
biological
functions
these
different
types
is
the
consequence
establishment
cell-type-specific
transcriptional
programs.
As
a
necessary
step
in
gaining
deeper
understanding
regulatory
mechanisms
controlling
plant
gene
expression,
we
report
use
single-nucleus
RNA
sequencing
(sNucRNA-seq)
assay
for
transposase
accessible
chromatin
(sNucATAC-seq)
technologies
on
Arabidopsis
roots.
comparison
our
transcriptomes
published
protoplast
validated
nuclei
as
entities
establish
transcriptomes.
Furthermore,
sNucRNA-seq
results
uncovered
additional
subtypes
not
identified
by
single-cell
RNA-seq.
transcriptomic
approach,
sNucATAC-seq
approach
led
distribution
into
distinct
clusters,
suggesting
differential
accessibility
between
groups
cells
according
their
identity.
To
reveal
impact
integrated
data
demonstrated
that
marker
genes
display
patterns
accessibility.
Our
suggest
critical
mechanism
regulate
activity
at
cell-type
level.
Nature Communications,
Journal Year:
2021,
Volume and Issue:
12(1)
Published: April 6, 2021
Abstract
Root
development
relies
on
the
establishment
of
meristematic
tissues
that
give
rise
to
distinct
cell
types
differentiate
across
defined
temporal
and
spatial
gradients.
Dissection
developmental
trajectories
transcriptional
networks
underlie
them
could
aid
understanding
function
root
apical
meristem
in
both
dicots
monocots.
Here,
we
present
a
single-cell
RNA
(scRNA)
sequencing
chromatin
accessibility
survey
rice
radicles.
By
profiling
individual
tip
cells
reconstruct
continuous
epidermal
ground
tissues,
elucidate
regulatory
underlying
fate
determination
these
lineages.
We
further
identify
characteristic
processes,
transcriptome
profiles,
marker
genes
for
reveal
conserved
divergent
pathways
between
Finally,
demonstrate
potential
platform
functional
genetic
studies
by
using
spatiotemporal
modeling
mutant
from
cell-specific
gene
cohort.
