Abstract
Research
on
how
plants
respond
to
hypoxia
has
concentrated
model
organisms
where
tissues
can
only
survive
hypoxic
conditions
for
a
few
hours
days.
In
contrast,
are
used
commercially
as
method
prolong
the
shelf
life
of
Malus
domestica
(apple)
fruit
up
year
storage
without
substantial
changes
in
quality,
not
mention
lack
tissue
death.
This
ability
apples
withstand
protracted
is
an
interesting
adaptation
that
had
limited
molecular
investigation
despite
its
economic
importance.
Here,
we
investigate
long‐term
apple
response
using
time‐course
RNA‐seq
analysis
several
postharvest
conditions.
We
use
phylogenetics,
differential
expression,
and
regulatory
networks
identify
genes
regulate
regulated
by
response.
potential
neofunctionalization
core‐hypoxia
apples,
including
novel
regulation
group
VII
ethylene
factor
(ERF
VII)
plant
cysteine
oxidase
(PCO)
family
members.
Genome Biology and Evolution,
Год журнала:
2022,
Номер
15(1)
Опубликована: Дек. 30, 2022
Abstract
Mycoheterotrophy
is
an
alternative
nutritional
strategy
whereby
plants
obtain
sugars
and
other
nutrients
from
soil
fungi.
associated
loss
of
photosynthesis
have
evolved
repeatedly
in
plants,
particularly
monocots.
Although
reductive
evolution
plastomes
mycoheterotrophs
well
documented,
the
dynamics
nuclear
genome
remains
largely
unknown.
Transcriptome
datasets
were
generated
four
three
families
(Orchidaceae,
Burmanniaceae,
Triuridaceae)
related
green
used
for
phylogenomic
analyses
to
resolve
relationships
among
mycoheterotrophs,
their
relatives,
representatives
across
Phylogenetic
trees
based
on
602
genes
mostly
congruent
with
plastome
phylogenies,
except
Asparagales
+
Liliales
clade
inferred
trees.
Reduction
chlorophyll
synthesis
photosynthetic
gene
expression
relaxation
purifying
selection
retained
progressive,
greater
older
nonphotosynthetic
lineages.
One
hundred
seventy-four
1375
plant
benchmark
universally
conserved
orthologous
undetected
any
mycoheterotroph
transcriptome
or
mycoheterotrophic
orchid
Gastrodia
but
expressed
providing
evidence
massively
convergent
We
designate
this
set
deleted
Missing
Mycoheterotrophs
(MIM).
MIM
encode
not
only
mainly
plastid
membrane
proteins
also
a
diverse
processes,
unknown
function,
mitochondrial,
cellular
processes.
Transcription
photosystem
II
(psb29)
all
lineages
implies
function
mycoheterotrophs.
Nonphotosynthetic
enable
novel
insights
into
as
shifts,
loss,
convergence
genomes.
Plants
have
complex
and
dynamic
immune
systems
that
evolved
to
resist
pathogens.
Humans
worked
enhance
these
defenses
in
crops
through
breeding.
However,
many
harbor
only
a
fraction
of
the
genetic
diversity
present
wild
relatives.
Increased
utilization
diverse
germplasm
search
for
desirable
traits,
such
as
disease
resistance,
is
therefore
valuable
step
towards
breeding
are
adapted
both
current
emerging
threats.
Here,
we
examine
defense
responses
across
four
populations
long-generation
tree
crop
Theobroma
cacao
L.,
well
non-cacao
species,
with
goal
identifying
elements
essential
protection
against
oomycete
pathogen
Phytophthora
palmivora.
PLoS ONE,
Год журнала:
2024,
Номер
19(3), С. e0297015 - e0297015
Опубликована: Март 6, 2024
Gene
expression
is
highly
impacted
by
the
environment
and
can
be
reflective
of
past
events
that
affected
developmental
processes.
It
therefore
expected
gene
serve
as
a
signal
current
or
future
phenotypic
traits.
In
this
paper
we
identify
sets
genes,
which
call
Prognostic
Transcriptomic
Biomarkers
(PTBs),
predict
firmness
in
Malus
domestica
(apple)
fruits.
apples,
all
individuals
cultivar
are
clones,
differences
fruit
quality
due
to
environment.
The
apples
transcriptome
responds
these
environment,
makes
PTBs
an
attractive
predictor
quality.
have
potential
enhance
supply
chain
efficiency,
reduce
crop
loss,
provide
higher
more
consistent
for
consumers.
However,
several
questions
must
addressed.
answer
question
two
common
modeling
approaches,
Random
Forest
ElasticNet,
outperforms
other.
We
if
with
few
genes
efficient
at
predicting
This
important
because
need
perform
qPCR,
qPCR
cost-effective
assay
input
modeled
using
high-throughput
RNA-seq.
To
do
this,
conducted
pilot
study
texture
‘Gala’
variety
across
postharvest
storage
regiments.
Fruit
controllable
post-harvest
treatments
good
candidate
explore
use
PTBs.
find
RandomForest
model
than
ElasticNet
predictive
(r2
=
0.78)
15
genes.
also
show
reasonably
RNA-seq
follow
up
experiment.
Results
promising
PTBs,
yet
work
needed
ensure
robust
various
environmental
conditions
treatments.
G3 Genes Genomes Genetics,
Год журнала:
2023,
Номер
13(8)
Опубликована: Июнь 1, 2023
Apples
grown
in
high
heat,
light,
and
low
humidity
environments
are
at
risk
for
sun
injury
disorders
like
sunburn
associated
crop
losses.
Understanding
the
physiological
molecular
mechanisms
underlying
will
support
improvement
of
mitigation
strategies
breeding
more
resilient
varieties.
Numerous
studies
have
highlighted
key
biochemical
processes
involved
injury,
such
as
phenylpropanoid
reactive
oxygen
species
(ROS)
pathways,
demonstrating
both
enzyme
activities
expression
related
genes
response
to
conditions.
Most
previous
focused
on
at-harvest
activity
a
small
number
heat
stress.
Thus,
it
remains
unclear
how
stress
events
earlier
season
affect
physiology
gene
expression.
Here,
we
applied
mid-season
apples
field
collected
tissue
along
time
course-24,
48,
72
h
following
stimulus-to
investigate
dynamic
changes
using
transcriptomic
lens.
We
found
relatively
differentially
expressed
(DEGs)
enriched
functional
terms
treatments.
Only
few
these
belonged
pathways
previously
described
be
sunburn,
AsA-GSH
pathway,
while
most
DEGs
had
not
yet
been
implicated
or
pome
fruit.
PeerJ,
Год журнала:
2023,
Номер
11, С. e16456 - e16456
Опубликована: Ноя. 27, 2023
kakapo
(kākāpō)
is
a
Python-based
pipeline
that
allows
users
to
extract
and
assemble
one
or
more
specified
genes
gene
families.
It
flexibly
uses
original
RNA-seq
read
GenBank
SRA
accession
inputs
without
performing
global
assembly
of
entire
transcriptomes
metatranscriptomes.
The
identifies
open
reading
frames
in
the
assembled
transcripts
annotates
them.
optionally
filters
raw
reads
for
ribosomal,
plastid,
mitochondrial
reads,
belonging
non-target
organisms
(
e.g.
,
viral,
bacterial,
human).
can
be
employed
targeted
assembly,
arbitrary
loci,
such
as
those
commonly
used
phylogenetic
inference
systematics
candidate
families
phylogenomic
metagenomic
studies.
We
provide
example
applications
discuss
how
its
use
offset
declining
value
GenBank’s
single-gene
databases
help
datasets
variety
analyses.
IGT/LAZY
proteins
play
a
central
role
in
determining
gravitropic
set
point
angle
and
orientation
of
lateral
organs
across
plant
species.
Recent
work
model
systems
has
demonstrated
that
interactions
between
BREVIS
RADIX
(BRX)-domain
containing
proteins,
such
as
PH,
RCC1,
AND
FYVE/RCC1-LIKE
DOMAIN
(PRAF/RLD),
LIKE
(BRXL)
family
members,
are
mechanistically
important
for
setting
angle.
Here,
we
identified
peach
PRAF/RLD
interactors
the
PpeLAZY1
DEEPER
ROOTING
1
(PpeDRO1)
from
yeast-two-hybrid
screen.
We
also
show
BRX
domains
these
interacting
have
high
sequence
similarity
with
rice
Arabidopsis.
Further,
all
expressed
at
relatively
levels
leaf,
meristem,
shoot
tip
tissues.
Together,
this
evidence
supports
importance
conservation
IGT/LAZY-BRX-domain
interactions,
which
underlie
angiosperms.
In
recent
years,
the
availability
of
high-throughput
genome/transcriptome
sequencing
data
and
sophisticated
bioinformatics
tools
facilitated
in
silico
identification
novel
genes
for
several
crops
including
wheat
using
well-characterized
from
other
species.
The
information
thus
generated
may
be
used
further
validation
marker-assisted
selection
(MAS),
gene
editing,
cloning.
this
chapter,
we
summarize
available
developments
field,
three
parts:
(i)
databases,
tools,
methodology
corresponding
proteins;
(ii)
present
status
families
identified
(including
contribution
authors
own
lab);
(iii)
use
current
future
improvement
programs.
This
chapter
is
a
suitable
reference
students/scientists
working
field
plant
genomics
cultivars.
Genes,
Год журнала:
2024,
Номер
15(9), С. 1140 - 1140
Опубликована: Авг. 29, 2024
Catharanthus
roseus
(C.
roseus)
can
produce
over
150
types
of
monoterpenoid
indole
alkaloids
(MIAs),
including
vinblastine
and
vincristine,
which
are
currently
the
primary
sources
these
alkaloids.
Exploring
complex
regulatory
mechanisms
C.
is
significant
for
resolving
MIA
biosynthesis.
The
Lateral
Organ
Boundaries
Domain
(LBD)
a
plant-specific
transcription
factor
family
that
plays
crucial
roles
in
physiological
processes
plant
growth,
stress
tolerance,
specialized
metabolism.
However,
LBD
gene
has
not
been
extensively
characterized
roseus,
whether
its
members
involved
biosynthesis
still
being
determined.
A
total
34
(CrLBD)
genes
were
identified.
RNA-Seq
data
investigated
to
examine
expression
patterns
CrLBD
various
tissues
methyl
jasmonate
(MeJA)
treatments.
results
revealed
Class
Ia
member
CrLBD4
positively
correlated
with
iridoid
biosynthetic
(p
<
0.05,
r
≥
0.8);
IIb
CrLBD11
negatively
≤
−0.8).
Further
validation
leaves
at
different
growth
stages
showed
exhibited
potential
trends
accumulation
vindoline
catharanthine.
Yeast
one-hybrid
(Y1H)
subcellular
localization
assays
demonstrated
could
bind
“aattatTCCGGccgc”
cis-element
localize
nucleus.
These
findings
suggest
may
be
candidates
regulating
roseus.
In
this
study,
we
systematically
analyzed
provided
insights
into
certain
CrLBDs
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 7, 2024
Abstract
Parasitic
plants
in
Orobanchaceae
are
noxious
agricultural
pests
that
severely
impact
crops
worldwide.
These
acquire
water
and
nutrients
from
their
hosts
through
a
specialized
organ
called
the
haustorium.
A
key
step
haustorium
development
involves
cell
wall
modification.
In
this
study,
we
identified
analyzed
evolutionary
relationships
of
pectate
lyase-like
(
PLL
)
genes
across
parasitic
other
non-parasitic
land
plant
lineages.
To
support
detailed
examination
gene
models
paralogous
family
members,
used
published
genomes,
as
well
recently
generated
draft
genome
assembly
annotation
Triphysaria
versicolor
.
One
particular
gene,
denoted
PLL1
Orobanchaceae,
emerged
an
important
candidate
for
parasitism,
highlighted
by
our
previous
comparative
transcriptomics
research;
it
belongs
to
largest
sub-clade
is
highly
upregulated
haustoria.
explore
its
function
development,
manipulated
expression
T.
,
model
species
using
direct
transformation
parasite
host-induced-gene-silencing
(HIGS).
For
HIGS,
transgenic
Medicago
truncatula
Arabidopsis
thaliana
expressing
hairpin
RNAs
targeting
Both
experimental
approaches
effectively
reduced
resulting
increased
frequency
poorly
adhered
parasites.
findings
demonstrate
plays
crucial
role
suggest
promising
target
managing
weeds.
Notably,
success
HIGS
even
before
establishment
functional
highlights
possibility
early
intervention
against
parasitism.