bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 22, 2023
ABSTRACT
We
developed
the
Maize
PeptideAtlas
resource
(
www.peptideatlas.org/builds/maize
)
to
help
solve
questions
about
maize
proteome.
Publicly
available
raw
tandem
mass
spectrometry
(MS/MS)
data
for
were
collected
from
ProteomeXchange
and
reanalyzed
through
a
uniform
processing
metadata
annotation
pipeline.
These
are
wide
range
of
genetic
backgrounds,
including
inbred
lines
B73
W22,
many
hybrids
their
respective
parents.
Samples
field
trials,
controlled
environmental
conditions,
(a)biotic
conditions
different
tissues,
cell
types
subcellular
fractions.
The
protein
search
space
included
genome
annotations
line
MaizeGDB,
UniProtKB,
NCBI
RefSeq
W22
line.
445
million
MS/MS
spectra
searched,
which
120
matched
0.37
distinct
peptides.
Peptides
66.2%
proteins
(one
isoform
per
coding
gene)
in
most
recent
nuclear
(v5).
Furthermore,
conserved
plastid-
mitochondrial-encoded
(NCBI
annotations)
identified.
identified
other
searched
will
aid
improve
annotation.
also
illustrate
high
confidence
detection
unique
proteins.
N-terminal
acetylation,
phosphorylation,
ubiquitination,
three
lysine
acylations
(K-acetyl,
K-malonyl,
K-hydroxyisobutyryl)
can
be
inspected
PTM
viewer
PeptideAtlas.
All
MS/MS-derived
peptide
linked
spectral,
technical
biological
metadata.
This
new
is
integrated
with
community
resources
MaizeGDB
at
https://www.maizegdb.org/
track
JBrowse.
Advanced Biotechnology,
Год журнала:
2024,
Номер
2(1)
Опубликована: Фев. 8, 2024
Alternative
splicing
(AS)
significantly
enriches
the
diversity
of
transcriptomes
and
proteomes,
playing
a
pivotal
role
in
physiology
development
eukaryotic
organisms.
With
continuous
advancement
high-throughput
sequencing
technologies,
an
increasing
number
novel
transcript
isoforms,
along
with
factors
related
to
their
associated
functions,
are
being
unveiled.
In
this
review,
we
succinctly
summarize
compare
different
mechanisms
across
prokaryotes
eukaryotes.
Furthermore,
provide
extensive
overview
recent
progress
various
studies
on
AS
covering
developmental
stages
diverse
plant
species
response
abiotic
stresses.
Additionally,
discuss
modern
techniques
for
studying
functions
quantification
transcripts,
as
well
protein
products.
By
integrating
genetic
studies,
quantitative
methods,
omics
techniques,
can
discover
isoforms
functional
factors,
thereby
enhancing
our
understanding
roles
modes
species.
Advanced Biotechnology,
Год журнала:
2023,
Номер
1(4)
Опубликована: Окт. 26, 2023
Water-saving
irrigation
techniques
play
a
crucial
role
in
addressing
water
scarcity
challenges
and
promoting
sustainable
agriculture.
However,
the
selection
of
appropriate
water-saving
methods
remains
challenge
agricultural
production.
Additionally,
molecular
regulatory
mechanisms
crops
under
are
not
yet
clear.
This
review
summarizes
latest
research
developments
application
different
technologies
to
five
important
(rice,
wheat,
soybeans,
maize,
cotton).
It
provides
an
overview
impact
on
crop
yield,
use
efficiency
(WUE),
physiology,
growth,
environmental
effects.
compares
contrasts
with
those
traditional
drought
stress,
emphasizing
significance
combining
genetic
engineering
for
developing
drought-resistant
varieties
improving
WUE.
Furthermore,
integration
various
can
stimulate
new
management
strategies,
optimize
resource
utilization,
enhance
sustainability,
representing
major
focus
future
research.
In
conclusion,
this
underscores
importance
technologies,
especially
when
combined
engineering,
scarcity,
increasing
yields,
Abstract
Main
conclusion
In
this
review,
we
give
an
overview
of
plant
sequencing
efforts
and
how
impacts
functional
genomics
research.
Plant
genome
sequence
information
greatly
facilitates
the
studies
biology,
genomics,
evolution
genomes
genes,
domestication
processes,
phylogenetic
relationships,
among
many
others.
More
than
two
decades
have
boosted
number
available
sequenced
genomes.
The
first
genome,
Arabidopsis,
was
published
in
year
2000
currently,
4604
from
1482
species
been
published.
Various
large
initiatives
are
running,
which
planning
to
produce
tens
thousands
near
future.
on
status
use
different
research
areas.
Advanced Agrochem,
Год журнала:
2023,
Номер
3(1), С. 26 - 38
Опубликована: Ноя. 18, 2023
Jasmonic
acid
is
a
crucial
phytohormone
that
plays
pivotal
role,
serving
as
regulator
to
balancing
plant
development
and
resistance.
However,
there
are
analogous
distinctive
characteristics
exhibited
in
JA
biosynthesis,
perception,
signal
transduction
pathways
both
herbaceous
woody
plants.
Moreover,
the
majority
of
research
subjects
have
predominantly
focused
on
function
model
or
Consequently,
significant
paucity
studies
investigating
regulation
networks
plants,
particularly
concerning
post-transcriptional
regulatory
events
such
alternative
splicing
(AS).
This
review
article
aims
conduct
comprehensive
summary
advancements
signals
regulate
across
various
species,
comparing
features
differences
counterparts.
In
addition,
we
summarized
involvement
AS
including
factor
(SF)
transcripts
network,
highlighting
effectiveness
high-throughput
proteogenomic
methods.
A
better
understanding
signaling
pathway
plants
has
implications
for
forestry
production,
optimizing
management
enhancing
secondary
metabolite
production.
Journal of Experimental Botany,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 8, 2025
Abstract
The
complex
gene
regulatory
landscape
underlying
early
flower
development
in
Arabidopsis
has
been
extensively
studied
through
transcriptome
profiling,
and
networks
controlling
floral
organ
have
derived
from
the
analyses
of
genome
wide
binding
key
transcription
factors.
In
contrast,
dynamic
nature
proteome
during
process
is
much
less
understood.
this
study,
we
characterized
at
different
stages
correlated
it
with
unbiased
transcript
expression
data.
Shotgun
proteomics
profiling
were
conducted
using
an
APETALA1-based
induction
system.
A
specific
analysis
pipeline
to
time-course
data
was
developed.
total,
8,924
proteins
23,069
transcripts
identified.
Co-expression
revealed
that
RNA-protein
pairs
clustered
various
pattern
modules.
An
overall
positive
correlation
between
RNA
protein
level
changes
observed,
but
subgroups
RNA/protein
anticorrelated
also
identified
found
be
enriched
hormone
responsive
pathways.
addition,
RNA-seq
dataset
reported
here
further
expanded
identification
genes
whose
development,
its
combination
previously
published
AP1
ChIP-seq
datasets
allowed
additional
direct
high-confidence
targets.
Proteomes,
Год журнала:
2025,
Номер
13(1), С. 4 - 4
Опубликована: Янв. 15, 2025
Nelumbo
nucifera
is
an
aquatic
plant
with
a
high
ornamental
value
due
to
its
flower.
Despite
the
release
of
several
versions
lotus
genome,
annotation
remains
inefficient,
which
makes
it
difficult
obtain
more
comprehensive
knowledge
when
–omic
studies
are
applied
understand
different
biological
processes.
Focusing
on
petaloid
flower,
we
conducted
comparative
proteomic
analysis
among
five
major
floral
organs.
The
proteogenomic
strategy
was
analyze
mass
spectrometry
data
in
order
dig
out
novel
proteoforms
that
involved
petaloids
results
revealed
total
4863
proteins
corresponding
genes
were
identified,
227
containing
single
amino
acid
variants
(SAAVs),
and
72
originating
from
alternative
splicing
(AS)
genes.
In
addition,
range
post-translational
modifications
(PTMs)
events
also
identified
lotus.
Through
functional
homology
24
closely
related
species,
candidate
associated
organ
development,
not
by
ordinary
analysis.
This
study
only
provides
new
insights
into
understanding
mechanism
but
helpful
identifying
improve
genome.
Journal of Proteome Research,
Год журнала:
2024,
Номер
23(9), С. 3984 - 4004
Опубликована: Авг. 5, 2024
This
study
presents
the
Maize
PeptideAtlas
resource
(www.peptideatlas.org/builds/maize)
to
help
solve
questions
about
maize
proteome.
Publicly
available
raw
tandem
mass
spectrometry
(MS/MS)
data
for
collected
from
ProteomeXchange
were
reanalyzed
through
a
uniform
processing
and
metadata
annotation
pipeline.
These
are
wide
range
of
genetic
backgrounds
many
sample
types
experimental
conditions.
The
protein
search
space
included
different
genome
annotations
B73
inbred
line
MaizeGDB,
UniProtKB,
NCBI
RefSeq,
W22
line.
445
million
MS/MS
spectra
searched,
which
120
matched
0.37
distinct
peptides.
Peptides
66.2%
proteins
in
most
recent
nuclear
annotation.
Furthermore,
conserved
plastid-
mitochondrial-encoded
(NCBI
RefSeq
annotations)
identified.
identified
other
will
improve
We
also
illustrate
high-confidence
detection
unique
proteins.
N-terminal
acetylation,
phosphorylation,
ubiquitination,
three
lysine
acylations
(K-acetyl,
K-malonyl,
K-hydroxyisobutyryl)
can
be
inspected
PTM
viewer
PeptideAtlas.
All
MS/MS-derived
peptide
linked
spectral,
technical,
biological
metadata.
new
is
integrated
MaizeGDB
with
track
JBrowse.
