Agronomy,
Год журнала:
2023,
Номер
14(1), С. 8 - 8
Опубликована: Дек. 19, 2023
Causal
discovery
is
a
highly
promising
tool
with
broad
perspective
in
the
field
of
biology.
In
this
study,
causal
structure
robustness
assessment
algorithm
proposed
and
employed
on
structures
obtained,
based
transcriptomic,
proteomic,
combined
datasets,
emerging
from
quantitative
proteogenomic
atlas
15
sweet
cherry
(Prunus
avium
L.)
cv.
‘Tragana
Edessis’
tissues.
The
assesses
impact
intervening
datasets
structures,
using
various
criteria.
results
showed
that
specific
tissues
exhibited
an
intense
were
considered.
addition,
case
demonstrated
biologically
related
referred
to
same
organ
induced
similar
considered,
as
was
expected.
However,
result
subtler
both
transcriptomic
proteomic
cases.
Furthermore,
single
omic
analysis
found
be
impacted
larger
extent,
compared
case,
probably
due
distinctive
biological
features
proteome
or
transcriptome.
This
study
showcases
significance
assessing
databases,
conjunction
discovery,
reveals
advantages
when
employing
multiomics
(proteogenomic)
single-omic
(transcriptomic,
proteomic)
analysis.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Янв. 2, 2025
Global
food
security
depends
heavily
on
a
few
staple
crops,
while
orphan
despite
being
less
studied,
offer
the
potential
benefits
of
environmental
adaptation
and
enhanced
nutritional
traits,
especially
in
changing
climate.
Major
crops
have
benefited
from
genomics-based
breeding,
initially
using
single
genomes
later
pangenomes.
Recent
advances
DNA
sequencing
enabled
pangenome
construction
for
several
offering
more
comprehensive
understanding
genetic
diversity.
Orphan
crop
research
has
now
entered
pangenomics
era
applying
these
pangenomes
with
advanced
selection
methods
genome
editing
technologies
can
transform
neglected
species
into
broader
agricultural
significance.
A
reference
is
not
enough
to
harness
full
variation
species.
Here,
authors
review
principles,
applications
improvement,
discuss
possible
ways
support
pangenomics-driven
molecular
breeding.
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.
Horticultural Plant Journal,
Год журнала:
2024,
Номер
10(6), С. 1274 - 1290
Опубликована: Авг. 14, 2024
The
pear
(Pyrus
spp.)
is
well
known
for
diverse
flavors,
textures,
and
global
horticultural
importance.
However,
the
genetic
diversity
responsible
its
extensive
phenotypic
variations
remains
largely
unexplored.
Here,
we
de
novo
assembled
annotated
genomes
of
maternal
(PsbM)
paternal
(PsbF)
lines
hybrid
'Yuluxiang'
constructed
pangenome
1.15
Gb
by
combining
these
two
with
five
previously
published
representing
cultivated
wild
germplasm.
Using
pangenome,
identified
21
224
gene
PAVs
(Presence-absence
variation)
1
158
812
SNPs
(Single
Nucleotide
Polymorphism)
in
non-reference
genome
that
were
absent
PsbM
reference
genome.
Compared
SNP
markers,
PAV-based
analysis
provides
additional
insights
into
population
structure.
In
addition,
some
genes
associated
fruit
quality
traits
have
differential
occurrence
frequencies
expression
between
Asian
European
populations.
Moreover,
our
revealed
a
mutated
an
insertion
promoter
region
PsbMGH3.1
potentially
enhance
sepal
shedding
'Xuehuali'
which
vital
quality.
may
play
role
IAA
pathway,
contributing
to
distinct
low-auxin
phenotype
observed
plants
heterologously
overexpressing
this
gene.
This
research
helps
capture
populations
genomic
resources
accelerating
breeding.
Journal of Integrative Plant Biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 15, 2025
In
plants,
proteins
are
fundamental
to
virtually
all
biological
processes,
such
as
photosynthesis,
signal
transduction,
metabolic
regulation,
and
stress
responses.
Studying
protein
distribution,
function,
modifications,
interactions
at
the
cellular
tissue
levels
is
critical
for
unraveling
complexities
of
these
pathways.
Protein
abundance
localization
highly
dynamic
vary
widely
across
proteome,
presenting
a
challenge
global
quantification
analysis.
Mass
spectrometry-based
proteomics
approaches
have
proven
be
powerful
tools
addressing
this
complex
issue.
review,
we
summarize
recent
advancements
in
research
their
applications
plant
biology,
with
an
emphasis
on
current
state
challenges
studying
post-translational
single-cell
proteomics,
protein-protein
interactions.
Additionally,
discuss
future
prospects
highlighting
potential
opportunities
that
technologies
offer
advancing
biology
research.
Pear
(Pyrus
ssp.)
belongs
to
Rosaceae
and
is
an
important
fruit
tree
widely
cultivated
around
the
world.
Currently,
challenges
cope
with
burgeoning
sets
of
multiomics
data
are
rapidly
increasing.
Here,
we
constructed
Multiomics
Database
(PearMODB)
by
integrating
genome,
transcriptome,
epigenome
population
variation
data,
aimed
provide
a
portal
for
accessing
analyzing
pear
data.
A
variety
online
tools
were
built
including
gene
search,
BLAST,
JBrowse,
expression
heatmap,
synteny
analysis
primer
design.
The
information
DNA
methylation
sites
single-nucleotide
polymorphisms
can
be
retrieved
through
custom
providing
opportunity
explore
genetic
linked
phenotype
variation.
Moreover,
different
families
involving
transcription
factors,
regulators
disease
resistance
(nucleotide-binding
site
leucine-rich
repeat)
identified
compiled
quick
search.
In
particular,
biosynthetic
clusters
(BGCs)
in
genomes,
specialized
webpages
set
up
show
detailed
BGCs,
laying
foundation
studying
metabolic
diversity
among
varieties.
Overall,
PearMODB
provides
platform
genomics,
genetics
breeding
studies.
URL
http://pearomics.njau.edu.cn.
Agronomy,
Год журнала:
2024,
Номер
15(1), С. 58 - 58
Опубликована: Дек. 28, 2024
Fruit
quality
is
one
of
the
most
important
economic
traits
fruit
crops,
directly
influencing
market
prices
and
orchard
revenues.
Enhancing
has
therefore
become
a
critical
objective
in
both
production
scientific
research.
External
fruits
typically
include
size,
coloration,
shape,
uniformity,
consistency.
Internal
refer
to
nutritional
value
fruits,
which
largely
determine
their
flavor
palatability.
Over
past
decade,
significant
progress
been
made
understanding
formation
regulatory
mechanisms
quality,
with
numerous
key
functional
genes
associated
being
identified.
While
substantial
advancements
have
achieved
studying
specific
aspects
there
remains
lack
comprehensive
systematic
reviews
addressing
overall
physiology
interplay
among
various
traits,
diversity
mechanisms.
Using
Chinese
pears
as
an
example,
this
review
summarizes
research
regulation
over
five
years.
Key
metabolic
such
sweetness,
color,
texture,
physiological
disorders;
factors
stone
cell
formation;
sugar
content
regulation;
roles
plant
hormones
including
ethylene,
gibberellins,
abscisic
acid;
translational
post-translational
modifications
ubiquitination,
methylation,
acetylation;
well
application
genomic
sequencing
technologies.
Furthermore,
offers
practical
suggestions
for
improving
pear
provides
insights
researchers
related
fields.
Finally,
future
trends
are
discussed,
offering
forward-looking
perspective
advancing
field.
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.
