Upgrading swin-B transformer-based model for accurately identifying ripe strawberries by coupling task-aligned one-stage object detection mechanism
Computers and Electronics in Agriculture,
Год журнала:
2024,
Номер
218, С. 108674 - 108674
Опубликована: Янв. 31, 2024
Язык: Английский
Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo
International Journal of Molecular Sciences,
Год журнала:
2023,
Номер
24(8), С. 7425 - 7425
Опубликована: Апрель 18, 2023
Moso
bamboo
is
capable
of
both
sexual
and
asexual
reproduction
during
natural
growth,
resulting
in
four
distinct
types
culms:
the
shoot-culm,
seedling
stem,
leptomorph
rhizome,
a
long-ignored
culm—the
outward-rhizome.
Sometimes,
when
outward
rhizomes
break
through
soil,
they
continue
to
grow
longitudinally
develop
into
new
individual.
However,
roles
alternative
transcription
start
sites
(aTSS)
or
termination
(aTTS)
as
well
splicing
(AS)
have
not
been
comprehensively
studied
for
their
development.
To
re-annotate
moso
genome
identify
genome-wide
aTSS,
aTTS,
AS
growing
culms,
we
utilized
single-molecule
long-read
sequencing
technology.
In
total,
169,433
non-redundant
isoforms
14,840
gene
loci
were
identified.
Among
1311
lncRNAs,
most
which
showed
positive
correlation
with
target
mRNAs,
one-third
these
IncRNAs
preferentially
expressed
winter
shoots.
addition,
predominant
type
observed
was
intron
retention,
while
aTSS
aTTS
events
occurred
more
frequently
than
AS.
Notably,
genes
also
accompanied
by
events.
Outward
rhizome
growth
associated
significant
increase
possibly
due
changes
environment.
As
different
culms
develop,
number
undergo
conserved
domains
regulation
result,
may
play
original
functions.
These
then
performed
functions
from
roles,
contributing
transcriptomic
complexity
bamboo.
Overall,
this
study
provided
comprehensive
overview
underlying
culm
Язык: Английский
Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis in Bactrocera dorsalis
Frontiers in Physiology,
Год журнала:
2024,
Номер
15
Опубликована: Июнь 17, 2024
Alternative
splicing
is
an
essential
post-transcriptional
regulatory
mechanism
that
diversifies
gene
function
by
generating
multiple
protein
isoforms
from
a
single
and
act
as
crucial
role
in
insect
environmental
adaptation.
Olfaction,
key
sense
for
adaptation,
relies
heavily
on
the
antennae,
which
are
primary
olfactory
organs
expressing
most
of
genes.
Despite
extensive
annotation
genes
within
antennal
tissues
facilitated
high-throughput
sequencing
technology
advancements,
systematic
analyses
alternative
still
relatively
less.
In
this
study,
we
focused
oriental
fruit
fly
(
Bactrocera
dorsalis
),
significant
pest
crops.
We
performed
detailed
analysis
its
antennae
utilizing
full-length
transcriptome
tissue
insect’s
genome.
The
results
revealed
8600
non-redundant
transcripts
identified
transcriptome,
spanning
4,145
loci.
Over
40%
these
loci
exhibited
isoforms.
Among
these,
161
showed
sex-biased
isoform
switching,
involving
seven
different
types
splicing.
Notably,
events
transcription
start
sites
(ATSS)
termination
(ATTS)
were
common.
Of
all
undergoing
ATSS
ATTS
between
male
female,
32
alternatively
spliced
coding
regions,
potentially
affecting
function.
These
categorized
based
length
isoforms,
with
highest
difference
fraction
(dIF)
associated
type,
including
such
BdorABCA13
,
BdorCAT2
BdorTSN3.
Additionally,
factor
binding
doublesex
upstream
both
BdorCAT2.
Besides
being
expressed
tissues,
also
mouthparts,
legs,
genitalia
female
adults,
suggesting
their
functional
diversity.
This
study
reveals
Bactrophora
two
aspects:
odorant
receptor
other
antennae.
not
only
provides
research
foundation
understanding
regulation
but
offers
new
insights
olfaction-based
behavioral
manipulation
techniques
to
manage
pest.
Язык: Английский
Direct RNA sequencing in plants: practical applications and future perspectives
Plant Communications,
Год журнала:
2024,
Номер
5(11), С. 101064 - 101064
Опубликована: Авг. 18, 2024
The
transcriptome
serves
as
a
bridge
that
links
genomic
variation
to
phenotypic
diversity.
A
vast
number
of
studies
using
next-generation
RNA
sequencing
(RNA-seq)
over
the
last
2
decades
have
emphasized
essential
roles
plant
in
response
developmental
and
environmental
conditions,
providing
numerous
insights
into
dynamic
changes,
evolutionary
traces,
elaborate
regulation
transcriptome.
With
substantial
improvement
accuracy
throughput,
direct
(DRS)
has
emerged
new
powerful
platform
for
precise
detection
native
full-length
transcripts,
overcoming
many
limitations
such
read
length
PCR
bias
are
inherent
short-read
RNA-seq.
Here,
we
review
recent
advances
dissecting
complexity
diversity
transcriptomes
DRS
main
technological
approach,
covering
aspects
metabolism,
including
novel
isoforms,
poly(A)
tails,
modification,
propose
comprehensive
workflow
processing
data.
Many
challenges
application
plants,
need
machine
learning
tools
tailored
transcriptomes,
remain
be
overcome,
together
outline
future
biological
questions
can
addressed
by
DRS,
allele-specific
modification.
This
technology
provides
convenient
support
on
which
connection
distinct
features
is
tightly
built,
sustainably
refining
our
understanding
functions
Язык: Английский
Comparative Analysis of Alternative Splicing in Moso Bamboo and Its Dwarf Mutant, Phyllostachys edulis ‘Tubaeformis’
Forests,
Год журнала:
2024,
Номер
15(7), С. 1233 - 1233
Опубликована: Июль 15, 2024
Internode
length
is
a
crucial
phenotypic
trait
of
bamboo,
significantly
impacting
its
processing
and
utilization.
Phyllostachys
edulis
‘Tubaeformis’
(Shengyin
Bamboo),
variety
Moso
exhibits
drastically
shortened
internodes,
making
it
valuable
ornamental
bamboo
species.
We
used
PacBio
single-molecule
long-read
sequencing
second-generation
to
identify
genome-wide
alternative
splicing
(AS)
events
in
dwarf
mutant,
Shengyin
compared
the
differences
between
two.
Our
data
unveiled
139,539
AS
events,
with
retained
introns
as
most
prevalent
events.
A
large
number
genes
were
differentially
alternatively
spliced
(DAS)
related
RNA
enriched.
The
high
expression
SR
isoforms
24th
internode
likely
main
factor
leading
greater
Alternative
affects
functional
domains
partial
GRF,
E2F,
NAM
isoforms,
loss
some
enabling
acquire
new
domains,
this
phenomenon
more
common
bamboo.
modifies
certain
GRF
frequently
resulting
domain
losses
or
endowing
novel
Bamboo
Язык: Английский
Strawberry biotechnology: A review on progress over past 10 years
Scientia Horticulturae,
Год журнала:
2024,
Номер
338, С. 113618 - 113618
Опубликована: Сен. 17, 2024
Язык: Английский
Comprehensive Assessment of Isoform Detection Methods for Third-Generation Sequencing Data
Research Square (Research Square),
Год журнала:
2022,
Номер
unknown
Опубликована: Ноя. 4, 2022
Abstract
The
advancement
of
Third-Generation
Sequencing
(TGS)
techniques
managed
to
increase
the
sequencing
length
several
kilobases,
which
leads
a
bright
future
for
completely
reserving
alternative
splicing
(AS)
events
and
isoform
expressions.
In
recent
years,
many
computational
methods
detection
from
long-read
data
have
been
developed
published.
However,
there
is
no
prior
comparative
study
that
systemically
evaluates
performance
software
implemented
with
different
algorithms.
Here
we
benchmarked
nine
in
seven
tools
can
identify
structures
TGS
RNA
analyzed
their
performances
various
aspects
using
both
simulated
datasets
produced
by
an
in-house
simulator
previously
published
experimental
data.
Our
results
comprehensively
demonstrate
relative
effectiveness
approaches
provide
guidance
as
well
recommendations
research
on
AS
analysis
further
improvement
Язык: Английский