Comparative analysis of chloroplast genomes on Meliaceae species: insights into the evolution and species identification
Frontiers in Plant Science,
Год журнала:
2025,
Номер
16
Опубликована: Март 11, 2025
Introduction
Meliaceae,
a
significant
group
in
Sapindales,
possesses
material
and
medicinal
value
due
to
its
applications
timber
bioactive
compounds.
However,
the
high
morphological
diversity
of
Meliaceae
species
lack
comparative
studies
chloroplast
(cp)
genomes
have
led
great
challenges
classification
identification
species.
Methods
In
this
study,
we
sequenced
complete
cp
three
Toona
(
fargesii
,
ciliata
sinensis
),
conducted
analyses
these
along
with
29
previously
published
Meliaceae.
Additionally,
performed
phylogenetic
estimated
divergence
times
Results
The
32
ranged
from
158,558
bp
160,978
length.
Specifically,
varied
159,242
159,617
These
contained
total
135
unique
genes,
comprising
90
protein-coding,
8
rRNA,
37
tRNA
genes.
Divergence
time
estimation
revealed
that
family
diverged
into
two
subfamilies
(Cedreloideae
Melioideae)
approximately
72.92
Ma
(95%
HPD:
60.62-87.01
Ma)
Late
Cretaceous.
diversification
Cedreloideae
(47.86
Ma,
95%
47.42-48.22
occurred
later
than
Melioideae
(66.60
55.41-79.73
Ma).
Furthermore,
genomic
analysis
identified
52
116
simple
sequence
repeats
(SSRs)
twelve
highly
variable
regions
(HVRs)
found
among
Discussion
indicates
most
relatively
recent
origin,
rapid
occurring
during
Oligocene
or
Early
Miocene
epochs.
Comparative
exhibits
relative
conservation
terms
genome
size,
inverted-repeat
(IR)
boundary,
structure,
HVRs
codon
patterns.
Although
differences
exist
between
subfamilies,
overall
similarity
remains
notably
high.
ycf
1,
trn
K-
rps
16,
ndh
F-
rpl
exhibited
highest
nucleotide
polymorphism
within
while
22
gene
displayed
genetic
both
subfamilies.
As
candidate
molecular
markers,
may
effectively
distinguish
findings
not
only
provide
insights
evolution
but
also
establish
scientific
foundation
for
future
systematics
Язык: Английский
Chloroplast Functionality at the Interface of Growth, Defense, and Genetic Innovation: A Multi-Omics and Technological Perspective
Plants,
Год журнала:
2025,
Номер
14(6), С. 978 - 978
Опубликована: Март 20, 2025
Chloroplasts
are
important
in
plant
growth,
development,
and
defense
mechanisms,
making
them
central
to
addressing
global
agricultural
challenges.
This
review
explores
the
multi-faceted
contributions
of
chloroplasts,
including
photosynthesis,
hormone
biosynthesis,
stress
signaling,
which
orchestrate
trade-off
between
growth
defense.
Advancements
chloroplast
genomics,
transcription,
translation,
proteomics
have
deepened
our
understanding
their
regulatory
functions
interactions
with
nuclear-encoded
proteins.
Case
studies
demonstrated
potential
chloroplast-targeted
strategies,
such
as
expression
elongation
factor
EF-2
for
heat
tolerance
flavodiiron
proteins
drought
resilience,
enhance
crop
productivity
adaptation.
Future
research
directions
should
focus
on
need
integrating
omics
data
nanotechnology
synthetic
biology
develop
sustainable
resilient
systems.
uniquely
integrates
recent
advancements
transcriptional
regulation,
present
a
holistic
perspective
optimizing
tolerance.
We
emphasize
role
chloroplast-driven
balancing
immunity,
leveraging
technologies
emerging
biotechnological
innovations.
comprehensive
approach
offers
new
insights
into
practices,
it
significant
contribution
field.
Язык: Английский
Chloroplast Genome of Myristica fragrans : Assembly, Annotation, and Phylogenetic Relationships
Forest Science and Technology,
Год журнала:
2025,
Номер
unknown, С. 1 - 8
Опубликована: Март 21, 2025
Myristica
fragrans
is
a
native
and
economically
significant
species
in
Indonesia.
However,
its
complete
chloroplast
genome,
particularly
from
Indonesia,
has
not
been
previously
reported.
In
this
study,
we
successfully
sequenced
assembled
the
genome
of
M.
using
next-generation
sequencing
technology.
The
total
length
155,868
bp
exhibits
typical
quadripartite
structure,
consisting
large
single-copy
(LSC)
region
(87,062
bp),
small
(SSC)
(20,664
pair
inverted
repeats
(IRs)
(24,071
each).
Genome
annotation
identified
126
genes,
including
83
protein-coding
8
ribosomal
RNA
35
transfer
genes.
A
141
simple
sequence
(SSRs)
were
detected,
with
mononucleotide
being
most
prevalent
(90.07%).
Phylogenetic
analysis
six
genomes
three
outgroup
confirmed
that
closely
related
to
argentea,
providing
new
insights
into
evolutionary
relationships
within
Myristicaceae
family.
Язык: Английский
Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae
BMC Genomics,
Год журнала:
2024,
Номер
25(1)
Опубликована: Окт. 23, 2024
The
use
of
complete
organelle
genomes,
including
chloroplast
and
mitochondrial
is
a
powerful
molecular
method
for
studying
biological
evolution
gene
transfer.
However,
in
the
case
Polygonaceae,
an
important
family
with
numerous
edible,
medicinal,
ornamental
species,
genomes
only
three
species
have
been
sequenced
analyzed.
In
this
study,
we
present
two
Tibetan
medicinal
plants,
Bistorta
viviparum
B.
macrophyllum.
All
are
assembled
into
single
circular
structure
contain
common
set
32
protein-coding
genes
(PCGs).
Some
such
as
rps2
ndhF
were
found
to
high
nucleotide
polymorphism
(Pi)
while
cox1,
mttB
rps12
showed
pronounced
Pi
values
genomes.
Furthermore,
our
analysis
revealed
that
most
PCGs
Polygonaceae
plants
under
purifying
selection.
few
genes,
psaJ
ccmFc,
atp8
nad4,
positive
selection
certain
indicated
by
Ka/Ks
ratio
greater
than
one.
Structural
variation
wealth
differences
between
five
particularly
notable
large-scale
inversion
observed
Reynoutria
japonica
Fallopia
aubertii.
homologous
sequences
rps7
has
transferred
from
genome
all
species.
Finally,
ecological
niche
models
constructed
macrophyllum,
indicating
mean
annual
temperature
altitude
main
climatic
factors
influencing
distribution
both
Although
current
significantly
wider
projections
suggest
optimal
growth
ranges
will
expand
future,
macrophyllum
potentially
exceeding
viviparum.
This
study
not
contributes
plastid
database
but
also
provides
theoretical
insights
adaptive
these
plants.
Язык: Английский
Comparative chloroplast genome analysis reveals powerful barcodes for combatting illegal logging of CITES-listed threatened Asian rosewoods (Dalbergia, Leguminosae, Papilionoideae)
Botanical Journal of the Linnean Society,
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 26, 2024
Abstract
Rosewoods
(Dalbergia)
are
among
the
most
heavily
trafficked
natural
resources
in
illegal
global
multibillion-dollar
wildlife
trade.
Consequently,
many
rosewood
species
experience
high
extinction
threats.
To
enforce
conservation
of
threatened
by
logging,
reliable
identification
is
required
to
distinguish
between
legally
and
illegally
traded
timber.
DNA
barcoding
considered
promising
approach
achieve
rapid
identification,
compared
morphological
biochemical
compound
analyses.
This
study
was
designed
establish
a
for
rosewoods
utilizing
whole-chloroplast
genome
sequences,
either
as
super-barcodes
or
sources
identify
short
but
highly
informative
regions.
these
objectives,
81
plastomes
that
cover
28
were
generated
de
novo.
The
phylogenomic
dataset
further
expanded
include
total
110
accessions
representing
31
Dalbergia.
chloroplast
structure
composition
found
be
conserved
across
all
studied.
phylogenetic
hypothesis
obtained
using
coding
sequences
data
fully
resolved
robust,
even
closely
related
species.
Five
loci
identified
powerful
barcodes
corresponded
sequence
variation
hotspots.
In
summary,
whole
genomes
super-barcodes,
while
up
five
plastome
small
barcode
regions
can
amplified
degraded
DNA.
successfully
establishes
necessary
carry
out
rosewoods,
serving
main
tool
provide
timber
market.
Язык: Английский