Scientific Reports,
Journal Year:
2023,
Volume and Issue:
13(1)
Published: Oct. 31, 2023
Abstract
The
genus
Cerastium
includes
about
200
species
that
are
mostly
found
in
the
temperate
climates
of
Northern
Hemisphere.
Here
we
report
complete
chloroplast
genomes
alpinum
,
C
.
arcticum
and
nigrescens
length
cp
ranged
from
147,940
to
148,722
bp.
Their
quadripartite
circular
structure
had
same
gene
organization
content,
containing
79
protein-coding
genes,
30
tRNA
four
rRNA
genes.
Repeat
sequences
varied
16
23
per
species,
with
palindromic
repeats
being
most
frequent.
number
identified
SSRs
20
they
were
mainly
composed
mononucleotide
A/T
units.
Based
on
Ka/Ks
ratio
values,
genes
subjected
purifying
selection.
newly
sequenced
characterized
by
a
high
frequency
RNA
editing,
including
both
U
conversion.
phylogenetic
relationships
within
family
Caryophyllaceae
reconstructed
based
71
topology
tree
was
consistent
systematic
position
studied
species.
All
representatives
gathered
single
clade
C.
glomeratum
sharing
least
similarity
others.
BMC Plant Biology,
Journal Year:
2025,
Volume and Issue:
25(1)
Published: Feb. 13, 2025
Abstract
Chloroplasts
are
essential
organelles
in
plants
and
eukaryotic
algae,
responsible
for
photosynthesis,
fatty
acid
synthesis,
amino
production,
stress
responses.
The
genus
Passiflora
,
known
its
species
diversity
dynamic
chloroplast
(cp)
genome
evolution,
serves
as
an
excellent
model
studying
structural
variations.
This
study
investigates
evolutionary
relationships
within
by
sequencing
11
new
genomes,
assessing
selective
pressures
on
cp
genes,
comparing
plastid
nuclear
phylogenies.
genomes
showed
significant
variations
size,
gene
content,
structure,
ranging
from
132,736
to
163,292
base
pairs,
especially
Decaloba
.
Structural
rearrangements
species-specific
repeat
patterns
were
identified.
Selective
pressure
tests
revealed
adaptive
evolution
certain
lineages,
with
several
including
clpP
petL
under
positive
selection.
Phylogenetic
analyses
confirmed
the
monophyly
of
subgenera
Astrophea
while
Deidamioides
appeared
polyphyletic.
Nuclear
phylogenetic
analysis
based
35S
rDNA
sequences
supported
but
inconsistencies
subgenus
compared
data.
highlights
complexity
demonstrating
evolution.
findings
underscore
effectiveness
phylogenomics
resolving
provide
insights
into
mechanisms
shaping
angiosperms.
Pharmacological Research - Modern Chinese Medicine,
Journal Year:
2024,
Volume and Issue:
10, P. 100354 - 100354
Published: Jan. 4, 2024
Various
medicinal
and
aromatic
plants
possess
bioactive
components
that
exhibit
therapeutic,
cosmetic
pharmaceutical
properties.
Allium
species
comprise
a
subgroup
of
these
which
offers
potential
advantages.
The
natural
volatile
oils
derived
from
have
broad
range
functions
owing
to
their
richness
in
components.
Therefore,
the
interest
presents
study
is
provide
an
updated
quantified
information
regarding
therapeutical
commercial
products,
chemical
composition,
biological
applications,
such
as
antioxidant
antimicrobial
activity
genus
essential
This
work
designed
using
mixed
methodology;
extensive
data
search
was
conducted
for
period
2000
2023
(July).
keywords
"Essential
oil",
"Allium
genus",
"Bioactive
components",
"Antimicrobial
activity",
"Antioxidant
potential",
were
utilised
extract
data.
literature
review
obtained
PubMed
database,
while
SCOPUS
online
database
used
bibliometric
analysis.
A
total
294
entries
found
PubMed,
out
only
42
studies
selected
comprehensive
based
on
experimental
approach,
including
vivo
(1)
vitro
(41)
studies.
Apart
this,
244
articles
subjected
analysis
VOSviewer
Bibliometrix
software.
one
most
representative
genera
Amaryllidaceae
family,
whose
therapeutic
benefits
are
properly
consolidated
wide
variety
ailments.
Traditionally,
been
consumed
China
spices
vegetables.
Although,
modern
Chinese
medicine
system
several
over
years
address
applications
commercially
available
products
containing
Allium.
In
this
sense,
concise
provides
overview
composition
(antioxidant
antimicrobial)
species-derived
oils.
results
published
works
also
illustrate
effective
microbial
can
be
exploited
multi-potent
drug
against
various
ailments
with
advanced
safety
efficacy.
integration
past
knowledge
current
research
underscores
enduring
significance
Furthermore,
it
highlights
patterns
future
trends
domain,
providing
valuable
insights
researchers
explore
domain
further.
International Journal of Molecular Sciences,
Journal Year:
2021,
Volume and Issue:
22(22), P. 12505 - 12505
Published: Nov. 19, 2021
The
polypeptides
encoded
by
the
chloroplast
ndh
genes
and
some
nuclear
form
thylakoid
NADH
dehydrogenase
(Ndh)
complex,
homologous
to
mitochondrial
complex
I.
Except
for
Charophyceae
(algae
related
higher
plants)
a
few
Prasinophyceae,
all
eukaryotic
algae
lack
genes.
Among
vascular
plants,
are
absent
in
epiphytic
species
scattered
among
different
genera,
families,
orders.
recent
identification
of
many
plants
lacking
plastid
allows
comparison
on
phylogenetic
trees
functional
investigations
protect
Angiosperms
under
various
terrestrial
stresses,
maintaining
efficient
photosynthesis.
On
edge
dispensability,
provide
test
natural
selection
photosynthesis-related
evolution.
Variable
evolutionary
environments
place
without
at
risk
extinction
and,
probably,
most
extant
ones
may
have
lost
recently.
Therefore,
they
endpoints
trees.
low
number
sequenced
DNA
long
lifespan
Gymnosperms
challenge
models
about
role
protecting
against
stress
promoting
leaf
senescence.
Additional
sequencing
into
molecular
mechanisms
their
response
will
unified
model
consequences
Genes,
Journal Year:
2022,
Volume and Issue:
13(7), P. 1279 - 1279
Published: July 19, 2022
With
the
development
of
molecular
sequencing
approaches,
many
taxonomic
and
phylogenetic
problems
genus
Allium
L.
have
been
solved;
however,
relationships
some
subgenera
or
sections,
such
as
section
Bromatorrhiza,
remain
unresolved,
which
has
greatly
impeded
our
full
understanding
species
among
major
clades
Allium.
In
this
study,
complete
chloroplast
(cp)
genomes
nine
in
sect.
Bromatorrhiza
were
determined
using
Illumina
paired-end
sequencing,
NOVOPlasty
de
novo
assembly
strategy,
PGA
annotation
method.
The
results
showed
that
cp
genome
exhibited
high
conservation
revealed
a
typical
circular
tetrad
structure.
Among
species,
gene
content,
SSRs,
codon
usage,
RNA
editing
site
similar.
structure
IR
regions’
fluctuation
investigated
while
genes,
CDSs,
non-coding
regions
extracted
for
phylogeny
reconstruction.
Evolutionary
rates
(Ka/Ks
values)
calculated,
positive
selection
analysis
was
further
performed
branch-site
model.
Five
hypervariable
identified
candidate
markers
authentication.
A
clear
relationship
detected
based
on
concatenated
genes
respectively,
suggested
is
monophyly.
addition,
there
three
with
higher
Ka/Ks
values
(rps2,
ycf1,
ycf2),
four
(rpoC2,
atpF,
atpI,
rpl14)
to
own
selected
sites.
These
provide
new
insights
into
plastome
component,
phylogeny,
evolution
species.
BMC Genomics,
Journal Year:
2023,
Volume and Issue:
24(1)
Published: Oct. 27, 2023
The
Begonia
species
are
common
shade
plants
that
mostly
found
in
southwest
China.
They
have
not
been
well
studied
despite
their
medicinal
and
decorative
uses
because
gene
penetration,
decreased
adaptability,
restricted
availability
all
caused
by
frequent
interspecific
hybridization.To
understand
the
patterns
of
mutation
chloroplast
genomes
different
Begonia,
as
evolutionary
relationships,
we
collected
seven
China
sequenced
genomes.
exhibit
a
quadripartite
structure
(157,634
-
169,694
bp),
consisting
two
pairs
inverted
repeats
(IR:
26,529
37,674
large
single
copy
(LSC:
75,477
86,500
small
(SSC:
17,861
18,367
bp).
128-143
genes
(comprising
82-93
protein-coding
genes,
8
ribosomal
RNAs,
36-43
transfer
RNAs)
Based
on
comparative
analyses,
this
taxon
has
relatively
similar
genome
structure.
A
total
six
substantially
divergent
DNA
regions
(trnT-UGU-trnL-UAA,
atpF-atpH,
ycf4-cemA,
psbC-trnS-UGA,
rpl32-trnL-UAG,
ccsA-ndhD)
seventeen
These
suitable
for
identification
phylogeographic
analysis.
Phylogenetic
analysis
shows
were
suited
to
comparable
environments
grouped
clade
formed
one
big
phylogenetic
tree,
supporting
genus'
monophyly.
In
addition,
positive
selection
sites
discovered
eight
(rpoC1,
rpoB,
psbE,
psbK,
petA,
rps12,
rpl2,
rpl22),
majority
which
involved
protein
production
photosynthesis.Using
these
resources,
can
resolve
deep-level
relationships
between
families,
leading
better
understanding
processes.
addition
enhancing
resolution,
results
demonstrate
utility
complete
phylogenetically
taxonomically
challenging
plant
groupings.
Frontiers in Plant Science,
Journal Year:
2022,
Volume and Issue:
13
Published: Dec. 9, 2022
The
chloroplast
(cp)
is
an
autonomous
plant
organelle
with
individual
genome
that
encodes
essential
cellular
functions.
architecture
and
gene
content
of
the
cp
highly
conserved
in
angiosperms.
plastome
Corydalis
belongs
to
Papaveraceae
family,
comprised
unusual
rearrangements
content.
Thus
far,
no
extensive
comparative
studies
have
been
carried
out
understand
evolution
genomes.Therefore,
platycarpa
was
sequenced,
wide-scale
were
conducted
using
publicly
available
twenty
plastomes.Comparative
analyses
showed
rearrangement
IR
expansion
occurred,
these
events
evolved
independently
species.
By
contrast,
plastomes
its
closely
related
subfamily
Papaveroideae
other
Ranunculales
taxa
are
conserved.
On
hand,
synapomorphy
characteristics
both
accD
ndh
loss
happened
common
ancestor
sub-clade
lineage,
respectively.
Corydalis-sub
clade
species
(ndh
lost)
distributed
predominantly
Qinghai-Tibetan
plateau
(QTP)
region.
phylogenetic
analysis
divergence
time
estimation
also
employed
for
species.The
(44.31
-
15.71
mya)
coincides
very
well
uplift
Qinghai-Tibet
Plateau
Oligocene
Miocene
periods,
maybe
during
this
period,
it
has
probably
triggered
radiation
species.To
best
authors'
knowledge,
first
large-scale
study
their
evolution.
present
may
provide
insights
into
molecular
Scientific Reports,
Journal Year:
2024,
Volume and Issue:
14(1)
Published: June 21, 2024
The
complete
cp
genomes
of
Pedicularis
chinensis
(GenBank
accession
number:
OQ587614)
and
kansuensis
OQ587613)
were
sequenced,
assembled,
annotated.
Their
chloroplast
(cp)
genome
lengths
146,452
bp,
146,852
respectively;
120
116
genes
identified,
comprising
75
72
protein-coding
(PCGs),
37
36
transfer
RNA
(tRNA)
genes,
8
ribosomal
(rRNA)
for
P.
kansuensis,
respectively.
A
simple
sequence
repeat
(SSR)
analysis
revealed
that
the
repetitive
sequences
mainly
composed
mononucleotide
repeats
(A/T
motif)
dinucleotide
(AT/TA
motif).
Comparative
genomics
identified
several
variant
(rpl22,
rps19,
rpl12,
ycf1,
trnH,
psbA,
ndhH)
regions
(trnS-GGA,
trnV-UAC,
ndhJ-trnV,
ycf4-cemA,
ndhE-nhdG,
rpl32-trnL)
with
a
high
Pi,
indicating
potential
to
serve
as
deoxyribo
nucleic
acid
(DNA)
barcodes
species
identification.
results
show
same
those
other
plants
in
Pedicularis,
different
degrees
AT
preference
codons.
Large
differences
number
SSRs
expansion
inverted
(IR)
region
showed
strong
variability
interspecific
differentiation
between
these
two
represented
genus
Pedicularis.
phylogenetic
had
closest
relationship
oliveriana,
aschistorhyncha.
These
will
facilitate
study
classification
evolution
plants.
Global Ecology and Conservation,
Journal Year:
2024,
Volume and Issue:
54, P. e03097 - e03097
Published: July 16, 2024
Geological
and
climatic
events
have
long
been
considered
to
profoundly
affect
population
evolution
demographic
history
of
species,
but
the
evolutionary
rare
endangered
herbaceous
plants
in
East
Asia
remains
less
well
understood.
In
this
study,
chloroplast
genomes,
environmental
variables
geographical
distribution
information
were
integrated
determine
dynamics
Bergenia
scopulosa
T.P.Wang,
an
medicinal
herb
endemic
central
China
(Qinling
Mountains).
Population
genomic
analysis
based
on
genomes
indicated
a
significant
degree
intraspecific
differentiation
within
B.
scopulosa,
where
two
separate
genetic
lineages
identified
eastern
western
groups
Qinling
Mountains,
respectively.
The
found
low
level
nucleotide
diversity.
Meanwhile,
ecological
niche
revealed
that
had
obvious
divergence.
Species
modeling
illustrated
experienced
prominent
contraction
from
interglacial
periods
present,
while
suitable
habitat
was
predicted
shift
higher
elevations
response
global
warming
future
scenarios.
These
findings
suggested
geological
factors
together
affected
divergence
Mountains
Asia.
particular,
geographic
isolation
appeared
play
greater
role
scopulosa.
Therefore,
conservation
units
should
be
correspondingly
established
for