BMC Plant Biology,
Journal Year:
2024,
Volume and Issue:
24(1)
Published: July 3, 2024
Abstract
Background
Cyperus
stoloniferus
is
an
important
species
in
coastal
ecosystems
and
possesses
economic
ecological
value.
To
elucidate
the
structural
characteristics,
variation,
evolution
of
organelle
genome
C.
,
we
sequenced,
assembled,
compared
its
mitochondrial
chloroplast
genomes.
Results
We
assembled
genomes
.
The
total
length
(mtDNA)
was
927,413
bp,
with
a
GC
content
40.59%.
It
consists
two
circular
DNAs,
including
37
protein-coding
genes
(PCGs),
22
tRNAs,
five
rRNAs.
(cpDNA)
186,204
containing
93
PCGs,
40
8
mtDNA
cpDNA
contained
81
129
tandem
repeats,
respectively,
346
1,170
dispersed
both
which
have
270
simple
sequence
repeats.
third
high-frequency
codon
(RSCU
>
1)
organellar
tended
to
end
at
A
or
U,
whereas
low-frequency
<
G
RNA
editing
sites
PCGs
were
relatively
few,
only
9
23
cpDNA,
respectively.
28
plastid
DNAs
(MTPTs)
derived
from
three
complete
trnT-GGU
trnH-GUG
trnS-GCU
Phylogeny
collinearity
indicated
that
relationship
between
rotundus
are
closest.
rns
gene
exhibited
greatest
nucleotide
variability,
variability
infA
Most
negatively
selected
highly
evolutionarily
conserved.
Only
six
Ka/Ks
1;
particular,
atp9
atp6
rps7
may
undergone
potential
positive
selection.
Conclusion
validated
contains
15,034
bp
reverse
complementary
sequence.
provides
valuable
genomic
resources
for
identification,
evolution,
comparative
research
Cyperaceae.
Mitochondrial DNA Part B,
Journal Year:
2025,
Volume and Issue:
10(1), P. 88 - 93
Published: Jan. 2, 2025
Carex
pseudochinensis
H.
Lév.
&
Vaniot
is
an
endemic
species
in
Korea
and
included
the
clade
of
section
Paludosae
recent
classification
system.
We
present
complete
mitochondrial
genome
sequence
C.
based
on
POLAP
pipeline
with
both
long-
short-read
sequences.
The
997,628
bp
length,
containing
two
large
regions
536.94
419.04
kbp,
respectively,
a
pair
direct
repeat
about
20.25
kbp.
contains
57
genes,
including
31
protein-coding
20
tRNAs,
6
rRNAs.
Phylogenetic
analysis
proteomes,
those
from
ten
related
taxa,
confirmed
close
phylogenetic
relationship
between
breviculmis
pseudochinensis.
BMC Genomics,
Journal Year:
2025,
Volume and Issue:
26(1)
Published: Feb. 17, 2025
Abstract
Background
Orobanche
is
a
parasitic
plant
distributed
in
the
temperate
zone
of
Northern
Hemisphere,
with
approximately
200
species
found
worldwide.
In
Republic
Korea,
two
,
namely
O.
coerulescens
Stephan
ex
Willd.
and
filicicola
Nakai
Hyun,
Y.
S.
Lim
&
H.
C.
Shin,
are
present,
being
endemic.
Genome
analysis
this
has
not
yet
been
performed,
characterizing
its
complete
organelle
genome
will
provide
valuable
insights
into
phylogeny
evolution
plants.
Results
The
chloroplast
mitochondrial
genomes
were
analyzed,
revealing
distinct
characteristics.
91,529
bp
long
GC
content
33.6%,
containing
33
protein-coding,
30
tRNA,
4
rRNA
genes.
contrast,
1,058,991
45.5%,
featuring
31
16
3
over
three
times
more
simple
sequence
repeats
longer
than
genome.
Analysis
synonymous
codon
usage
protein-coding
genes
from
nine
Orobanchaceae
revealed
significant
differences
between
chloroplasts
mitochondria,
codons
ending
A
or
T
exhibiting
higher
coding
rates.
Ka/Ks
ratio
calculations
indicated
that
psbI
atpB
had
smallest
largest
ratios
chloroplasts,
respectively,
while
ccmFC
was
identified
as
only
gene
under
positive
selection
mitochondria
genomes.
Sequence
alignment
homologous
fragments
genomes,
totaling
7,247
bp.
Comparison
’s
related
showed
loss
conserved
inverted
repeat
sequences.
Numerous
collinear
blocks
species,
but
some
regions
lacked
homology.
Phylogenetic
identical
topologies
for
forming
strong
monophyletic
group.
Conclusions
Characterizing
enabled
comprehensive
genome,
providing
important
baseline
data
structure
evolution.
Frontiers in Plant Science,
Journal Year:
2025,
Volume and Issue:
16
Published: March 20, 2025
Introduction
Blechnopsis
orientalis
(L.)
C.
Presl
is
a
medicinal
and
edible
fern
species
belonging
to
the
Blechnaceae
family.
Currently,
complete
mitochondrial
genome
of
B.
,
as
well
those
other
species,
remains
unreported,
studies
on
are
limited.
Methods
In
this
study,
was
sequenced
using
both
Nanopore
PromethION
Illumina
NovaSeq
6000
platforms.
Genome
annotation
performed
MITOFY
MFANNOT,
with
structural
visualization
via
OGDRAW.
In-depth
analyses
were
conducted,
including
assessments
non-synonymous/synonymous
mutation
ratios
(Ka/Ks),
codon
usage
bias,
repeat
sequence
identification,
RNA
editing
site
prediction,
collinearity,
identification
homologous
fragments
between
chloroplast
genomes.
Finally,
we
employed
maximum
likelihood
(ML)
Bayesian
(BI)
methods
analyze
phylogenetic
relationships
among
nine
lycophyte
species.
Results
The
has
complex
structure
comprising
80
contigs,
total
length
501,663
bp
GC
content
48.53%.
A
179
genes
identified,
40
protein-coding
(PCGs),
98
tRNA
genes,
rRNA
one
pseudogene
(
rps11
).
Phylogenetic
analysis
based
PCGs
from
aligned
described
in
Pteridophyte
Phylogeny
Group
I
(PPG
I)
system.
Further
comparison
ten
reported
revealed
that
these
plants
highly
conserved,
despite
significant
rearrangements
genome.
Discussion
findings
study
provide
valuable
insights
into
evolutionary
contribute
understanding
characteristics
ferns
lycophytes.
Frontiers in Plant Science,
Journal Year:
2025,
Volume and Issue:
16
Published: May 8, 2025
Introduction
The
genus
Rosa
belongs
to
the
family
Rosaceae
within
order
Rosales,
which
is
one
of
more
ancient
plant
lineages.
At
present,
complete
mitochondrial
genome
spp.
still
rarely
reported,
and
studies
on
are
limited.
Methods
In
this
study,
R.
laevigata
was
sequenced
using
both
Pacbio
Sequel
II
DNB-SEQ-T7
platforms.
second-
third-generation
data
for
other
five
species
were
downloaded
from
NCBI
database.
Genome
annotation
performed
Geneious,
with
structural
visualization
via
CPGview.
In-depth
analyses
conducted,
including
assessments
non-synonymous/synonymous
mutation
ratios
(Ka/Ks),
codon
usage
bias,
collinearity,
identification
homologous
fragments
between
chloroplast
genomes.
Finally,
we
employed
maximum
likelihood
(ML)
methods
analyze
phylogenetic
relationships
among
species.
Results
sizes
ranged
156,342
bp
(
)
157,214
agrestis
).
GC
content
varied
37.2%
37.3%,
number
genes
129
131.
genomes
all
circular,
lengths
271,191
338,975
bp,
containing
52
59
genes.
Codon
analysis
indicated
a
preference
A/T-ending
codons
in
Four
highly
differentiated
regions
rps19
,
ndhF
ycf1
psbM-trnD-GUC
plastomes
7
identified,
can
serve
as
molecular
markers
future
genetic
diversity.
Compared
PCGs
plastome,
displayed
higher
non-synonymous
synonymous
ratio.
We
also
observed
extensive
gene
transfer
mitochondria
chloroplasts,
particularly
rrn16
rpl23
genes,
commonly
found
These
events
likely
occurred
ancestor
around
4.46
Mya.
Estimates
divergence
indicate
that
rapid
differentiation
took
place
Mya,
potentially
influenced
by
uplift
Qinghai-Tibet
Plateau
during
Late
Miocene.
Discussion
This
study
enriches
resources
lays
groundwork
development
markers,
analyses,
research
into
evolution
organelle
