Research Square (Research Square),
Journal Year:
2023,
Volume and Issue:
unknown
Published: July 10, 2023
Abstract
Background
Punica
granatum
is
an
essentially
important
fruit
tree
that
has
economic,
medicinal
and
ornamental
properties.
At
present,
there
are
few
reports
on
the
mitochondrial
genome
of
pomegranate.
To
further
understand
organization,
variation,
evolution
pomegranate
mitogenomes,
P.
mitogenome
was
sequenced
assembled
in
study.
Results
The
structure
multi-chromosomes
with
seven
circular
chromosomes,
measuring
382,774
bp
length
a
45.91%
GC
content.
It
contained
74
genes,
including
46
protein-coding
25
tRNA
three
rRNA
genes.
There
were
188
pairs
dispersed
repeats
lengths
greater
than
or
equal
to
30,
which
mainly
reverse
complementary
repeats.
analysis
identified
114SSRs
466
RNA
editing
sites.
Analyses
codon
usage,
nucleotide
diversity
gene
migration
from
chloroplast
also
conducted.
collinear
comparative
structures
between
its
proximal
species
indicated
closely
related
Lagerstroemia
indica.
Phylogenetic
examination
based
confirmed
evolutionary
relationship.
Conclusion
results
provided
predominant
information
for
biology
promote
germplasm
utilization.
International Journal of Molecular Sciences,
Journal Year:
2024,
Volume and Issue:
25(3), P. 1578 - 1578
Published: Jan. 27, 2024
Epipogium
roseum,
commonly
known
as
one
of
the
ghost
orchids
due
to
its
rarity
and
almost
transparent
color,
is
a
non-photosynthetic
fully
mycoheterotrophic
plant.
Given
special
nutritional
strategies
evolutionary
significance,
mitogenome
was
first
characterized,
three
plastomes
sampled
from
Asia
were
assembled.
The
found
be
smallest
among
Orchidaceae,
with
lengths
ranging
18,339
19,047
bp,
exhibited
high
sequence
variety.
For
mitogenome,
total
414,552
bp
in
length,
comprising
26
circular
chromosomes,
identified.
A
54
genes,
including
38
protein-coding
13
tRNA
3
rRNA
annotated.
Multiple
repeat
sequences
spanning
length
203,423
(45.47%)
discovered.
Intriguingly,
six
plastid
regions
via
intracellular
gene
transfer
four
horizontal
observed.
phylogenomics,
incorporating
90
56
mitogenomes,
consistently
revealed
sister
relationship
Gastrodia,
bootstrap
percentage
100%.
These
findings
shed
light
on
organelle
evolution
Orchidaceae
plants.
BMC Genomics,
Journal Year:
2023,
Volume and Issue:
24(1)
Published: Nov. 23, 2023
Abstract
Background
Forsythia
suspensa
(Thunb.)
Vahl
is
a
valuable
ornamental
and
medicinal
plant.
Although
the
nuclear
chloroplast
genomes
of
F.
have
been
published,
its
complete
mitochondrial
genome
sequence
has
yet
to
be
reported.
In
this
study,
genomic
DNA
yellowish
leaf
material
was
extracted,
sequenced
by
using
mixture
Illumina
Novaseq6000
short
reads
Oxford
Nanopore
PromethION
long
reads,
sequencing
data
were
assembled
annotated.
Result
The
obtained
in
length
535,692
bp
with
circular
structure,
GC
content
44.90%.
contains
60
genes,
including
36
protein-coding
21
tRNA
three
rRNA
genes.
We
further
analyzed
RNA
editing
relative
synonymous
codon
usage,
repeats
based
on
data.
There
25
homologous
sequences
between
mitochondria
genome,
which
involved
transfer
8
9473
genomes.
Analysis
nucleic
acid
substitution
rate,
diversity,
collinearity
genes
revealed
that
majority
may
undergone
purifying
selection,
exhibiting
slower
rate
evolution
relatively
conserved
structure.
phylogenetic
relationships
among
different
species
most
closely
related
Olea
europaea
subsp.
Europaea.
Conclusion
we
sequenced,
assembled,
annotated
high-quality
genome.
results
study
will
enrich
,
lay
foundation
for
development
promote
evolutionary
analysis
Oleaceae
species.
BMC Plant Biology,
Journal Year:
2023,
Volume and Issue:
23(1)
Published: Oct. 25, 2023
Abstract
Background
Punica
granatum
is
a
fundamentally
important
fruit
tree
that
has
economic,
medicinal
and
ornamental
properties.
At
present,
there
are
few
reports
on
the
mitochondrial
genome
of
pomegranate.
Hence,
in
this
study
P.
mitogenome
was
sequenced
assembled
to
further
understanding
organization,
variation,
evolution
mitogenomes
species.
Results
The
structure
multi-chromosomes
with
seven
circular
contigs,
measuring
382,774
bp
length
45.91%
GC
content.
It
contained
74
genes,
including
46
protein-coding
25
tRNA
three
rRNA
genes.
There
were
188
pairs
dispersed
repeats
lengths
30
or
greater,
primarily
consisting
reverse
complementary
repeats.
analysis
identified
114SSRs
466
RNA
editing
sites.
Analyses
codon
usage,
nucleotide
diversity
gene
migration
from
chloroplast
also
conducted.
collinear
comparative
structures
between
its
proximal
species
indicated
‘Taishanhong’
closely
related
‘Qingpitian’
Lagerstroemia
indica.
Phylogenetic
examination
based
confirmed
evolutionary
relationship.
Conclusion
results
offered
crucial
information
biology
pomegranate
highlighted
ways
promote
utilization
species’
germplasm.
International Journal of Molecular Sciences,
Journal Year:
2025,
Volume and Issue:
26(2), P. 562 - 562
Published: Jan. 10, 2025
Danxiaorchis
yangii
is
a
fully
mycoheterotrophic
orchid
that
lacks
both
leaves
and
roots,
belonging
to
the
genus
in
subtribe
Calypsoinae.
In
this
study,
we
assembled
annotated
its
mitochondrial
genome
(397,867
bp,
GC
content:
42.70%),
identifying
55
genes,
including
37
protein-coding
genes
(PCGs),
16
tRNAs,
2
rRNAs,
conducted
analyses
of
relative
synonymous
codon
usage
(RSCU),
repeat
sequences,
horizontal
gene
transfers
(HGTs),
selective
pressure
(dN/dS).
Additionally,
sequenced
plastome,
which
has
reduced
size
110,364
bp
(GC
36.60%),
comprising
48
PCGs,
26
4
rRNAs.
We
identified
64
potential
chloroplast
DNA
fragments
transferred
mitogenome.
Phylogenomic
analysis
focusing
on
33
mitogenomes,
with
Vitis
vinifera
as
outgroup,
indicated
D.
grouped
follows:
+
((Dendrobium
wilsonii
Dendrobium
henanense)
Phalaenopsis
aphrodite).
Phylogenetic
based
83
plastid
PCGs
from
these
species
showed
(D.
Pha.
aphrodite)
(Den.
Den.
henanense).
Gene
revealed
most
are
under
purifying
selection,
ensuring
functional
stability,
certain
may
have
undergone
positive
selection
or
adaptive
evolution,
reflecting
species’
adaptation
specific
ecological
environments.
Our
study
provides
valuable
data
plastomes
mitogenomes
lays
groundwork
for
future
research
genetic
variation,
evolutionary
relationships,
breeding
orchids.
Life,
Journal Year:
2025,
Volume and Issue:
15(1), P. 102 - 102
Published: Jan. 15, 2025
Navicula
incerta,
a
marine
benthic
diatom,
holds
promise
for
human
nutrition
and
health
as
well
aquaculture
applications.
However,
the
scarcity
of
organelle
genome
data
within
clade
has
impeded
comprehensive
understanding
utilization
this
group.
Our
research
presents
pioneering
exploration
into
complete
mitochondrial
chloroplast
sequences
N.
incerta
CACC
0356,
shedding
light
on
its
phylogeny
evolutionary
history.
The
(mtDNA)
spans
61,320
bp
with
GC
content
29.87%,
comprising
one
circular
DNA
molecule
that
encodes
34
protein-coding
genes,
24
tRNAs,
rRNAs.
Whereas,
(cpDNA)
is
larger
at
129,090
bp,
encompassing
127
30
7
Notably,
cpDNA
approximately
2.1
times
size
mtDNA.
annotation
identified
four
genes
are
partially
situated
in
homologous
regions
between
mitogenome
genome,
totaling
372
which
represents
0.61%
entire
mitogenome.
Comparative
analyses
revealed
0356
closely
affiliated
Fistulifera
saprophila
solaris,
both
members
Naviculaceae
order.
This
study
significantly
expands
genomic
resources
algae
lays
foundation
development
genetic
diversity
algae.
Frontiers in Plant Science,
Journal Year:
2025,
Volume and Issue:
15
Published: Jan. 20, 2025
Introduction
Garuga
forrestii
W.
Sm.
is
a
tree
species
of
the
Burseraceae
family,
endemic
to
China,
found
in
hot/warm-dry
valleys.
This
plays
crucial
role
maintaining
biodiversity
these
ecosystems.
Methods
We
performed
de
novo
assembly
mitochondrial
genome
using
PMAT
(v.1.5.4),
resulting
typical
circular
molecule
606,853
bp.
The
consists
31
tRNA
genes,
3
rRNA
35
protein-coding
and
1
pseudogene.
study
also
investigates
RNA
editing
sites
evolutionary
patterns.
Results
exhibits
low
proportion
repetitive
sequences
(3.30%),
suggesting
highly
conserved
structure.
A
high
copy
number
trnM-CAT
gene
(4
copies)
noted,
which
may
contribute
genomic
rearrangement
adaptive
evolution.
Among
476
sites,
hydrophilic-hydrophobic
hydrophobic-hydrophobic
events
are
most
common,
accounting
for
77.10%.
Negative
selection
predominates
among
genes
(Ka/Ks
<
1),
while
few
(e.g.,
matR
,
nad3
rps1
rps12
rps4
)
show
signs
positive
>
potentially
conferring
advantages.
Additionally,
significant
A/T
bias
observed
at
third
codon
position.
Phylogenomic
analysis
supports
APG
IV
classification,
with
no
evidence
horizontal
transfer.
Discussion
offers
valuable
insights
into
mechanisms
processes
.
It
enhances
our
understanding
species'
biogeography
tropical
Southeast
Asia
Southwest
providing
key
information
on
history
this
genus.
Biomolecules,
Journal Year:
2025,
Volume and Issue:
15(3), P. 343 - 343
Published: Feb. 27, 2025
Thymus
mongolicus
(Lamiaceae)
is
a
plant
commonly
found
throughout
China,
in
which
it
widely
used
chemical
products
for
daily
use,
traditional
medicinal
preparations,
ecological
management,
and
cooking.
In
this
study,
we
have
assembled
annotated
the
first
time
entire
mitochondrial
genome
(mitogenome)
of
T.
mongolicus.
The
composed
monocyclic
structure,
with
an
overall
size
450,543
base
pairs
(bp)
GC
composition
45.63%.
It
contains
32
unique
protein-encoding
genes.
repetitive
sequences
mitogenome
include
165
forward
200
palindromic
sequences,
addition
to
88
simple
sequence
repeats,
tetramers
accounted
highest
proportion
(40.91%).
An
analysis
codons
revealed
that
synonymous
generally
end
A/U.
With
exception
nad4L,
uses
ACG/ATG
as
initiation
codon,
all
other
genes
begin
ATG
start
codon.
Codon
also
showed
leucine
(909)
are
most
abundant
amino
acid,
while
tryptophan
(134)
least
prevalent.
total,
374
RNA
editing
sites
were
detected.
Moreover,
180
homologous
segments
totaling
105,901
bp
when
chloroplast
genomes
compared.
Phylogenetic
further
indicated
closely
related
Prunella
vulgaris
Lamiaceae
family.
Our
findings
offer
important
genetic
insights
research
on
species.
To
best
our
knowledge,
study
description
Frontiers in Plant Science,
Journal Year:
2025,
Volume and Issue:
15
Published: Feb. 27, 2025
Iris
domestica
is
a
perennial
herb
valued
for
both
its
ornamental
and
medicinal
properties.
Despite
significance,
no
comprehensive
analysis
of
mitochondrial
genome
has
been
previously
reported.
Plant
genomes
are
known
their
large
size,
structural
complexity,
frequent
recombination
events.
This
study
aims
to
provide
the
first
complete
assembly
characterization
I.
domestica,
with
focus
on
structure,
gene
content,
repeat
elements,
RNA
editing
sites.
We
used
GetOrganelle
Unicycler
software
hybrid
assemble
Nanopore
Illumina
data
obtain
domestica.
The
consists
four
contigs:
contig1
(222,498
bp),
contig2
(90,780
contig3
(42,563
contig4
(39,247
bp).
Two
sequences,
R1
(7,784
bp)
R2
(3,519
facilitate
conformation
three
circular
chromosomes,
suggesting
complex
multi-chromosomal
structure.
A
total
34
protein-coding
genes,
including
24
core
genes
10
non-core
were
identified.
Analysis
tandem
elements
revealed
significant
variability,
Chromosome
1
showing
highest
diversity
SSRs
scattered
repeats.
Additionally,
20
homologous
fragments
identified
between
chloroplast
genomes,
accounting
1.10%
genome.
Phylogenetic
based
conserved
placed
in
close
relation
Crocus
sativus.
Furthermore,
545
sites
identified,
notable
variations
across
that
plays
role
regulating
expression.
reveals
multichromosomal
structure
characterized
by
high
number
presence
transferred
plastid
DNA
highlight
dynamic
nature
genome,
contributing
adaptability
evolution.
These
findings
genetic
foundation
into
plant's
properties,
adaptive
mechanisms,
potential
environmental
resilience.
