Characterize the Complete Mitogenome of Semiaquilegia guangxiensis and Assess the Efficiency of the Mitochondrial Genes in Ranunculales Phylogeny
Ecology and Evolution,
Год журнала:
2025,
Номер
15(4)
Опубликована: Март 27, 2025
ABSTRACT
Plant
mitochondrial
genome
(mitogenome)
has
crucial
functions
underpinning
survive,
development,
and
reproduction
of
organisms.
However,
the
complete
mitogenomes
have
been
far
less
assembled
annotated
than
plastomes
even
nuclear
genomes
in
plants,
due
to
their
highly
frequent
long
repeat
sequences
genomic
structural
variations.
These
further
hinder
understanding
mitogenome
evolution
restrict
potential
applications
phylogenetic
analyses.
In
this
study,
we
sequenced,
assembled,
Semiaquilegia
guangxiensis
explored
its
usefulness
phylogenetics.
The
results
showed
that
was
composed
two
independent
molecules,
which
had
a
total
length
522,981
bp,
GC
content
45.69%,
58
genes
including
34
protein‐coding
(PCGs),
21
tRNA
genes,
three
rRNA
genes.
A
generalized
codon
usage
preference
observed
among
PCGs,
665
RNA
editing
sites
were
identified
across
all
base
C‐to‐U
edits.
Moreover,
large
number
repetitive
chloroplast‐sourced
transferred
detected.
largest
collinear
block
between
S.
Paropyrum
anemonoides
4282
bp
length.
analyses
based
on
gene
resolved
relationships
within
Ranunculales,
close
.
19
PCGs
ranked
according
efficiencies
resolution
several
metrics,
combined
metric
suggested
mat
R,
rps
3,
nad
5
top
loci
contributing
most
phylogeny.
As
first
reported
,
our
findings
enrich
limited
library
reecho
complex
evolutionary
dynamics
mitogenome,
highlight
Язык: Английский
Mitochondrial genome of Lonicera macranthoides: features, RNA editing, and insights into male sterility
Frontiers in Plant Science,
Год журнала:
2025,
Номер
15
Опубликована: Янв. 10, 2025
Mitochondria
are
essential
organelles
that
provide
energy
for
plants.
They
semi-autonomous,
maternally
inherited,
and
closely
linked
to
cytoplasmic
male
sterility
(CMS)
in
Lonicera
macranthoides,
a
widely
used
medicinal
plant
from
the
Caprifoliaceae
family,
is
rich
chlorogenic
acid
(CGA)
its
analogues,
which
known
their
antiviral
anticancer
properties.
However,
studies
on
mitogenome
of
L.
macranthoides
still
remain
limited.
The
mitochondrial
DNA
contained
whole
genome
was
extracted
sterile
cultivar
named
'Yulei
1'.
Next-generation
sequencing
(NGS)
third-generation
(TGS)
technologies
were
combined
obtain
mitogenome.
RNA
editing
events
identified
by
integrating
data
with
leaf,
stem,
flower
tissues.
potential
causes
1'
analyzed
based
loss
functional
genes,
rearrangements,
events,
open
reading
frames
(ORFs).
complete
obtained
first
time,
length
1,002,202
bp.
It
contains
48
protein-coding
genes
(PCGs),
26
tRNA
3
rRNA
genes.
Additionally,
79
simple
sequence
repeats
(SSRs),
39
tandem
repeats,
99
dispersed
identified.
Among
these,
two
direct
(RP1a/1b,
RP2a/2b)
inverse
(RP3a/b,
RP4a/b)
may
facilitate
recombination.
Gene
transfer
analysis
revealed
4.36%
21.98%
mitogenomic
sequences
mapped
chloroplast
nuclear
genomes,
respectively.
Phylogenetic
indicated
closest
japonica
at
level.
Notably,
varied
across
different
tissues,
357
sites
30
PCGs
leaves,
138
24
flowers,
68
13
stems.
Finally,
all
indications
CMS
screened,
including
detection
ORFs,
findings
showed
no
mutations
would
explain
Overall,
our
study
provides
will
aid
genetic
marker
exploration,
evolutionary
relationship
analysis,
breeding
programs.
Язык: Английский
The first complete mitochondrial genome of Curcuma amarissima (Zingiberaceae): insights into multi-branch structure, codon usage, and phylogenetic evolution
BMC Genomics,
Год журнала:
2025,
Номер
26(1)
Опубликована: Апрель 5, 2025
As
a
key
genus
in
Zingiberaceae,
Curcuma
is
widely
studied
for
its
taxonomic
diversity,
the
presence
of
bioactive
curcuminoids
and
volatile
oils,
extensive
applications
traditional
medicine
economic
products
such
as
spices
cosmetics.
Although
chloroplast
genomes
have
been
assembled
published
over
20
species,
mitochondrial
genomic
data
remain
limited.
We
successfully
sequenced,
assembled,
annotated
mitogenome
amarissima
(C.
amarissima)
using
both
Illumina
short
reads
Nanopore
long
reads,
achieving
first
complete
characterization
Zingiberaceae
family.
The
C.
features
unique
multi-branched
structure,
spanning
6,505,655
bp
consisting
39
distinct
segments.
It
contains
total
43
protein-coding
genes,
63
tRNA
4
rRNA
with
GC
content
44.04%.
Codon
usage
analysis
indicated
weak
bias,
neutrality
plot
suggesting
natural
selection
factor
shaping
codon
amarissima.
provides
valuable
insights
into
genome
size,
coding
structural
features,
RNA
editing,
repetitive
sequences,
sequence
migration,
enhancing
our
understanding
evolution
molecular
biology
mitochondria
Zingiberaceae.
high
frequency
repeat
sequences
may
contribute
to
stability
mitochondria.
Comparing
genome,
phylogenetic
based
on
establishes
foundation
further
exploration
evolutionary
relationships
within
In
short,
characterized
here
advances
organization
offers
useful
resources
that
support
future
breeding,
germplasm
conservation,
studies,
though
research
necessary.
Язык: Английский
De Novo Assembly and Comparative Analysis of the Complete Mitochondrial and Chloroplast Genome of Melicope Pteleifolia (Rutaceae)
Опубликована: Янв. 1, 2024
Язык: Английский
Characterization of the complete chloroplast genome and development of molecular markers of Salix
Scientific Reports,
Год журнала:
2024,
Номер
14(1)
Опубликована: Ноя. 18, 2024
Salix,
an
economically
and
ecologically
multifunctional
tree
species
widely
distributed
in
China,
encompasses
five
ornamental
sequenced
this
study,
which
are
highly
beneficial
for
plant
phytoremediation
due
to
their
ability
absorb
heavy
metals.
This
research
utilized
high-throughput
sequencing
acquire
chloroplast
genome
sequences
of
analyzing
gene
composition
structural
characteristics,
identifying
potential
molecular
markers,
laying
a
foundation
Salix
identification
resource
classification.
Chloroplast
DNA
was
extracted
from
the
leaves
argyracea,
dasyclados,
eriocephala,
integra
'Hakuro
Nishiki',
suchowensis
using
optimized
CTAB
method.
Sequencing
conducted
on
Illumina
NovaSeq
PE150
platform,
bioinformatics
tools
were
employed
compare
features
variations
within
genomes
Salix.
Analysis
revealed
high
similarity
among
species,
with
subsequent
examination
276,
269,
270,
273,
273
SSR
loci,
respectively,
along
unique
simple
repeat
each
variety.
Comparison
across
22
highlighted
regions
such
as
matK-trnQ,
ndhC-trnV,
psbE-petL,
rpl36-rps8,
ndhB-rps7,
may
serve
valuable
markers
willow
classification
studies.
In
analysis
not
only
enhances
genetic
resources
but
also
forms
critical
basis
development
exploration
interspecific
phylogeny
genus.
Язык: Английский