Frontiers in Plant Science,
Год журнала:
2024,
Номер
15
Опубликована: Июнь 28, 2024
Water
hyacinth
(
Pontederia
crassipes
Mart.)
is
a
monocotyledonous
aquatic
plant
renowned
for
its
rapid
growth,
extensive
proliferation,
biological
invasiveness,
and
ecological
resilience
to
variations
in
pH,
nutrients,
temperature.
The
International
Union
Conservation
of
Nature
(IUCN)
has
listed
P.
among
the
top
100
invasive
species.
However,
comprehensive
genomic
information,
particularly
concerning
mitochondrial
genome
(mitogenome),
remains
surprisingly
limited.
In
this
study,
complete
mitogenome
was
analyzed
using
bioinformatics
approaches.
399,263
bp
long
contains
38
protein-coding
genes
(PCGs),
24
tRNA
genes,
3
rRNA
genes.
Sequence
analysis
revealed
that
species
3,289
dispersed
repeats,
765
RNA
editing
sites
possessed
un-conserved
structures,
including
sequence
transfer
between
chloroplasts
mitochondria.
Our
study
on
offers
critical
insights
into
evolutionary
patterns
phylogenetic
relationships
with
related
taxa.
This
research
enhances
our
understanding
species,
known
significant
biomass
overgrowth
environments.
Abstract
Background
Red
raspberry
(
Rubus
idaeus
L.)
is
a
renowned
fruit
plant
with
significant
medicinal
value.
Its
nuclear
genome
and
chloroplast
(plastome)
have
been
reported,
while
there
lack
of
genetic
information
on
its
mitogenome.
We
sequenced
assembled
the
complete
mitogenome
R.
,
conducted
series
investigations
comparing
it
genomes,
so
as
to
better
gain
comprehensive
understanding
species’
background.
Results
The
represented
by
one
circular
chromosome
438,947
bp.
Twenty-four
core
genes,
nine
variable
26
tRNAs,
three
rRNAs
were
annotated.
A
total
52
SSRs
38
tandem
repeat
sequences
identified.
533
pairs
dispersed
repeats
detected,
among
which
found
mediated
homologous
recombination,
resulting
in
major
conformation
seven
minor
conformations.
Furthermore,
between
plastome
identified,
including
six
protein-coding
genes
12
tRNA
genes.
also
detected
828
fragments
mitogenome,
trn
M-CAU
gene.
Conclusions
In
this
study,
we
presented
for
first
time
based
data
obtained
from
Illumina
Oxford
Nanopore
sequencing
platforms.
Key
characteristics
examined,
gene
composition,
repetitive
elements,
DNA
fragments.
Additionally,
identified
multiple
recombination
events
high-quality
well-annotated
known
red
will
provide
essential
species
classification,
evolution
analysis,
even
improvement
future.
Fritillaria
ussuriensis
is
an
endangered
medicinal
plant
known
for
its
notable
therapeutic
properties.
Unfortunately,
population
has
drastically
declined
due
to
the
destruction
of
forest
habitats.
Thus,
effectively
protecting
F.
from
extinction
poses
a
significant
challenge.
A
profound
understanding
genetic
foundation
crucial.
To
date,
research
on
complete
mitochondrial
genome
not
yet
been
reported.
Rehmannia
chingii
is
an
important
medicinal
plant
with
immense
value
in
scientific
research.
However,
its
mitochondrial
genome
(mitogenome)
has
not
yet
been
characterized.
Herein,
based
on
whole-genome
Illumina
short
reads
and
PacBio
HiFi
reads,
we
obtained
the
complete
mitogenome
of
R.
through
a
de
novo
assembly
strategy.
We
carried
out
comparative
genomic
analyses
found
that,
comparison
plastid
(plastome)
showing
high
degree
structural
conservation,
structure
relatively
complex,
intricate
ring
16
connections,
owing
to
five
repetitive
sequences.
The
was
783,161
bp
GC
content
44.8%
contained
77
genes,
comprising
47
protein-coding
genes
(CDS),
27
tRNA
3
rRNA
genes.
counted
579
RNA
editing
events
CDS
12,828
codons
all
CDSs
mitogenome.
Furthermore,
24
unique
sequence
transfer
fragments
were
between
plastome,
8
plastome
corresponding
2.39%
Mitogenomes
had
shorter
but
more
collinear
regions,
evidenced
by
organelles
non-parasitic
chingii,
hemiparasitic
Pedicularis
chinensis,
holoparasitic
Aeginetia
indica
Orobanchaceae
family.
Moreover,
from
species,
size
mitogenomes
species
did
decrease
gradually.
Instead,
smallest
P.
225,612
bp.
findings
fill
gap
research
promote
progress
organelle
family,
provide
clues
for
molecular
breeding.
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.
Frontiers in Plant Science,
Год журнала:
2024,
Номер
15
Опубликована: Фев. 6, 2024
Corydalis
saxicola
,
an
endangered
medicinal
plant
endemic
to
karst
habitats,
is
widely
used
in
Traditional
Chinese
Medicine
treat
hepatitis,
abdominal
pain,
bleeding
hemorrhoids
and
other
conditions.
However,
date,
the
mitochondrial
(mt)
genome
of
C.
has
not
been
reported,
which
limits
our
understanding
genetic
biological
mechanisms
.
Here,
mt
was
assembled
by
combining
Nanopore
Illumina
reads.
The
represented
a
circular
chromosome
587,939
bp
length,
with
overall
GC
content
46.50%.
40
unique
protein-coding
genes
(PCGs),
22
tRNA
three
rRNA
were
identified.
Codon
usage
PCGs
investigated
167
simple
sequence
repeats
Twelve
homologous
fragments
identified
between
ct
genomes
accounting
for
1.04%
entire
genome.
Phylogenetic
examination
30
taxa
provided
their
evolutionary
relationships.
We
also
predicted
779
RNA
editing
sites
C
successfully
validated
506
(65%)
these
using
PCR
amplification
Sanger
sequencing.
In
addition,
we
transcriptionally
profiled
24
core
roots
treated
different
concentrations
CaCl
2
as
well
organs.
These
investigations
will
be
useful
effective
utilization
molecular
breeding,
provide
reference
further
studies
genus
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.
Frontiers in Plant Science,
Год журнала:
2023,
Номер
14
Опубликована: Дек. 8, 2023
Introduction
Prunus
pedunculata
(Prunoideae:
Rosaceae),
a
relic
shrub
with
strong
resistance
and
multiple
application
values,
is
endangered
in
China.
Extensive
research
had
been
devoted
to
gene
expression,
molecular
markers,
plastid
genome
analysis,
genetic
background
investigations
of
P.
.
However,
the
mitochondrial
this
species
has
not
systematically
described,
owing
complexity
plant
mitogenome.
Methods
In
present
research,
complete
was
assembled,
annotated,
characterized.
The
genomic
features,
content
repetitive
sequences
were
analyzed.
variation
phylogenetic
analysis
have
extensively
enumerated.
Results
discussion
mitogenome
circular
molecule
total
length
405,855
bp
GC
45.63%,
which
are
smallest
size
highest
among
known
genomes.
encodes
62
genes,
including
34
unique
protein-coding
genes
(PCGs,
excluding
three
possible
pseudogenes),
ribosomal
RNA
19
transfer
genes.
rich
sequences,
counting
112
simple
sequence
repeats,
15
tandem
50
interspersed
repeat
11,793
bp,
accounting
for
2.91%
genome.
Leucine
(Leu)
predominant
amino
acid
PCGs,
frequency
10.67%,
whereas
cysteine
(Cys)
tryptophan
(Trp)
least
adopted.
most
frequently
used
codon
UUU
(Phe),
relative
synonymous
usage
(RSCU)
value
1.12.
Selective
pressure
calculated
based
on
20
shared
PCGs
mitogenomes
32
species,
subjected
purifying
selection
(Ka/Ks
<
1),
ccmC
ccmFn
underwent
positive
selection.
A
262
potential
editing
sites
26
identified.
Furthermore,
56
chloroplast-derived
fragments
ascertained
mitogenome,
ranging
from
30
858
mainly
located
across
IGS
(intergenic
spacer)
regions
or
rRNA
These
findings
verify
occurrence
intracellular
events
chloroplast
mitochondria.
relationship
supported
by
data
other
taxa
Rosaceae
family.
Understanding
characteristics
great
importance
promote
comprehension
its
study
provides
basis
breeding
Frontiers in Plant Science,
Год журнала:
2024,
Номер
15
Опубликована: Март 6, 2024
,
native
to
Guangdong,
Guangxi,
and
Hainan
provinces
in
China,
has
long
been
utilized
as
an
herbal
remedy
ancient
China.
In
this
study,
we
assembled
annotated
the
complete
mitochondrial
genome
(mitogenome)
of
Mitochondrial DNA Part B,
Год журнала:
2024,
Номер
9(4), С. 452 - 456
Опубликована: Апрель 2, 2024
Konjac
glucomannan
consists
of
D-mannose
and
D-glucose
units
is
a
hydrocolloid
obtained
from
the
corm
Amorphophallus
species.
Due
to
its
bioactive
properties,
biodegradability,
hydrophilic
ability,
widely
used
in
fields
food,
medicine,
industry.
species
have
been
cultivated
as
cash
crops
many
Asian
countries.
kachinensis
Engler
&
Gehrmann
1911
naturally
distributed
southwestern
China,
Laos,
northern
Thailand.
To
help
genetic
assessment
conservation
this
species,
first
chloroplast
genome
A.
was
sequenced
on
Illumina
sequencing
platform.
We
assembled
using
software
GetOrganelle
annotated
by
Geseq
Cpgavas
2.
The
173,330
bp
long,
average
GC
content
35%
(GenBank
accession
number:
PP072244).
contained
one
large
single
copy,
small
two
inverted
repeats,
with
lengths
92,030
bp,
15,118
33,091
respectively.
successfully
132
genes
across
genome,
which
consistent
other
phylogenetic
tree
indicates
sub-divergence
genus
main
groups
detected
among
eight
should
be
treated
distinct
evolutionarily
significant
when
making
strategies.
Our
study
enriched
resources
could
future
phylogeographic
studies,
protection,
utilization
wild
resources.
Mitochondrial DNA Part B,
Год журнала:
2024,
Номер
9(4), С. 522 - 526
Опубликована: Апрель 2, 2024
The
mountainous
region
of
southern
China
has
been
characterized
by
its
complicated
environment
and
topography.
Amorphophallus
kiusianus
Makino
1913
is
a
representative
species
extreme
habitat
preference
that
resides
mainly
in
this
region.
To
help
study
the
genetic
differentiation
mechanisms
A.
populations,
we
sequenced
first
chloroplast
genome
using
next-generation
sequencing.
was
166,269
bp
length
with
an
average
GC
content
36%
(GenBank
accession
number:
PP072243).
lengths
large
single-copy
(LSC),
small
(SSC),
two
inverted
repeats
(IRs)
were
90,701
bp,
14,802
31,383
respectively.
One
hundred
twenty-nine
genes
annotated
genome,
including
84
protein-coding
genes,
8
rRNA
37
tRNA
genes.
phylogenetic
tree
suggested
close
relationship
among
kiusianus,
yunnanensis,
coaetaneus.
reported
provides
valuable
genomic
resources
for
future
phylogeographic
research
kiusianus.