Research Square (Research Square),
Год журнала:
2023,
Номер
unknown
Опубликована: Июль 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.
Abstract
In
this
study,
we
investigated
the
codon
bias
of
twelve
mitochondrial
core
protein
coding
genes
(PCGs)
in
eight
Pleurotus
strains,
two
which
are
from
same
species.
The
results
revealed
that
codons
all
strains
had
a
preference
for
ending
A/T.
Furthermore,
correlation
between
base
compositions
and
adaptation
index
(CAI),
(CBI)
frequency
optimal
(FOP)
indices
was
also
detected,
implying
influence
composition
on
bias.
P.
ostreatus
species
were
found
to
have
differences
various
indicators.
average
effective
number
(ENC)
PCGs
be
less
than
35,
indicating
strong
.
neutrality
plot
analysis
PR2-Bias
further
suggested
natural
selection
plays
an
important
role
Additionally,
six
ten
(ΔRSCU
>
0.08
RSCU
1)
identified
with
UGU
ACU
being
most
widely
used
Finally,
based
combined
sequence
value,
genetic
relationship
different
deduced,
showing
large
variations
them.
This
research
has
improved
our
understanding
synonymous
usage
characteristics
evolution
fungal
group.
Mitochondrial DNA Part B,
Год журнала:
2025,
Номер
10(4), С. 292 - 297
Опубликована: Март 13, 2025
Tyromyces
fissilis
(Berk.
&
M.A.Curtis)
Donk
1933,
a
globally
renowned
white-rot
basidiomycete
belonging
to
the
Polyporales
order,
holds
significant
potential
for
lignin
degradation,
yet
its
mitochondrial
genome
has
received
comparatively
little
attention.
Our
study
concentrates
on
specimen
designated
T.
NEFU_01,
sourced
from
Forest
Botanical
Garden
in
Heilongjiang
Province,
China.
Utilizing
next-generation
sequencing
(NGS)
technology,
we
have
successfully
delineated
complete
of
this
isolate.
The
is
composed
15
protein-coding
genes
(PCGs),
an
array
24
transfer
RNAs
(tRNAs),
and
pair
ribosomal
(rRNAs),
encompassing
total
163,380
base
pairs
(bp).
Additionally,
encodes
28
LAGLIDADG-
10
GIY-YIG-homing
endonucleases.
nucleotide
composition
characterized
by
adenine
(A)
at
37.02%,
cytosine
(C)
12.91%,
guanine
(G)
13.04%,
thymine
(T)
37.03%,
culminating
GC
content
25.95%.
Subsequently,
undertook
phylogenetic
analysis,
employing
dataset
25
genomes
construct
tree.
This
research
represents
first
comprehensive
foray
into
understanding
relationships
with
Basidiomycete
kin,
particularly
sister-group
relationship
Phlebia
radiata
Fr.
(1821),
thereby
laying
substantive
groundwork
subsequent
evolutionary
taxonomic
studies
within
mycological
cohort.
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.
Plants,
Год журнала:
2024,
Номер
13(4), С. 468 - 468
Опубликована: Фев. 6, 2024
Heat
shock
protein
20
(HSP20)
serves
as
a
chaperone
and
plays
roles
in
numerous
biological
processes,
but
the
codon
usage
bias
(CUB)
of
its
genes
has
remained
unexplored.
This
study
identified
140
HSP20
from
four
cruciferous
species,
Arabidopsis
thaliana,
Brassica
napus,
rapa,
Camelina
sativa,
that
were
Ensembl
plants
database,
we
subsequently
investigated
their
CUB.
As
result,
base
composition
analysis
revealed
overall
GC
content
was
below
50%.
The
significantly
correlated
with
constituents
at
three
positions,
implying
both
mutation
pressure
natural
selection
might
contribute
to
relatively
high
ENc
values
suggested
CUB
species
weak.
Subsequently,
exhibited
negative
correlation
gene
expression
levels.
Analyses,
including
ENc-plot
analysis,
neutral
PR2
bias,
mainly
shaped
patterns
these
species.
In
addition,
total
12
optimal
codons
(ΔRSCU
>
0.08
RSCU
1)
across
A
neighbor-joining
phylogenetic
based
on
coding
sequences
(CDS)
showed
strictly
distinctly
clustered
into
subfamilies.
Principal
component
cluster
relative
synonymous
(RSCU)
supported
fact
pattern
consistent
genetic
relationship
level
(or)
These
results
will
not
only
enrich
resource
also
advance
our
understanding
genes,
which
may
underlie
theoretical
basis
for
exploration
evolutionary
pattern.
The
sect.
Chrysantha
Chang
of
plants
with
yellow
flowers
Camellia
species
as
the
"Queen
Tea
Family",
most
these
are
narrowly
distributed
endemics
China
and
currently
listed
Grde-II
in
National
Key
Protected
Wild
Plant
China.
They
commercially
important
horticultural
medicinal
scientific
research
value.
However,
study
genetics
still
its
infancy,
to
date,
mitochondrial
genome
has
been
unexplored.
Mitochondria
are
crucial
for
energy
production
in
plant
tissues,
but
their
quantity
and
activity
vary
different
tissues
developmental
processes.
Determining
the
factors
underlying
differential
molecular
evolutionary
rates
has
long
been
a
central
question
biology,
with
expression
level
emerging
as
prime
predictor.
Although
we
have
previously
observed
an
anti-correlation
between
(E)
rate
(R)
chloroplast
genes,
it
remains
unclear
whether
such
exists
mitochondrial
genes.
Ophioglossum
vulgatum
is
typical
belonging
to
Ophioglossaceae,
characterized
by
its
unique
morphology
only
single
leaf
above
ground.
It
holds
significant
scientific
medicinal
value.
Using
genome
transcriptome
data
of
O.
vulgatum,
first
analyzed
correlation
gene
expression,
codon
usage
bias,
tissues.
Our
findings
indicated
that
was
strongest
stem
leaf,
while
weakest
sporangium
root.
Kruskal-Wallis
tests
revealed
differences
across
various
tissue
types.
Codon
bias
influenced
both
mutation
selection,
selection
exerting
greater
impact.
The
Spearman's
rank
coefficients
adaptation
index
levels
sporangium,
stem,
root
were
0.1178,
0.3926,
0.4463,
0.2945,
respectively,
significance
(P
<
0.05).
nonsynonymous
substitution
(dN)
-0.0840,
-0.1786,
-0.1714,
-0.0857,
yet
none
statistically
significant.
coefficient
synonymous
(dS)
negative,
whereas
those
dS
positive,
although
they
not
dN/dS
ratio
exhibited
negative
For
time,
our
study
well
rates,
vulgatum.
Moreover,
also
provide
novel
insights
into
understanding
effects
on
patterns.
Arthropod Systematics & Phylogeny,
Год журнала:
2024,
Номер
82, С. 133 - 150
Опубликована: Март 22, 2024
Longhorn
beetles
(Cerambycidae)
play
a
vital
role
in
global
ecosystems.
Some
of
them
contribute
to
nutrient
cycling
and
pollination,
while
others,
pose
threat
forestry
production.
Despite
their
ecological
importance,
there
has
been
lack
comprehensive
analyses
on
the
mitochondrial
genomes
Cerambycidae
beetles.
In
this
study,
we
have
conducted
genome
sequencing
annotation
for
four
beetles:
Monochamus
sutor
,
guerryi
galloprovincialis
latefasciatus
.
Our
analysis
revealed
high
degree
conservation
these
genomes,
with
rare
gene
rearrangements
observed
across
family.
Additionally,
notable
bias
towards
AT
content
was
identified,
most
genes
using
ATN
as
start
codon
TAA
stop
codon.
Except
trnS1,
all
tRNA
showed
typical
cloverleaf
secondary
structures.
Phylogenetic
IQ-TREE
Phylobayes
consistently
produced
congruent
topologies.
At
level
analyses,
our
results
highlighted
remarkable
COX1
gene.
Furthermore,
at
species
level,
strong
adaptability
Spondylidinae
Lepturinae
subfamilies.
We
also
offer
insights
into
contentious
aspects
phylogeny.
Overall,
research
contributes
deeper
understanding
phylogeny
evolution
Cerambycidae,
laying
groundwork
future
population
genetic
investigations.
Forests,
Год журнала:
2023,
Номер
14(11), С. 2136 - 2136
Опубликована: Окт. 26, 2023
Hemlocks
(Pinaceae:
Tsuga)
are
widely
distributed
in
North
America
and
East
Asia,
forming
a
reticulate
evolutionary
structure
Asia
with
significant
ecological
importance.
To
clarify
the
chloroplast
genome
characteristics
phylogenetic
relationships
among
Tsuga
species,
we
analyzed
genomes
of
T.
chinensis
var.
tchekiangensis,
chinensis,
diversifolia,
dumosa,
forrestii,
sieboldii,
performing
associated
analyses.
The
results
reveal
that
lengths
six
species
vary
from
120,520
to
121,010
bp,
encompassing
about
108
112
genes,
including
35/32
tRNA
genes
4
rRNA
genes.
A
codon
usage
analysis
highlighted
preference
for
A/U-ending
codons,
all
nucleotide
types
have
A/T
bases
prevalence
mononucleotides.
Notably,
exhibit
inverted
repeat
(IR)
contractions
possess
unique
hexanucleotides
absent
other
Pinaceae,
potentially
making
them
more
susceptible
gene
recombination
or
rearrangement
during
evolution.
While
most
variations
observed
non-coding
regions,
particularly
intergenic
fragments,
substantial
variation
sites
also
present
within
tree,
constructed
using
genomes,
substantiates
sister
taxa
relationship
between
Nothotsuga.
Furthermore,
it
confirms
tchekiangensis
exhibits
closer
forrestii
than
chinensis.
These
findings
not
only
provide
partial
evidence
may
constitute
monophyletic
but
underscore
necessity
reevaluating
taxonomic
status
tchekiangensis.
In
addition,
while
RSCU
cluster
is
basically
consistent
analysis,
highlights
distinct
differentiation
Nothotsuga
Tsuga.
This
study
provides
molecular-level
classification
Pinaceous
genera
via
analyses
offers
compelling
further
exploring
delimitation
hemlocks
Asia.
