Scientific Reports,
Год журнала:
2021,
Номер
11(1)
Опубликована: Июнь 3, 2021
Abstract
Adrinandra
megaphylla
Hu
is
a
medicinal
plant
belonging
to
the
genus,
which
well-known
for
its
potential
health
benefits
due
bioactive
compounds.
This
study
aimed
assemble
and
annotate
chloroplast
genome
of
A.
as
well
compare
it
with
previously
published
cp
genomes
within
genus.
The
was
reconstructed
using
de
novo
reference-based
assembly
paired-end
reads
generated
by
long-read
sequencing
total
genomic
DNA.
size
156,298
bp,
comprised
large
single-copy
(LSC)
region
85,688
small
(SSC)
18,424
pair
inverted
repeats
(IRa
IRb)
26,093
bp
each;
51
SSRs
48
repeat
structures
were
detected.
includes
131
functional
genes,
containing
86
protein-coding
37
transfer
RNA
8
ribosomal
genes.
indicated
that
gene
content
structure
are
highly
conserved.
phylogenetic
reconstruction
complete
sequences,
matK
trnL
genes
from
Pentaphylacaceae
species
exhibited
genetic
relationship.
Among
them,
sequence
better
candidate
resolution.
first
report
.
Camellia
reticulata
Lindl.
(C.
reticulata)
is
the
tallest
ornamental
camellia
globally,
with
wild
populations
comprising
a
polyploid
complex
of
diploids
(2×),
tetraploids
(4×),
and
hexaploids
(6×).
The
type
specimen
C.
heteroploid
hexaploid
derived
from
2
×
ancestors,
including
pitardii,
saluenensis,
reticulata.
Currently,
limited
information
exists
regarding
evolutionary
characteristics
chloroplast
genomes
at
different
ploidy
levels,
phylogenetic
position
4
remains
unclear.
This
study
sequenced,
assembled,
annotated
reticulata,
comparing
them
those
6
other
closely
related
species.
results
indicated
that
genome
sizes
ranged
156,519
to
156,927
bp,
gene
counts,
distributions,
GC
content,
codon
usage
being
similar
across
levels.
ycf1
exhibited
significant
differentiation
among
species,
was
identified
as
candidate
for
adaptive
evolution
in
Additionally,
11
highly
differentiated
intergenic
regions
were
identified,
six
hotspots
variation
can
serve
molecular
markers
genetic
studies
populations.
Analysis
selection
pressure
four
genes
under
positive
selection.
Phylogenetic
analysis
revealed
along
mairei,
formed
well-supported
clade.
distances
between
its
three
ancestors
relatively
small.
mairei
may
have
participated
allopolyploidization
both
potential
independent
classification.
These
findings
provide
valuable
insights
into
alterations
following
allopolyploidization,
establishing
crucial
foundation
understanding
systematic
history
various
levels
Frontiers in Plant Science,
Год журнала:
2021,
Номер
11
Опубликована: Фев. 11, 2021
In
this
study,
we
assembled
and
annotated
the
chloroplast
(cp)
genome
of
Euonymus
species
fortunei
,
phellomanus
maackii
performed
a
series
analyses
to
investigate
gene
structure,
GC
content,
sequence
alignment,
nucleic
acid
diversity,
with
objectives
identifying
positive
selection
genes
understanding
evolutionary
relationships.
The
results
indicated
that
cp
was
156,860–157,611bp
in
length
exhibited
typical
circular
tetrad
structure.
Similar
majority
angiosperm
genomes,
yielded
large
single-copy
region
(LSC)
(85,826–86,299bp)
small
(SSC)
(18,319–18,536bp),
separated
by
pair
sequences
(IRA
IRB;
26,341–26,700bp)
same
encoding
but
opposite
directions.
130–131
genes,
including
85–86
protein
coding
37
tRNA
eight
rRNA
contents
37.26–37.31%.
content
variable
among
regions
highest
inverted
repeat
(IR)
region.
IR
boundary
happened
expanding
resulting
rps19
entered
into
doubled
completely.
Such
fluctuations
at
border
positions
might
be
helpful
determining
relationships
.
simple-sequence
repeats
(SSRs)
were
composed
primarily
single
nucleotides
(A)n
(T)n,
mostly
10–12bp
length,
an
obvious
A/T
bias.
We
identified
several
loci
suitable
polymorphism
potential
use
as
molecular
markers
for
inferring
phylogeny
within
genus
Signatures
seen
rpoB
genes.
Based
on
data
from
whole
genome,
common
copy
LSC,
SSC,
regions,
constructed
tree
related
species,
which
consistent
traditional
taxonomic
classifications.
It
showed
E.
sister
japonicus
whereby
appeared
hamiltonianus
Our
study
provides
important
genetic
information
support
further
investigations
phylogenetic
development
adaptive
evolution
species.
Scientific Reports,
Год журнала:
2021,
Номер
11(1)
Опубликована: Июнь 3, 2021
Abstract
Adrinandra
megaphylla
Hu
is
a
medicinal
plant
belonging
to
the
genus,
which
well-known
for
its
potential
health
benefits
due
bioactive
compounds.
This
study
aimed
assemble
and
annotate
chloroplast
genome
of
A.
as
well
compare
it
with
previously
published
cp
genomes
within
genus.
The
was
reconstructed
using
de
novo
reference-based
assembly
paired-end
reads
generated
by
long-read
sequencing
total
genomic
DNA.
size
156,298
bp,
comprised
large
single-copy
(LSC)
region
85,688
small
(SSC)
18,424
pair
inverted
repeats
(IRa
IRb)
26,093
bp
each;
51
SSRs
48
repeat
structures
were
detected.
includes
131
functional
genes,
containing
86
protein-coding
37
transfer
RNA
8
ribosomal
genes.
indicated
that
gene
content
structure
are
highly
conserved.
phylogenetic
reconstruction
complete
sequences,
matK
trnL
genes
from
Pentaphylacaceae
species
exhibited
genetic
relationship.
Among
them,
sequence
better
candidate
resolution.
first
report
.
