Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications
Frontiers in Plant Science,
Год журнала:
2024,
Номер
15
Опубликована: Апрель 30, 2024
The
genus
Argentina
Hill
belongs
to
the
tribe
Potentilleae
Sweet
and
contains
approximately
75
species
predominantly
distributed
in
Sino-Himalayan
region
Malesian
archipelago.
So
far
we
have
less
knowledge
on
phylogenetic
relationships
within
owing
limited
sampling
of
taxa
or
gene
fragments
previous
studies.
Moreover,
date
there
is
no
study
from
perspective
comparative
chloroplast
(cp)
genomics.
Here
performed
genomic
analyses
cp
genomes
39
accessions
representing
18
.
presented
typical
quadripartite
structure,
with
sizes
ranging
155
096
bp
157
166
bp.
contained
a
set
112
unique
genes,
comprising
four
ribosomal
RNA
(rRNA)
30
transfer
(tRNA)
as
well
78
protein-coding
genes
(PCGs).
genome
organization,
content
order
were
highly
conserved,
but
some
visible
divergences
present
IR/SC
boundary
regions.
Ten
regions
(
trnH-GUG-psbA,
trnG-GCC-trnfM-CAU,
trnD-GUC-trnY-GUA,
rpl32-trnL-UAG,
atpH-atpI,
rps16-trnQ-UUG,
trnS-GCU-trnG-UCC,
ndhF-rpl32,
trnR-UCU-atpA,
accD-psaI
)
identified
excellent
candidate
DNA
markers
for
future
studies
identification,
population
genetics
phylogeny
Our
results
indicated
that
monophyletic.
In
current
sampling,
A.
smithiana
-
anserina
clade
was
sister
remainder
corroborated
taxonomic
treatments
phanerophlebia
micropetala
Sibbaldia
L.
showed
close
among
stenophylla
,
microphylla
taliensis
tatsienluensis
congruent
based
morphology
these
species.
Twenty-six
rps3,
rps15,
rps16,
rps19,
rpl16,
rpl20,
rpl22,
rpoA,
rpoB,
rpoC1,
rpoC2,
atpA,
atpF,
psbB,
psbF,
ndhA,
ndhB,
ndhC,
ndhD,
ndhF,
rbcL,
accD,
ccsA,
matK,
ycf1,
ycf2
sites
under
positive
selection,
adaptive
evolution
might
played
crucial
roles
adaptation
harsh
mountain
environment.
This
will
facilitate
work
taxonomy,
phylogenetics,
Язык: Английский
Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics
Plant Diversity,
Год журнала:
2023,
Номер
46(2), С. 219 - 228
Опубликована: Авг. 3, 2023
Here,
we
infer
the
historical
biogeography
and
evolutionary
diversification
of
genus
Lilium.
For
this
purpose,
used
complete
plastomes
64
currently
accepted
species
in
Lilium
(14
were
newly
sequenced)
to
recover
phylogenetic
backbone
a
time-calibrated
framework
estimate
biogeographical
history
scenarios
rates
Our
results
suggest
that
ancient
climatic
changes
geological
tectonic
activities
jointly
shaped
distribution
range
drove
radiation
Lilium,
including
Middle
Miocene
Climate
Optimum
(MMCO),
late
global
cooling,
as
well
successive
uplift
Qinghai-Tibet
Plateau
(QTP)
strengthening
monsoon
climate
East
Asia
during
Pliocene.
This
case
study
suggests
unique
events
Neogene
Asia,
particular
QTP
enhancement
monsoonal
climate,
may
have
played
an
essential
role
formation
uneven
plant
diversity
Northern
Hemisphere.
Язык: Английский
Comparative chloroplast genome analysis of <i>Camellia oleifera</i> and <i>C. meiocarpa</i>: phylogenetic relationships, sequence variation and polymorphic markers
Tropical Plants,
Год журнала:
2024,
Номер
3(1), С. 0 - 0
Опубликована: Янв. 1, 2024
Tea-oil
Camellia,
a
prominently
woody
oil
crop,
serves
as
crucial
source
of
edible
oil,
protein
feed,
and
industrial
raw
materials.
Notably,
C.
Oleifera
meiocarpa
yield
higher
production
larger
cultivation
areas
than
other
Camellia
species.
However,
the
taxonomy
phylogenetic
relationship
between
these
species
remain
elusive,
complicating
their
commercial
application.
Here,
we
sequenced
analyzed
complete
chloroplast
genomes
two
species,
compared
them
with
related
developed
DNA
markers
to
distinguish
them.
The
genome
was
157,009
bp
(HZP)
156,549
(CKX)
156,512
(XG)
in
length.
Comparative
analysis
indicated
that
distinct
differences
HZP
CKX
(or
XG)
XG.
repetitive
sequences
interspecific
variations
among
showed
number
distribution
XG
were
smaller
those
HZP.
Phylogenetic
not
closely
oleifera.
A
total
56
pairs
primers
test
polymorphism
After
PCR
sequencing
verification,
detected
target
17
primers.
data
derived
from
newly
are
invaluable
for
understanding
relationships,
assessing
genetic
diversity
tea-oil
germplasm
resources.
Язык: Английский
The Complete Chloroplast Genome of Trigonotis cavaleriei (Boraginaceae) Analysis and Phylogenetics from Guizhou
Russian Journal of Plant Physiology,
Год журнала:
2025,
Номер
72(2)
Опубликована: Апрель 1, 2025
Язык: Английский
Comparative Analysis of Plastomes of Artemisia and Insights into the Infra-Generic Phylogenetic Relationships Within the Genus
Genes,
Год журнала:
2025,
Номер
16(6), С. 659 - 659
Опубликована: Май 29, 2025
Background:
Artemisia
is
a
large
and
complex
genus
comprising
about
500
species.
Currently,
only
limited
number
of
plastomes
(the
chloroplast
genome)
are
available.
Their
structures
have
not
been
comparatively
analyzed,
phylogenetic
backbone
based
on
plastome-scale
data
still
lacking.
This
situation
has
greatly
hindered
our
understanding
the
plastome
variation
patterns
infra-generic
relationships
genus.
Methods:
We
newly
sequenced
34
representing
30
species
three
varieties.
Combining
this
with
previously
published
plastomes,
we
analyzed
their
structure
constructed
using
protein-coding
sequences
(CDS)
plastomes.
Results:
Our
analyses
indicated
that
conserved
in
terms
structure,
GC
content,
gene
number,
order.
The
sequence
divergence
higher
LSC
SSC
regions
than
IR
regions.
Three
genes
four
non-coding
regions,
i.e.,
accD,
petG,
ycf1,
rpoC1-rpoC2,
rpoC2-rps2,
trnG(UCC)-trnfM(CAU),
ndhG-ndhI,
were
highly
diverse
could
be
chosen
as
candidates
DNA
barcodes.
Phylogenetic
trees
divided
into
several
clades,
all
main
subgenera
monophyletic.
Additionally,
position
A.
stracheyi
controversial.
Conclusions:
Plastomes
can
provide
important
information
for
constructions.
study
provides
insights
within
also
lays
foundation
future
evolutionary
studies
Язык: Английский
Phylogeny, biogeography, and character evolution of Anaphalis (Gnaphalieae, Asteraceae)
Frontiers in Plant Science,
Год журнала:
2024,
Номер
15
Опубликована: Фев. 7, 2024
The
HAP
clade,
mainly
including
Helichrysum
Mill,
Anaphalis
DC.,
and
Pseudognaphalium
Kirp.,
is
a
major
component
of
tribe
Gnaphalieae
(Asteraceae).
In
this
represents
the
largest
genus
Asian
Gnaphalieae.
intergeneric
relationships
among
its
related
genera
infrageneric
taxonomy
are
complex
remain
controversial.
However,
there
few
studies
that
have
focused
on
these
issues.
Herein,
based
current
most
comprehensive
sampling
especially
,
we
conducted
phylogenetic
analyses
using
chloroplast
(cp)
genome
nuclear
ribosomal
DNA
(nrDNA)
to
evaluate
within
test
monophyly
examine
genus.
Meanwhile,
morphological
characters
were
verified
determine
circumscription
system
.
Additionally,
biogeographical
history,
diversification
processes,
evolution
crucial
estimated
inferred.
Our
suggested
polyphyletic
because
it
nested
with
Two
four
main
clades
identified
in
cp
nrDNA
trees,
respectively.
Compared
trees
more
effective
for
resolution.
After
comprehensively
analyzing
evidence,
was
concluded
achene
surface
ornamentation
leaf
base
showed
less
homoplasy
supported
two
lineages
inferred
from
genome.
indicated
clade
underwent
rapid
late
Miocene
Pliocene.
appeared
originated
Africa,
then
spread
Western
Southern
Asia,
subsequently
moved
into
Southwestern
China
forming
diversity
center.
dispersal
patterns
different.
One
dispersed
around
world,
except
Africa
South
America.
other
one
Eastern
Southeastern
Asia
ancestral
origin
region.
Язык: Английский
Comparative analysis of Artemisia plastomes and insights into the infra-generic phylogenetic relationships of the genus
Опубликована: Июль 16, 2024
Abstract
Background
The
genus
Artemisia
is
a
taxonomically
difficult
group
comprising
400–500
species
mainly
distributed
in
northern
hemisphere.
Only
limited
number
of
plastomes
are
currently
available.
Their
structure
has
not
been
comparatively
analyzed,
and
the
phylogenetic
backbone
based
on
plastome-scale
data
reported
with
dense
taxon
sampling.
This
situation
greatly
hindered
our
understanding
plastome
variation
patterns
infra-generic
relationships
genus.
With
advancement
next
generation
sequencing
technologies,
it
becoming
easier
to
obtain
analyze
plastome,
use
construct
phylogeny.
Results
In
this
study,
we
newly
sequenced
34
representing
30
three
varieties.
Combing
38
previously
published
plastomes,
total
72
complete
were
analyzed.
results
indicated
that
conserved
terms
structure,
GC
content,
gene
order.
All
have
typical
quadripartite
87
protein
coding,
37
tRNA,
8
rRNA
genes.
IR
regions
similar
length
among
compared
generic
more
than
intergenic
spacer
regions.
sequence
divergence
higher
LSC
SSC
Three
protein-coding
genes
four
non-coding
regions,
i.e.,
accD,
petG,
ycf1,
rpoC1-
rpoC2,
rpoC2-
rps2,
trnG(UCC)-
trnfM(CAU),
ndhG-
ndhI,
found
be
highly
diverse,
could
chosen
as
candidates
DNA
barcode.
Phylogenetic
constructed
using
coding
divided
into
several
clades
did
match
previous
divisions
Artemisia,
subgenera
monophyletic.
Furthermore,
they
also
inconsistent
those
nuclear
markers.
And
position
A.
stracheyi
still
controversial.
Conslusions
study
reveals
conservative,
especially
CDS
further
confirmed
natural.
lay
foundation
for
future
evolutionary
studies
Artemisia.
Язык: Английский
Complete Chloroplast Genome Sequences of Two Ehretia Trees (Ehretia cymosa and Ehretia obtusifolia): Genome Structures and Phylogenetic Analysis
Forests,
Год журнала:
2023,
Номер
14(7), С. 1486 - 1486
Опубликована: Июль 20, 2023
Ehretiaceae
is
a
family
in
the
order
Boraginales.
It
contains
more
than
150
species.
The
classification
has
remained
elusive
and
changed
over
time
from
subfamily
to
family,
or
vice
versa.
In
this
paper,
we
sequenced,
characterized,
analyzed
complete
chloroplast
(cp)
genomes
of
Ehretia
cymosa
obtusifolia,
their
cp
were
compared
those
related
length
E.
was
156,328
bp,
whereas
that
obtusifolia
155,961
bp.
Each
genome
contained
114
genes,
including
80
protein-coding
4
rRNA
30
tRNA
genes.
Repeat
analysis
revealed
complement,
forward,
palindromic,
reverse
repeats
present
both
Simple
sequence
repeat
showed
comprise
141
139
microsatellites,
respectively.
Phylogenetic
based
on
Bayesian
maximum
likelihood
analyses
divided
Boraginales
into
two
well-supported
clades.
first
clade
includes
single
(Boraginaceae),
second
three
families
(Ehretiaceae,
Cordiaceae,
Heliotropiaceae).
This
study
provides
valuable
genomic
resources
insights
evolutionary
relationships
within
Язык: Английский