Plants,
Journal Year:
2024,
Volume and Issue:
13(5), P. 612 - 612
Published: Feb. 23, 2024
Erigeron
represents
the
third
largest
genus
on
Juan
Fernández
Islands,
with
six
endemic
species,
five
of
which
occur
exclusively
younger
Alejandro
Selkirk
Island
one
species
both
islands.
While
its
continental
sister
is
unknown,
Islands
appears
to
be
monophyletic
and
most
likely
evolved
from
South
American
progenitor
species.
We
characterized
complete
chloroplast
genomes
including
accessions
E.
fernandezia
each
Robinson
Crusoe
purposes
elucidating
molecular
evolution
phylogenetic
relationships.
found
highly
conserved
in
size,
gene
order
contents,
further
identified
several
mutation
hotspot
regions.
In
addition,
we
two
positively
selected
genes
(ccsA
ndhF)
among
The
plastome
sequences
confirmed
monophyly
islands
corroborated
previous
relationships
New
findings
current
study
include
(1)
major
lineages,
turricola–E.
luteoviridis
fernandezia–E.
ingae–E.
rupicola,
(2)
non-monophyly
occurring
islands,
(3)
alpine
ingae
complex.
American Journal of Botany,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 14, 2025
Magnoliids
are
a
strongly
supported
clade
of
angiosperms.
Previous
phylogenetic
studies
based
primarily
on
analyses
limited
number
mostly
plastid
markers
have
led
to
the
current
classification
magnoliids
into
four
orders
and
18
families.
However,
uncertainty
remains
regarding
placement
several
For
first
comprehensive
phylogenomic
analysis
as
whole,
we
sampled
235
species
from
199
(74%)
genera
representing
all
families
most
subfamilies
tribes.
We
analyzed
newly
generated
data
Angiosperms353
probe
set
using
both
coalescent
concatenation
testing
impact
multiple
filtering
alignment
strategies.
While
our
results
generally
provide
further
support
for
previously
established
relationships
in
whole
large
including
Annonaceae
Lauraceae,
they
also
new
evidence
ambiguous
relationships.
In
particular,
found
position
Hydnoraceae
sister
remainder
Piperales,
though
was
conflicting,
resolved
backbone
among
Myristicaceae.
Different
analytical
strategies
tended
rather
small
effects
branch
topology.
Although
some
by
low
gene
recovery
taxa
significant
tree
conflict
relationships,
this
study
represents
step
toward
reconstructing
evolutionary
history
major
lineage
Based
these
results,
present
an
updated
magnoliids,
recognizing
21
families,
summarizing
tribes,
describing
tribes
American Journal of Botany,
Journal Year:
2021,
Volume and Issue:
108(7), P. 1166 - 1180
Published: July 1, 2021
PREMISE
The
inference
of
evolutionary
relationships
in
the
species‐rich
family
Orchidaceae
has
hitherto
relied
heavily
on
plastid
DNA
sequences
and
limited
taxon
sampling.
Previous
studies
have
provided
a
robust
phylogenetic
framework,
which
was
used
to
classify
orchids
investigate
drivers
orchid
diversification.
However,
extent
based
genome
is
congruent
with
nuclear
been
only
poorly
assessed.
METHODS
We
inferred
higher‐level
likelihood
ASTRAL
analyses
294
low‐copy
genes
sequenced
using
Angiosperms353
universal
probe
set
for
75
species
(representing
69
genera,
16
tribes,
24
subtribes)
concatenated
analysis
78
264
(117
18
28
subtribes).
compared
informativeness
support
hypotheses.
RESULTS
Phylogenetic
data
sets
provides
well‐supported
that
are
highly
between
analyses.
Comparisons
gene
trees
supermatrix
tree
showed
mostly
congruent,
but
revealed
instances
strongly
supported
incongruence
both
shallow
deep
time.
individual
general
better
than
most
genes.
CONCLUSIONS
Our
study
first
phylogenomic
framework
an
assessment
intragenomic
discordance,
plastid‐nuclear
incongruence,
across
family.
results
also
demonstrate
what
long
known
rarely
thoroughly
documented:
can
contain
discordances,
this
must
be
reconciled
prior
interpretation
studies,
such
as
taxonomy,
biogeography,
character
evolution.
Botanical Journal of the Linnean Society,
Journal Year:
2021,
Volume and Issue:
197(1), P. 1 - 14
Published: Jan. 26, 2021
Abstract
Using
DNA
barcoding
for
species
identification
remains
challenging
many
plant
groups.
New
sequencing
approaches
such
as
complete
plastid
genome
may
provide
some
increased
power
and
practical
benefits
beyond
standard
barcodes.
We
undertook
a
case
study
comparing
to
discrimination
in
the
ecologically
economically
important
family
Lauraceae,
using
191
genomes
131
from
25
genera,
representing
largest
plastome
data
set
Lauraceae
date.
found
that
sequences
were
useful
correcting
errors
finding
new
cryptic
species.
However,
overall
only
able
discriminate
c.
60%
of
our
sample,
with
this
modest
improvement
40
50%
success
Beyond
discrimination,
revealed
complex
relationships
family,
12/25
genera
being
non-monophyletic
extensive
incongruence
relative
nuclear
ribosomal
DNA.
These
results
highlight
although
improving
phylogenetic
resolution
providing
species-level
insights,
partially
improve
reinforces
need
large-scale
among
closely
related
Molecular Ecology,
Journal Year:
2023,
Volume and Issue:
32(11), P. 2850 - 2868
Published: Feb. 27, 2023
The
evergreen
versus
deciduous
leaf
habit
is
an
important
functional
trait
for
adaptation
of
forest
trees
and
has
been
hypothesized
to
be
related
the
evolutionary
processes
component
species
under
paleoclimatic
change,
potentially
reflected
in
dynamic
history
broadleaved
forests
(EBLFs)
East
Asia.
However,
knowledge
about
shift
with
impact
change
using
genomic
data
remains
rare.
Here,
we
focus
on
Litsea
complex
(Lauraceae),
a
key
lineage
dominant
EBLFs,
gain
insights
into
how
shifted,
providing
origin
historical
dynamics
EBLFs
Asia
Cenozoic
climate
change.
We
reconstructed
robust
phylogeny
genome-wide
single-nucleotide
variants
(SNVs)
eight
clades
resolved.
Fossil-calibrated
analyses,
diversification
rate
shifts,
ancestral
habit,
ecological
niche
modelling
reconstruction
were
employed
estimate
its
pattern.
Taking
account
studies
other
plant
lineages
dominating
Asia,
it
was
revealed
that
prototype
probably
emerged
Early
Eocene
(55-50
million
years
ago
[Ma]),
facilitated
by
greenhouse
warming.
As
response
cooling
drying
Middle
Late
(48-38
Ma),
habits
evolved
Up
Miocene
(23
prevailing
Asian
monsoon
increased
extreme
seasonal
precipitation
accelerated
emergence
lineages,
ultimately
shaped
vegetation
resembling
today.
BMC Plant Biology,
Journal Year:
2025,
Volume and Issue:
25(1)
Published: March 6, 2025
Neocinnamomum
plants
are
considered
a
promising
feedstock
for
biodiesel
in
China,
due
to
the
richness
long-chain
fatty
acids
(LCFAs)
found
their
seeds.
However,
mitochondrial
genome
(mitogenome)
of
this
genus
has
not
yet
been
systematically
described,
and
exploration
species
relationships
within
using
mitogenome
sequences
is
also
an
uncharted
territory.
This
hindered
our
understanding
diversity
evolutionary
Neocinnamomum.
In
study,
total
24
individuals
representing
seven
distinct
taxa
from
were
subjected
Illumina
sequencing,
N.
delavayi
was
sequenced
Oxford
Nanopore
sequencing
technology.
We
successfully
assembled
delavayi,
which
778,066
bp
size
exhibits
single
circular
structure.
The
analysis
identified
659
dispersed
repeats,
211
simple
sequence
repeats
(SSRs),
30
tandem
mitogenome.
Additionally,
37
homologous
fragments,
totaling
9929
bp,
between
plastid
(plastome).
codons
41
protein-coding
genes
(PCGs)
had
preference
ending
A/T,
codon
usage
bias
majority
these
influenced
by
natural
selection
pressures.
Comparative
genomic
revealed
low
collinearity
significant
gene
rearrangements
species.
Phylogenetic
resulted
classification
into
six
clades,
contradicting
previous
findings
based
on
complete
plastomes
nuclear
ribosomal
cistron
(nrDNA).
PCGs
individuals,
86
mutation
events
identified,
included
three
indels
83
SNPs.
Notably,
ccmC
underwent
positive
pairwise
comparisons
pairs.
Furthermore,
748
RNA
editing
sites
predicted
study
enriches
knowledge
mitogenomes
family
Lauraceae,
provides
valuable
data
foundation
evolution
research,
genetic
resource
conservation,
molecular
breeding
Scientific Reports,
Journal Year:
2022,
Volume and Issue:
12(1)
Published: Jan. 21, 2022
The
genus
Ocotea
(Lauraceae)
includes
about
450
species,
of
which
90%
are
Neotropical,
while
the
rest
is
from
Macaronesia,
Africa
and
Madagascar.
In
this
study
we
present
first
complete
chloroplast
genome
sequences
seven
six
Neotropical
one
Macaronesia.
Genome
sizes
range
152,630
(O.
porosa)
to
152,685
bp
aciphylla).
All
plastomes
contain
a
total
131
(114
unique)
genes,
among
87
(80
encode
proteins.
order
genes
(if
present)
same
in
all
Lauraceae
examined
so
far.
Two
hypervariable
loci
were
found
LSC
region
(psbA-trnH,
ycf2),
three
SSC
(ycf1,
ndhH,
trnL(UAG)-ndhF).
pairwise
cp
genomic
alignment
between
taxa
showed
that
regions
more
variable
compared
IR
regions.
protein
coding
comprise
25,503-25,520
codons
examined.
most
frequent
amino
acids
encoded
leucine,
isoleucine,
serine.
SSRs
be
two
dioecious
species
than
four
bisexual
gynodioecious
(87
vs.
75-84
SSRs).
A
preliminary
phylogenetic
analysis
based
on
69
shows
as
sister
group
Cinnamomum
sensu
lato.
Sequence
divergence
appears
much
lower
closely
related,
likewise
species-rich
genera
Cinnamomum,
Lindera
Litsea.
BMC Plant Biology,
Journal Year:
2022,
Volume and Issue:
22(1)
Published: Jan. 13, 2022
Abstract
Background
The
East
Asian
subtropical
evergreen
broad-leaved
forests
(EBLFs)
harbor
remarkable
biodiversity.
However,
their
historical
assembly
remains
unclear.
To
gain
new
insights
into
the
of
this
biome,
we
generated
a
molecular
phylogeny
one
its
essential
plant
groups,
tribe
Perseeae
(Lauraceae).
Results
Our
plastid
tree
topologies
were
robust
to
analyses
based
on
different
regions
and
strategies
for
data
partitioning,
nucleotide
substitution
saturation,
gap
handling.
We
found
that
comprised
six
major
clades
began
colonize
EBLFs
Asia
in
early
Miocene.
diversification
rates
accelerated
twice
late
Conclusions
findings
suggest
intensified
precipitation
Miocene
may
have
facilitated
range
expansions
establishment
within
biome.
By
Miocene,
species
had
become
rapid.
Frontiers in Plant Science,
Journal Year:
2023,
Volume and Issue:
14
Published: July 7, 2023
The
genus
Neocinnamomum
is
considered
to
be
one
of
the
most
enigmatic
groups
in
Lauraceae,
mainly
distributed
tropical
and
subtropical
regions
Southeast
Asia.
contains
valuable
oilseed
medicinal
tree
species.
However,
there
are
few
studies
on
at
present,
its
interspecific
relationship
still
unclear.
In
order
explore
genetic
structure
evolutionary
characteristics
chloroplast
genome
resolve
species
relationships
within
genus,
comparative
genomic
phylogenetic
analyses
were
performed
whole
sequences
51
samples
representing
seven
taxa.
size
ranged
from
150,753-150,956
bp,
with
a
GC
content
38.8%-38.9%.
A
total
128
genes
annotated
genome,
including
84
protein
coding
genes,
8
rRNA
36
tRNA
genes.
Between
71-82
SSRs
detected,
among
which
A/T
base
repeats
common.
contained
31
preferred
codons.
Three
highly
variable
regions,
trnN
-
GUU
ndhF
,
petA
psbJ
ccsA
ndhD
identified
Pi
values
>
0.004.
Based
tree,
taxa
determined.
N.
delavayi
fargesii
closely
related
species,
lecomtei
was
as
basal
taxon.
this
study,
sequence
variation
genomes
revealed,
clarified.
results
study
will
provide
reference
for
subsequent
molecular
marker
development
research
.
RSC Advances,
Journal Year:
2024,
Volume and Issue:
14(15), P. 10481 - 10498
Published: Jan. 1, 2024
We
introduce
a
liquid
chromatography
-
mass
spectrometry
with
data-independent
acquisition
(LC-MS/DIA)-based
strategy,
specifically
tailored
to
achieve
comprehensive
and
reliable
glycosylated
flavonoid
profiling.
This
approach
facilitates
in-depth
simultaneous
exploration
of
all
detected
precursors
fragments
during
data
processing,
employing
the
widely-used
open-source
MZmine
3
software.
It
was
applied
dataset
six
Ocotea
plant
species.
framework
suggested
49
flavonoids
potentially
newly
described
for
these
species,
alongside
45
known
features
within
genus.
Flavonols
kaempferol
quercetin,
both
exhibiting
O-glycosylation
patterns,
were
particularly
prevalent.
Gas-phase
fragmentation
reactions
further
supported
findings.
For
first
time,
apigenin
flavone
backbone
also
annotated
in
most
examined
Apigenin
derivatives
found
mainly
C-glycoside
form,
O.
porosa
displaying
highest
:
flavonol
ratio.
The
allowed
an
unprecedented
detection
quercetin
it
has
underscored
untapped
potential
LC-MS/DIA
broad
Our
study
more
than
50
backbones
each
surpassing
current
literature.