Research Square (Research Square),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Dec. 7, 2022
Abstract
Background
Lilium
(Liliaceae)
is
an
economically
important
genus
with
great
medicinal,
ornamental,
and
edible
values,
however
evolutionary
history
of
the
remains
poorly
understood
due
to
lack
robust
phylogeny.
Based
on
a
large
plastome
data
set,
this
study
aims
recover
backbone
phylogeny
infer
its
historical
biogeography
diversification.
Results
Complete
plastomes
representing
50
currently
accepted
species
in
were
sampled
for
phylogenetic
analysis,
among
which,
14
newly
sequenced
study.
Under
time-calibrated
framework,
biogeographic
scenarios
diversification
explored.
Phylogenetic
analysis
recovered
,
which
most
nodes
fully
supported;
however,
failed
resolve
all
intrageneric
sections
as
monophyletic.
Ancestral
area
reconstruction
proposed
that
ancestor
might
widely
distribute
throughout
temperate
regions
Northern
Hemisphere,
has
experienced
multiple
dispersal,
extinction,
vicariance
events
during
course.
The
rate
sharply
accelerated
since
late
Miocene
(
ca.
9
Ma)
kept
increasing
Pliocene
Pleistocene.
Conclusions
results
suggest
ancient
climatic
changes
geological
tectonic
activities,
such
Middle
Climate
Optimum
(MMCO),
global
cooling,
well
successive
uplift
Qinghai-Tibetan
Plateau
(QTP)
enhancement
monsoonal
climate
East
Asia
Pliocene,
jointly
shaped
distribution
range
drove
radiation
.
Resulted
from
radiative
divergence
distant
dispersal
events,
may
have
incomplete
lineage
sorting
(ILS)
morphological
convergence.
QTP
dramatically
triggered
species,
accounting
higher
diversity
than
Central
Asia,
Europe,
North
America.
findings
shed
light
crucial
role
unique
Neogene
establishment
climate,
shaping
uneven
plant
Hemisphere.
BMC Plant Biology,
Journal Year:
2024,
Volume and Issue:
24(1)
Published: Jan. 24, 2024
Abstract
Background
The
genus
Sanicula
L.
is
a
unique
perennial
herb
that
holds
important
medicinal
values.
Although
the
previous
studies
on
provided
us
with
good
research
basis,
its
taxonomic
system
and
interspecific
relationships
have
not
been
satisfactorily
resolved,
especially
for
those
endemic
to
China.
Moreover,
evolutionary
history
of
this
also
remains
inadequately
understood.
plastid
genomes
possessing
highly
conserved
structure
limited
rate
proved
be
an
effective
tool
studying
plant
phylogeny
evolution.
Results
In
current
study,
we
newly
sequenced
assembled
fifteen
complete
plastomes.
Combined
two
previously
reported
plastomes,
performed
comprehensively
phylogenomics
analyses
gain
novel
insights
into
genus.
comparative
results
indicated
seventeen
plastomes
exhibited
high
degree
conservation
similarity
in
terms
their
structure,
size,
GC
content,
gene
order,
IR
borders,
codon
bias
patterns
SSRs
profiles.
Such
as
all
them
displayed
typical
quadripartite
including
large
single
copy
region
(LSC:
85,074–86,197
bp),
small
(SSC:
17,047–17,132
bp)
separated
by
pair
inverted
repeat
regions
(IRs:
26,176–26,334
bp).
And
had
similar
boundaries
adjacent
genes
were
identical.
rps
19
was
located
at
junction
LSC/IRa,
IRa/SSC
between
trn
N
ndh
F
gene,
ycf
1
appeared
SSC/IRb
IRb/LSC
boundary
rpl
12
H
gene.
Twelve
specific
mutation
hotspots
(
atp
F,
cem
A,
acc
D,
22,
rbc
L,
mat
K,
1,
-psb
4
-cem
L
-acc
E
-trn
T
G
R)
identified
can
serve
potential
DNA
barcodes
species
identification
within
.
Furthermore,
data
Internal
Transcribed
Spacer
(ITS)
sequences
reconstruct
Sanicula.
tree
topologies
incongruent,
both
strong
evidence
supporting
monophyly
Saniculoideae
Apioideae.
addition,
sister
groups
Apioideae
strongly
suggested.
involved
study
clustered
clade,
Eryngium
together.
However,
it
clearly
observed
sections
respectively
recovered
monophyletic
group.
Molecular
dating
analysis
explored
origin
occurred
during
late
Eocene
period,
approximately
37.84
Ma
(95%
HPD:
20.33–52.21
Ma)
years
ago
diversification
early
Miocene
18.38
10.68–25.28
Ma).
Conclusion
plastome-based
ITS-based
generated
incongruences,
which
may
attributed
event
hybridization/introgression,
incomplete
lineage
sorting
(ILS)
chloroplast
capture.
Our
highlighted
power
plastome
significantly
improve
phylogenetic
supports
resolutions,
efficiently
explore
Miocene,
largely
influenced
prevalence
East
Asian
monsoon
uplift
Hengduan
Mountains
(HDM).
summary,
our
provides
evolution,
relationships,
framework
evolution
Frontiers in Plant Science,
Journal Year:
2024,
Volume and Issue:
15
Published: March 27, 2024
The
former
genus
Nomocharis
,
which
has
been
merged
as
a
clade
within
the
Lilium
(Liliaceae),
represents
one
of
most
complicated
and
unclear
groups
included
in
latter.
Research
on
members
quite
limited
due
to
sampling
difficulties
caused
by
its
selective
environmental
preferences.
In
this
study,
we
propose
new
species
clade,
liangiae
further
bridge
connecting
with
other
Lilium.
We
conducted
morphological
clustering,
phylogenetic,
comparative
genomics
analyses
nuclear
internal
spacers
newly
generated
complete
chloroplast
genome,
conjunction
previously
published
sequences,
performed
ancestral
state
reconstruction
clarify
evolutionary
pattern
important
traits
.
clustering
results
38
indicated
that
is
allied
Nomocharis,
increasing
polymorphism
phylogenetic
both
supported
L.
belonging
subclade
Ecristata
closest
affinity
being
gongshanense
Inconsistencies
relationships
were
detected
between
plastid
datasets,
possibly
ancient
hybridization
ongoing
introgression.
Comparative
revealed
conservation
similarity
their
genomes,
variations
observed
expansion
contraction
IR
regions.
A/T
palindromic
repeat
sequences
abundant.
Seven
highly
variable
regions
(Pi≥0.015)
identified
potential
molecular
markers
based
genomes
47
Both
genes
exhibited
very
low
variability
contrasting
appearance.
analysis
suggests
campanulate
flower
form,
arose
at
least
three
times
revealing
parallel
evolution
Overall,
study
adds
genetic
evidence
for
understanding
patterns
Scientific Reports,
Journal Year:
2022,
Volume and Issue:
12(1)
Published: June 7, 2022
Lilium
ledebourii
(Baker)
Boiss
is
a
rare
species,
which
exhibits
valuable
traits.
However,
before
its
genetic
diversity
and
evolutionary
were
uncovered,
wild
resources
jeopardized.
Moreover,
some
ambiguities
in
phylogenetic
relationships
of
this
genus
remain
unresolved.
Therefore,
obtaining
the
whole
chloroplast
sequences
L.
comparative
analysis
along
with
other
species
crucial
pivotal
to
understanding
evolution
as
well
populations.
A
multi-scale
genome-level
analysis,
especially
selection
pressure,
was
conducted.
Detailed
third‑generation
sequencing
revealed
genome
151,884
bp,
an
ordinary
quadripartite
protected
structure
comprising
37.0%
GC.
Overall,
113
different
genes
recognized
genome,
consisting
30
distinct
tRNA
genes,
four
ribosomal
RNAs
79
unique
protein-encoding
genes.
Here,
3234
SSRs
2053
complex
repeats
identified,
comprehensive
performed
for
IR
expansion
contraction,
codon
usage
bias.
genome-wide
sliding
window
variability
rpl32-trnL-ccsA,
petD-rpoA,
ycf1,
psbI-trnS-trnG,
rps15-ycf1,
trnR,
trnT-trnL,
trnP-psaJ-rpl33
higher
among
48
cp
genomes,
displaying
nucleotide
SC
regions.
Following
1128
pairwise
comparisons,
ndhB,
psbJ,
psbZ,
ycf2
exhibit
zero
synonymous
substitution,
revealing
divergence
or
restriction.
Furthermore,
out
78
protein-coding
we
found
that
accD
rpl36
under
positive
selection:
however,
at
entire-chloroplast
protein
scale,
have
gone
through
purifying
selection.
Also,
new
tree
rebuilt,
believe
classification
clearer
than
before.
The
provided
here
will
aid
future
studies
identification,
population
genetics,
conservation.
Plant Diversity,
Journal Year:
2023,
Volume and Issue:
46(2), P. 219 - 228
Published: Aug. 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.
Abstract
Calochortus
tolmiei
Hook.
&
Arn.,
a
bulbous
monocot
with
cat’s
ear
flowers
in
the
angiosperm
family
Liliaceae,
is
perennial
herb
native
to
northern
California,
Oregon,
and
Washington.
exhibits
substantial
morphological
karyotype
diversity
multiple
floral
forms
haploid
chromosome
number
varying
from
six
10.
Here,
we
present
first
high-quality
reference
assembly
Liliaceae
for
C.
tolmiei,
scaffolded
of
2.9
Gbp
N50
296
Mbp.
Notably,
92%
assembled
genome
into
10
pseudomolecules,
matching
documented
count
tolmiei.
The
contains
31,049
protein-coding
genes,
86.2%
being
functionally
annotated.
closest
reference-quality
Chionographis
japonica
(Willd.)
Maxim.
(Melianthiaceae),
which
diverged
approximately
83
MYA,
providing
valuable
genomic
resource
Liliales,
an
order
lacks
resources.
BMC Biology,
Journal Year:
2025,
Volume and Issue:
23(1)
Published: April 28, 2025
Phylogenetic
research
in
Tulipa
(Liliaceae),
a
genus
of
significant
economic
and
horticultural
value,
has
relied
on
limited
nuclear
(mostly
ribosomal
internal
transcribed
spacer,
nrITS)
plastid
DNA
sequences,
resulting
low-resolution
phylogenetic
trees
uncertain
intrageneric
classifications.
The
genus,
noted
for
its
large
genome,
presents
discordant
relationships
among
Amana,
Erythronium,
Tulipa,
likely
due
to
incomplete
lineage
sorting
(ILS)
and/or
reticulate
evolution.
Thus,
phylogenomic
approaches
are
needed
clarify
these
the
conflicting
signals
within
tribe
Tulipeae.
We
newly
sequenced
50
transcriptomes
46
species
Tulipeae
(including
multiple
accessions
all
four
genera)
one
outgroup
sister
Lilieae
(Notholirion
campanulatum),
downloaded
15
previously
published
supplement
sampling.
One
dataset
(74
protein-coding
genes,
PCGs)
(2594
orthologous
OGs)
were
constructed,
with
latter
used
tree
inference
based
maximum
likelihood
(ML)
multi-species
coalescent
(MSC)
methods.
To
investigate
causes
gene
discordance,
"site
con/discordance
factors"
(sCF
sDF1/sDF2)
calculated
first,
after
which
nodes
displaying
high
or
imbalanced
sDF1/2
selected
network
analyses
polytomy
tests
determine
whether
ILS
evolution
best
explain
incongruence.
Key
not
resolved
by
this
technique,
especially
those
further
investigated
applying
D-statistics
QuIBL.
failed
reconstruct
reliable
unambiguous
evolutionary
history
pervasive
evolution,
caused
either
obscured
minority
signal
differing
genomic
compartments.
However,
we
confirmed
monophyly
most
subgenera,
exception
two
small
subgenus
Orithyia,
heterophylla
was
recovered
as
remainder
whereas
T.
sinkiangensis
clustered
Tulipa.
In
contrast,
traditional
sections
found
be
non-monophyletic.
Mitochondrial DNA Part B,
Journal Year:
2025,
Volume and Issue:
10(6), P. 474 - 479
Published: May 14, 2025
Lilium
leichtlinii
var.
maximowiczii,
native
to
Northeast
Asia,
shows
morphological
differences
between
Korean
and
Japanese
varieties.
This
study
analyzed
chloroplast
(cp)
genomes
of
three
diploid
L.
groups:
(KR),
broad-leaved
(JB),
narrow-leaved
(JN).
Genome
sizes
ranged
from
152,053
bp
152,588
with
GC
contents
37.02-37.06%.
All
had
typical
quadripartite
structures
contained
129
genes.
Phylogenetic
analysis
48
cp
revealed
at
least
distinct
Most
genomic
variation
was
found
in
non-coding
regions,
providing
insights
into
intraspecific
diversity
leichtlinii.
Frontiers in Plant Science,
Journal Year:
2022,
Volume and Issue:
13
Published: July 22, 2022
Lilies
are
one
of
the
most
important
ornamental
flowers
worldwide
with
approximately
100
wild
species
and
numerous
cultivars,
but
phylogenetic
relationships
among
their
contributions
to
these
cultivars
poorly
resolved.
We
collected
major
Lilium
assembled
plastome
sequences.
Our
reconstruction
using
114
plastid
genomes,
including
70
representing
all
sections
42
six
hybrid
divisions
two
outgroups,
uncovered
well-supported
genetic
within
.
The
were
separated
into
distinct
groups
(groups
A
B)
associated
geographical
distribution,
which
further
diversified
eight
different
clades
that
phylogenetically
well
supported.
Additional
support
was
provided
by
distributions
indels
single-nucleotide
variants,
consistent
topology.
Archelirion,
Sinomartagon
III,
Leucolirion
6a
6b
maternal
donors
for
Oriental
hybrids,
Asiatic
Trumpet
Longiflorum
respectively.
OT
hybrids
originated
from
Archelirion
6a,
LA
derived
study
provides
an
basis
clarifying
infrageneric
classification
origin
in