Journal of Systematics and Evolution,
Journal Year:
2021,
Volume and Issue:
59(5), P. 1124 - 1138
Published: July 21, 2021
Abstract
With
the
decreasing
cost
and
availability
of
many
newly
developed
bioinformatics
pipelines,
next‐generation
sequencing
(NGS)
has
revolutionized
plant
systematics
in
recent
years.
Genome
skimming
been
widely
used
to
obtain
high‐copy
fractions
genomes,
including
plastomes,
mitochondrial
DNA
(mtDNA),
nuclear
ribosomal
(nrDNA).
In
this
study,
through
simulations,
we
evaluated
optimal
(minimum)
depth
performance
for
recovering
single‐copy
genes
(SCNs)
from
genome
data,
by
subsampling
resequencing
data
generating
10
sets
with
different
coverage
silico
.
We
tested
four
(plastome,
nrDNA,
mtDNA,
SCNs)
obtained
based
on
phylogenetic
analyses
Vitis
clade
at
genus
level
Vitaceae
family
level,
respectively.
Our
results
showed
that
minimum
high‐quality
SCNs
assembly
via
was
about
10×
coverage.
Without
steps
synthesizing
baits
enrichment
experiments,
coupled
incredibly
low
costs,
showcase
deep
(DGS)
is
as
effective
capturing
large
Hyb‐Seq
approach,
addition
entire
nrDNA
repeats.
DGS
may
serve
an
efficient
economical
alternative
be
superior
popular
target
enrichment/Hyb‐Seq
approach.
Molecular Phylogenetics and Evolution,
Journal Year:
2021,
Volume and Issue:
157, P. 107068 - 107068
Published: Jan. 9, 2021
Gesneriaceae
(ca.
3400
species)
is
a
pantropical
plant
family
with
wide
range
of
growth
form
and
floral
morphology
that
are
associated
repeated
adaptations
to
different
environments
pollinators.
Although
systematics
has
been
largely
improved
by
the
use
Sanger
sequencing
data,
our
understanding
evolutionary
history
group
still
far
from
complete
due
limited
number
informative
characters
provided
this
type
data.
To
overcome
limitation,
we
developed
here
Gesneriaceae-specific
gene
capture
kit
targeting
830
single-copy
loci
(776,754
bp
in
total),
including
279
genes
Universal
Angiosperms-353
kit.
With
an
average
557,600
reads
87.8%
recovery,
target
was
successful
across
also
other
families
Lamiales.
From
bait
set,
selected
most
418
resolve
phylogenetic
relationships
entire
using
maximum
likelihood
coalescent-based
methods.
Upon
testing
performance
baits
on
78
taxa
representing
20
out
24
subtribes
within
family,
showed
data
high
support
for
among
major
lineages,
were
able
provide
resolution
more
recent
radiations.
Overall,
molecular
resources
open
new
perspectives
study
phylogeny
at
taxonomical
levels
identification
factors
underlying
diversification
group.
Molecular Ecology Resources,
Journal Year:
2022,
Volume and Issue:
23(2), P. 424 - 439
Published: Oct. 11, 2022
Cymbidium
is
an
orchid
genus
that
has
undergone
rapid
radiation
and
high
ornamental,
economic,
ecological
cultural
importance,
but
its
classification
based
on
morphology
controversial.
The
plastid
genome
(plastome),
as
extension
of
plant
standard
DNA
barcodes,
been
widely
used
a
potential
molecular
marker
for
identifying
recently
diverged
species
or
complicated
groups.
In
this
study,
we
newly
generated
237
plastomes
50
(at
least
two
individuals
per
species)
by
skimming,
covering
71.4%
members
the
Cymbidium.
Sequence-based
analyses
(barcoding
gaps
automatic
barcode
gap
discovery)
tree-based
(maximum
likelihood,
Bayesian
inference
multirate
Poisson
tree
processes
model)
were
conducted
identification
Our
work
provides
comprehensive
reference
library
identification.
results
show
compared
with
barcodes
(rbcL
+
matK)
well
trnH-psbA,
rate
plastome
increased
moderately
from
58%
to
68%.
At
same
time,
propose
optimized
strategy
species.
cannot
completely
resolve
Cymbidium,
main
reasons
being
incomplete
lineage
sorting,
artificial
cultivation,
natural
hybridization
chloroplast
capture.
To
further
explore
use
nuclear
data
in
species,
Skmer
method
was
adopted
72%.
It
appears
have
vital
role
are
expected
be
next-generation
barcodes.
Journal of Integrative Plant Biology,
Journal Year:
2024,
Volume and Issue:
66(10), P. 2242 - 2261
Published: Aug. 21, 2024
ABSTRACT
The
woody
bamboos
(Bambusoideae)
exhibit
distinctive
biological
traits
within
Poaceae,
such
as
highly
lignified
culms,
rapid
shoot
growth,
monocarpic
mass
flowering
and
nutlike
or
fleshy
caryopses.
Much
of
the
remarkable
morphological
diversity
across
subfamily
exists
a
single
hexaploid
clade,
paleotropical
(PWB),
making
it
ideal
to
investigate
factors
underlying
evolution
in
bamboos.
However,
origin
biogeographical
history
PWB
remain
elusive,
does
effect
environmental
on
their
characters.
We
generated
robust
time‐calibrated
phylogeny
using
nucleotide
polymorphisms
retrieved
from
optimized
double
digest
restriction
site
associated
DNA
sequencing,
explored
evolutionary
trends
habit,
inflorescence,
caryopsis
type
relation
including
climate,
soil,
topography.
inferred
that
started
diversify
Oligocene–Miocene
boundary
formed
four
major
clades,
is,
Melocanninae,
Racemobambosinae
s.l.
(comprising
Dinochloinae,
Greslanlinae,
s.str.
Temburongiinae),
Hickeliinae
Bambusinae
plus
Holttumochloinae).
ancestor
was
reconstructed
having
erect
indeterminate
inflorescence
basic
caryopsis.
characters
climbing/scrambling
determinate
nucoid/bacoid
have
since
undergone
multiple
changes
reversals
during
diversification
PWB.
all
three
correlated
with,
hence
likely
influenced
by,
aspects
topography,
with
climate
most
strongly
traits,
soil
least
so.
topography
had
more
influence
than
whereas
both
greater
bacoid
did
soil.
Our
results
provide
novel
insights
into
adaptive
for
future
ecological
research.
Annals of Botany,
Journal Year:
2023,
Volume and Issue:
131(6), P. 953 - 966
Published: May 9, 2023
Abstract
Background
and
Aims
Hybridization
has
long
been
recognized
as
an
important
process
for
plant
evolution
is
often
accompanied
by
polyploidization,
another
prominent
force
in
generating
biodiversity.
Despite
its
pivotal
importance
evolution,
the
actual
prevalence
distribution
of
hybridization
across
tree
life
remain
unclear.
Methods
We
used
whole-genome
shotgun
(WGS)
sequencing
cytological
data
to
investigate
evolutionary
history
Henckelia,
a
large
genus
family
Gesneriaceae
with
high
frequency
suspected
polyploidization
events.
generated
WGS
at
about
10×
coverage
26
Chinese
Henckelia
species
plus
one
Sri
Lankan
species.
To
untangle
history,
we
separately
extracted
whole
plastomes
thousands
single-copy
nuclear
genes
from
data,
reconstructed
phylogenies
based
on
both
plastid
data.
also
explored
sources
genealogical
cytonuclear
conflicts
identified
signals
introgression
within
our
phylogenomic
dataset
using
several
statistical
methods.
Additionally,
test
evaluated
chromosome
counts
45
populations
27
studied.
Key
Results
obtained
well-supported
phylogenetic
relationships
concatenation-
coalescent-based
However,
were
highly
inconsistent
phylogeny,
observed
intensive
discordance
among
gene
trees.
Further
analyses
suggested
that
incomplete
lineage
sorting
flow
contributed
discordance.
Our
networks
revealed
complex
Henckelia.
In
addition,
species,
found
independent
events
occurred
after
different
Conclusions
findings
demonstrated
are
common
Furthermore,
results
H.
oblongifolia
not
member
redefined
they
other
taxonomic
treatments
this
genus.
American Journal of Botany,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 10, 2025
Centropogon
subgenus
comprises
55
species
found
primarily
in
midelevation
Andean
forests
featuring
some
of
the
most
curved
flowers
among
angiosperms.
Floral
curvature
is
linked
to
coevolution
with
sicklebill
hummingbird,
which
pollinates
species.
Despite
charismatic
flowers,
there
limited
knowledge
about
phylogenetic
relationships
and
floral
evolution.
We
conducted
first
densely
sampled
phylogenomic
analysis
clade
using
methods
that
account
for
incomplete
lineage
sorting
on
a
sequence
capture
dataset
generated
lineage-specific
probe
set.
Using
comparative
methods,
we
test
correlated
evolution
two
traits
central
pollination.
improve
understanding
by
more
than
doubling
past
taxon
sampling.
confirm
monophyly
sections,
non-monophyly
remaining
sections.
The
characterized
high
gene
tree
discordance.
Three
widespread
display
contrasting
dynamics,
C.
cornutus
forming
granulosus
solanifolius
non-monophyletic,
biogeographically
clustered
lineages.
Correlated
inflorescence
structure
has
led
multiple
putative
losses
adds
growing
body
literature
plant
clades
This
phylogeny
serves
as
foundational
framework
further
macroevolutionary
investigations
into
environmental
biogeographic
factors
shaping
pollination-related
traits.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: April 24, 2024
Abstract
The
tree
of
blobs
a
species
network
shows
only
the
tree-like
aspects
relationships
taxa
on
network,
omitting
information
substructures
where
hybridization
or
other
types
lateral
transfer
genetic
occur.
By
isolating
such
regions
inference
can
serve
as
starting
point
for
more
detailed
investigation,
indicate
limit
what
may
be
inferrable
without
additional
assumptions.
Building
our
theoretical
work
identifiability
from
gene
quartet
distributions
under
Network
Multispecies
Coalescent
model,
we
develop
an
algorithm,
TINNiK,
statistically
consistent
inference.
We
provide
examples
its
application
to
both
simulated
and
empirical
datasets,
utilizing
implementation
in
MSCquartets
2.0
R
package.
MSC
Classification
92D15,
92D20
