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
.
Journal of Biogeography,
Год журнала:
2019,
Номер
46(12), С. 2678 - 2689
Опубликована: Сен. 30, 2019
Abstract
Aim
The
Hengduan
Mountains
(HDM)
of
southwest
China
is
a
biodiversity
hotspot
and
harbours
one
the
world's
richest
temperate
floras.
However,
origin
evolution
its
biota
remain
largely
unresolved.
Here
we
explore
impact
mountain
uplift
on
diversification
process
in
this
using
alpine
bamboos.
Location
HDM
region,
China.
Taxon
Alpine
Methods
We
used
ddRAD‐seq
data
from
most
complete
sampling
bamboos
undertaken
to
date
(79%
species
diversity),
investigate
their
evolutionary
history.
ancestral
area
these
was
reconstructed
time‐calibrated
phylogeny
BioGeoBEARS
rates
were
inferred
BAMM
analyses.
In
addition,
divergence
evaluated
trait‐dependent
models
diversification.
Results
strongly
supported
as
monophyletic,
relationships
within
them
robustly
resolved.
Fargesia
found
be
polyphyletic
Yushania
resolved
monophyletic.
originated
outside
region
during
late
Miocene,
spread
Pliocene,
undergoing
significant
acceleration
net
diversification,
which
temporally
congruent
with
orogeny.
speciation
rate
increased
altitude
high
rate,
estimated
0.75
per
million
years,
detected
for
distributed
elevations.
Main
Conclusions
Our
study
demonstrates
that
heterogeneous
habitats
geographical
isolation
bamboos,
have
limited
dispersal
ability,
are
important
drivers
rapid
This
also
highlights
power
complementary
analyses
revealing
link
between
past
geological
changes.
Systematic Biology,
Год журнала:
2020,
Номер
70(4), С. 756 - 773
Опубликована: Сен. 25, 2020
Rapid
evolutionary
radiations
are
among
the
most
challenging
phylogenetic
problems,
wherein
different
types
of
data
(e.g.,
morphology
and
molecular)
or
genetic
markers
nuclear
organelle)
often
yield
inconsistent
results.
The
tribe
Arundinarieae,
that
is,
temperate
bamboos,
is
a
clade
tetraploid
originated
22
Ma
subsequently
radiated
in
East
Asia.
Previous
studies
Arundinarieae
have
found
conflicting
relationships
and/or
low
support.
Here,
we
obtain
from
ddRAD
for
213
taxa
parallel
sampling
chloroplast
genomes
genome
skimming
147
taxa.
We
first
assess
feasibility
using
ddRAD-seq
estimates
paleopolyploid
rapidly
lineages,
optimize
clustering
thresholds,
analysis
workflow
orthology
identification.
Reference-based
assembly
approaches
perform
well
strongly
supported
generally
concordant
with
morphology-based
taxonomy.
recover
five
major
two
which
notable
(the
pachymorph
leptomorph
lineages),
they
correspond
distinct
rhizome
morphologies.
By
contrast,
phylogeny
differed
significantly.
Based
on
multiple
lines
evidence,
tree
favored
as
best
species
estimation
bamboos.
Using
time-calibrated
tree,
find
diversified
around
mid-Miocene
corresponding
intensification
Asian
monsoon
evolution
key
innovations
including
rhizomes.
Our
results
provide
highly
resolved
shed
new
light
radiation
reticulate
history
this
tribe,
an
empirical
example
study
recalcitrant
plant
radiations.
[Arundinarieae;
ddRAD;
paleopolyploid;
skimming;
rapid
diversification;
incongruence.].
Annals of Botany,
Год журнала:
2022,
Номер
129(4), С. 457 - 471
Опубликована: Янв. 16, 2022
Theaceae,
with
three
tribes,
nine
genera
and
more
than
200
species,
are
of
great
economic
ecological
importance.
Recent
phylogenetic
analyses
based
on
plastomic
data
resolved
the
relationships
among
tribes
intergeneric
within
two
those
tribes.
However,
generic-level
largest
tribe,
Theeae,
were
not
fully
resolved.
The
role
putative
whole-genome
duplication
(WGD)
events
in
family
possible
hybridization
Theeae
also
remain
to
be
tested
further.Transcriptomes
or
low-depth
sequencing
57
species
as
well
additional
plastome
sequence
data,
generated.
Using
a
dataset
low-copy
nuclear
genes,
we
reconstructed
using
concatenated,
tree
network
approaches.
We
further
conducted
molecular
dating
inferred
WGD
by
examining
distribution
number
synonymous
substitutions
per
site
(Ks)
for
paralogues
each
species.
For
plastid
protein-coding
sequences
,
phylogenies
comparison
results
obtained
from
analysis
dataset.Based
610
genes
(858
606
bp
length)
investigated,
Stewartieae
was
sister
other
Within
Apterosperma-Laplacea
clade
grouped
Pyrenaria,
leaving
Camellia
Polyspora
sister.
estimated
ages
Theaceae
largely
consistent
previous
studies
mainly
data.
Two
reticulation
one
between
common
ancestor
Gordonia
Schima
found.
All
members
tea
shared
events,
an
older
At-γ
recent
Ad-β;
both
outgroups
(Diapensiaceae,
Pentaphylacaceae,
Styracaceae
Symplocaceae).Our
improved
understanding
at
tribal
generic
levels
previously
proposed
but
position
needs
attention.
There
is
no
evidence
extensive
Theaceae-specific
event.
Land
bridges
(e.g.
Bering
land
bridge)
during
Late
Oligocene
may
have
permitted
intercontinental
plant
movements
that
facilitated
ancient
introgression
Schima.
Molecular Ecology,
Год журнала:
2023,
Номер
32(11), С. 2850 - 2868
Опубликована: Фев. 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.
Communications Biology,
Год журнала:
2025,
Номер
8(1)
Опубликована: Март 3, 2025
Orphan
genes
play
crucial
roles
in
diverse
biological
processes,
but
the
evolutionary
trajectories
and
functional
divergence
remain
largely
unexplored.
The
Theaceae
family,
including
economically
culturally
important
tea
plant,
offers
a
distinctive
model
to
examine
these
aspects.
Here,
we
integrated
Nanopore
long-read
sequencing,
Illumina
short-read
Hi-C
methods
decode
pseudo-chromosomal
genome
assembly
of
Stewartia
sinensis,
from
earliest-diverging
tribe
Theaceae,
spanning
2.95
Gb.
Comparative
genomic
analysis
revealed
absence
recent
whole-genome
duplication
events
ancestor,
highlighting
tandem
duplications
as
predominant
mechanism
gene
expansion.
We
identified
31,331
orphan
genes,
some
which
appear
have
ancient
origins,
suggesting
early
emergence
with
frequent
gains
losses,
while
others
seem
more
specific
recent.
Notably,
are
distinguished
by
shorter
lengths,
fewer
exons
domains
compared
that
originate
much
earlier,
like
transcription
factors.
Moreover,
contributes
significantly
adaptive
evolution
characteristic
diversity
it
is
also
major
driving
origination
genes.
This
study
illuminates
dynamics
providing
valuable
resource
for
understanding
origin
plant
flavor
enhancing
genetic
breeding
efforts.
nearly
complete
an
early-diverging
species,
phylogenomic
studies
provide
insights
into
Theaceae.