Annals of Botany,
Journal Year:
2023,
Volume and Issue:
132(1), P. 15 - 28
Published: Jan. 31, 2023
Species
of
the
genus
Buddleja
in
Asia
are
mainly
distributed
Sino-Himalayan
region
and
form
a
challenging
taxonomic
group,
with
extensive
hybridization
polyploidization.
A
phylogenetic
approach
to
unravelling
history
reticulation
this
lineage
will
deepen
our
understanding
speciation
biodiversity
hotspots.
Horticulture Research,
Journal Year:
2023,
Volume and Issue:
10(1)
Published: Jan. 1, 2023
Abstract
Cultivated
strawberry
(Fragaria
×
ananassa),
a
perennial
herb
belonging
to
the
family
Rosaceae,
is
complex
octoploid
with
high
heterozygosity
at
most
loci.
However,
there
no
research
on
haplotype
of
genome.
Here
we
aimed
obtain
high-quality
genome
cultivated
cultivar,
“Yanli”,
using
single
molecule
real-time
sequencing
and
high-throughput
chromosome
conformation
capture
technology.
The
“Yanli”
was
823
Mb
in
size,
long
terminal
repeat
assembly
index
14.99.
phased
into
two
haplotypes,
Hap1
(825
contig
N50
26.70
Mb)
Hap2
(808
27.51
Mb).
Using
combination
Hap2,
obtained
for
first
time
haplotype-resolved
56
chromosomes
strawberry.
We
identified
~
10
inversion
translocation
2-1.
104
957
102
356
protein-coding
genes
were
annotated
respectively.
Analysis
related
anthocyanin
biosynthesis
pathway
revealed
structural
diversity
complexity
expression
alleles
F.
ananassa
In
summary,
ananassa,
which
will
provide
foundation
investigating
gene
function
evolution
Science Advances,
Journal Year:
2024,
Volume and Issue:
10(6)
Published: Feb. 7, 2024
Butylphthalide
is
one
of
the
first-line
drugs
for
ischemic
stroke
therapy,
while
no
biosynthetic
enzyme
butylphthalide
has
been
reported.
Here,
we
present
a
haplotype-resolved
genome
Journal of Integrative Plant Biology,
Journal Year:
2022,
Volume and Issue:
64(8), P. 1487 - 1501
Published: June 24, 2022
Cultivated
hawthorn
(Crataegus
pinnatifida
var.
major)
is
an
important
medicinal
and
edible
plant
with
a
long
history
of
use
for
health
protection
in
China.
Herein,
we
provide
de
novo
chromosome-level
genome
sequence
the
cultivar
"Qiu
Jinxing."
We
assembled
823.41
Mb
encoding
40
571
genes
further
anchored
779.24
into
17
pseudo-chromosomes,
which
account
94.64%
genome.
Phylogenomic
analyses
revealed
that
cultivated
diverged
from
other
species
within
Maleae
(apple
tribe)
at
approximately
35.4
Mya.
Notably,
involved
flavonoid
triterpenoid
biosynthetic
pathways
have
been
significantly
amplified
In
addition,
our
results
indicated
share
unique
ancient
tetraploidization
event;
however,
no
recent
independent
whole-genome
duplication
event
was
specifically
detected
hawthorn.
The
amplification
non-specific
terminal
repeat
retrotransposons
contributed
most
to
expansion
Furthermore,
identified
two
paleo-sub-genomes
extant
found
these
sub-genomes
showed
different
rearrangement
mechanisms.
also
reconstructed
ancestral
chromosomes
Rosaceae
discussed
possible
paleo-polyploid
origin
patterns
(autopolyploidization
or
allopolyploidization)
Maleae.
Overall,
study
provides
improved
context
understanding
evolution
species,
this
new
high-quality
reference
useful
resource
horticultural
improvement
Horticulture Research,
Journal Year:
2024,
Volume and Issue:
11(6)
Published: April 9, 2024
Ginseng
(Panax
ginseng)
is
a
representative
of
Chinese
traditional
medicine,
also
used
worldwide,
while
the
triterpene
saponin
ginsenoside
most
important
effective
compound
within
it.
an
allotetraploid,
with
complex
genetic
background,
making
study
its
metabolic
evolution
challenging.
In
this
study,
we
assembled
telomere-to-telomere
ginseng
reference
genome,
constructed
3.45
Gb
24
chromosomes
and
77
266
protein-coding
genes.
Additionally,
genome
was
divided
into
two
subgenomes,
designated
as
subgenome
A
B.
Subgenome
contains
larger
number
genes,
whereas
B
has
general
expression
advantage,
suggesting
that
subgenomes
experienced
asymmetric
gene
loss
biased
expression.
The
separated
approximately
6.07
million
years
ago,
shows
closest
relation
to
Panax
vietnamensis
var.
fuscidiscus.
Comparative
genomics
revealed
expansion
families
associated
biosynthesis
in
both
subgenomes.
Furthermore,
tandem
duplications
proximal
play
crucial
roles
biosynthesis.
We
screened
functional
genes
identified
previous
research
found
some
these
located
colinear
regions
between
have
divergence
functions,
revealing
unbalanced
pathway
ginseng.
Our
work
provides
resources
for
future
studies
breeding
programs
ginseng,
well
ginsenosides.
BMC Biology,
Journal Year:
2024,
Volume and Issue:
22(1)
Published: April 23, 2024
Transposable
elements
(TEs)
have
a
profound
influence
on
the
trajectory
of
plant
evolution,
driving
genome
expansion
and
catalyzing
phenotypic
diversification.
The
pangenome,
comprehensive
genetic
pool
encompassing
all
variations
within
species,
serves
as
an
invaluable
tool,
unaffected
by
confounding
factors
intraspecific
diversity.
This
allows
for
more
nuanced
exploration
TE
evolution.
Communications Biology,
Journal Year:
2024,
Volume and Issue:
7(1)
Published: Aug. 17, 2024
Biological
invasions
pose
a
significant
threat
to
ecosystems,
disrupting
local
biodiversity
and
ecosystem
functions.
The
genomic
underpinnings
of
invasiveness,
however,
are
still
largely
unknown,
making
it
difficult
predict
manage
invasive
species
effectively.
common
reed
(Phragmites
australis)
is
dominant
grass
in
wetland
ecosystems
has
become
particularly
when
transferred
from
Europe
North
America.
Here,
we
present
high-quality
gap-free,
telomere-to-telomere
genome
assembly
Phragmites
australis
consisting
24
pseudochromosomes
B
chromosome.
Fully
phased
subgenomes
demonstrated
considerable
subgenome
dominance
revealed
the
divergence
diploid
progenitors
approximately
30.9
million
years
ago.
Comparative
genomics
using
chromosome-level
scaffolds
for
three
other
lineages
previously
published
draft
an
lineage
that
gene
family
expansions
form
tandem
duplications
may
have
contributed
invasiveness
lineage.
This
study
sheds
light
on
evolution
Arundinoideae
grasses
suggests
genetic
drivers,
such
as
duplications,
underly
processes
biological
invasion
plants.
These
findings
provide
crucial
step
toward
understanding
managing
basis
plant
species.
Scientific Data,
Journal Year:
2024,
Volume and Issue:
11(1)
Published: June 22, 2024
Synthetic
hexaploid
wheats
(SHWs)
are
effective
genetic
resources
for
transferring
agronomically
important
genes
from
wild
relatives
to
common
wheat
(Triticum
aestivum
L.).
Dozens
of
reference-quality
pseudomolecule
assemblies
have
been
generated,
but
none
is
reported
SHW-derived
cultivars.
Here,
we
generated
a
chromosome-scale
assembly
the
cultivar
'Chuanmai
104'
based
on
PacBio
HiFi
reads
and
chromosome
conformation
capture
sequencing.
The
total
size
was
14.81
Gb
with
contig
N50
length
58.25
Mb.
A
BUSCO
analysis
yielded
completeness
score
99.30%.
In
total,
repetitive
elements
comprised
81.36%
genome
122,554
high-confidence
protein-coding
gene
models
were
predicted.
summary,
first
chromosome-level
presents
promising
outlook
study
utilization
SHWs
in
improvement,
which
essential
meet
global
food
demand.