Origin and evolution of the bread wheat D genome
Nature,
Год журнала:
2024,
Номер
633(8031), С. 848 - 855
Опубликована: Авг. 14, 2024
Bread
wheat
(Triticum
aestivum)
is
a
globally
dominant
crop
and
major
source
of
calories
proteins
for
the
human
diet.
Compared
with
its
wild
ancestors,
modern
bread
shows
lower
genetic
diversity,
caused
by
polyploidisation,
domestication
breeding
bottlenecks
Язык: Английский
Isoform‐resolved genome annotation enables mapping of tissue‐specific betalain regulation in amaranth
New Phytologist,
Год журнала:
2024,
Номер
243(3), С. 1082 - 1100
Опубликована: Апрель 8, 2024
Summary
Betalains
are
coloring
pigments
produced
in
some
families
of
the
order
Caryophyllales,
where
they
replace
anthocyanins
as
pigments.
While
betalain
pathway
itself
is
well
studied,
tissue‐specific
regulation
remains
mostly
unknown.
We
enhance
high‐quality
Amaranthus
hypochondriacus
reference
genome
and
produce
a
substantially
more
complete
annotation,
incorporating
isoform
details.
annotate
anthocyanin
genes
along
with
their
regulators
amaranth
map
genetic
control
pathway.
Our
improved
annotation
allowed
us
to
identify
causal
mutations
that
lead
knock‐out
red
betacyanins
natural
accessions
amaranth.
reveal
flower
color
via
previously
uncharacterized
MYB
transcription
factor,
AhMYB2
.
Downregulation
leads
reduced
expression
key
enzyme
loss
color.
represents
most
date
valuable
resource
for
research.
High
similarity
regulator
partially
conserved
interaction
motif
support
co‐option
possible
reason
mutual
exclusiveness
two
Язык: Английский
Domestication shaped the chromatin landscape of grain amaranth
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 18, 2025
Plant
domestication
has
had
profound
impacts
on
the
morphology
and
genetic
diversity
of
crops.
Beyond
sequence
diversity,
changes
in
chromatin
structure
can
play
an
important
role
plant
adaptation.
However,
interplay
between
landscape
remains
unclear.
We
present
a
high-quality
genome
assembly
map
ancient
pseudo-cereal,
amaranth.
Using
ATAC-sequencing
multiple
accessions
three
grain
amaranth
species
two
wild
relatives,
we
show
that
overall
amount
accessible
is
highly
conserved,
about
2.5%
all
switched
states,
with
higher
fraction
repeatedly
opening
during
processes.
These
differentially
regions,
crops
their
ancestor,
were
species-specific
significantly
associated
selective
sweeps
-
reflecting
repeated
independent
Our
findings
reveal
dynamic
landscape,
highlighting
additional
layer
Язык: Английский
Genome-Wide Resequencing Revealed the Genetic Diversity of Fraxinus platypoda Oliv. in Northwestern China
Forests,
Год журнала:
2025,
Номер
16(5), С. 860 - 860
Опубликована: Май 21, 2025
Fraxinus
platypoda
Oliv.
(Oleaceae),
an
ecologically
and
economically
valuable
tree
species
with
key
distribution
areas
in
northwestern
China,
faces
conservation
challenges
due
to
its
fragmented
groups
scarce
individual
numbers.
To
investigate
the
genetic
consequences
of
this
demographic
crisis,
we
analyzed
65
individuals
from
11
natural
region
using
whole-genome
resequencing.
We
identified
a
total
60,503,092
single
nucleotide
polymorphisms
(SNPs),
after
further
filtering,
retained
3,394,299
SNPs
for
subsequent
analysis.
Population
structure
analysis
(Neighbor-Joining
tree,
STRUCTURE,
kinship
coefficients)
revealed
two
distinct
clusters
(K
=
2),
principal
component
(PCA)
confirming
subdivision.
Cluster
I,
composed
eight
Groups
3,
5,
8,
11,
is
highly
differentiated
II
may
be
ancestral
it.
Among
groups,
3
show
high
diversity
differentiation,
Tajima’s
D
>
0,
indicating
long
evolutionary
history
balancing
selection.
The
remaining
nine
have
low
diversity,
frequent
gene
flow,
<
suggesting
directional
A
mantel
test
showed
no
significant
link
between
variation
geographic
isolation
(p
0.460).
differentiation
I
flow
are
maintained
by
factors
like
reproductive
systems.
highlighted
as
important
resources
deserving
priority
protection.
This
study
offers
genomic
data
conserving
future
adaptability
research.
Язык: Английский
Origin and evolution of the bread wheat D genome
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Ноя. 29, 2023
Abstract
Bread
wheat
(
Triticum
aestivum
)
is
a
globally
dominant
crop
and
major
source
of
calories
proteins
for
the
human
diet.
Compared
to
its
wild
ancestors,
modern
bread
shows
lower
genetic
diversity
caused
by
polyploidisation,
domestication,
breeding
bottlenecks
1,2
.
Wild
relatives
represent
reservoirs,
harbouring
beneficial
alleles
that
have
not
been
incorporated
into
wheat.
Here,
we
establish
analyse
pangenome
resources
Tausch’s
goatgrass,
Aegilops
tauschii
,
donor
D
genome.
This
new
facilitated
cloning
disease
resistance
gene
haplotype
analysis
across
complex
locus,
allowing
us
discern
from
paralogous
copies.
We
also
reveal
composition
history
genome,
involving
previously
unreported
contributions
genetically
geographically
discrete
Ae.
subpopulations.
Together,
our
results
genome
demonstrate
potential
in
improvement.
Язык: Английский
Isoform-resolved genome annotation enables mapping of tissue-specific betalain regulation in amaranth
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Авг. 25, 2023
Summary
•
Betalains
are
coloring
pigments
produced
in
some
families
of
the
order
Caryophyllales,
where
they
replace
anthocyanins
as
pigments.
While
betalain
pathway
itself
is
well
studied,
tissue-specific
regulation
remains
mostly
unknown.
We
enhance
high-quality
Amaranthus
hypochondriacus
reference
genome
and
produce
a
substantially
more
complete
annotation,
incorporating
isoform
details.
annotate
anthocyanin
genes
along
with
their
regulators
amaranth
map
genetic
control
pathway.
Our
improved
annotation
allowed
us
to
identify
causal
mutations
that
lead
knock-out
red
betacyanins
natural
accessions
amaranth.
reveal
flower
color
via
previously
uncharacterized
MYB
transcription
factor,
AhMYB2
.
Downregulation
leads
reduced
expression
key
enzyme
loss
color.
represents
most
date
valuable
resource
for
research.
High
similarity
regulator
partially
conserved
interaction
motif
support
co-option
possible
reason
mutual
exclusiveness
two
Язык: Английский