Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Апрель 17, 2024
Abstract
Poaceae
members
shared
a
whole-genome
duplication
called
rho.
However,
little
is
known
about
the
evolutionary
pattern
of
rho-derived
duplicates
among
lineages
and
implications
in
adaptive
evolution.
Here
we
present
phylogenomic/phylotranscriptomic
analyses
363
grasses
covering
all
12
subfamilies
report
nine
previously
unknown
duplications.
Furthermore,
duplications
from
single
were
mapped
to
multiple
nodes
on
species
phylogeny;
was
likely
by
woody
bamboos
with
possible
gene
flow
herbaceous
bamboos;
recent
paralogues
tetraploid
Oryza
are
implicated
tolerance
seawater
submergence.
Moreover,
rho
showing
differential
retention
include
those
functions
environmental
adaptations
or
morphogenesis,
including
ACOT
for
aquatic
environments
(Oryzoideae),
CK2β
cold
responses
(Pooideae),
SPIRAL1
rapid
cell
elongation
(Bambusoideae),
PAI1
drought/cold
(Panicoideae).
This
study
presents
profile
evidence
mechanisms
that
contribute
losses.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Март 20, 2024
Abstract
Subgenome
dominance
has
been
reported
in
diverse
allopolyploid
species,
where
genes
from
one
subgenome
are
preferentially
retained
and
more
highly
expressed
than
those
other
subgenome(s).
However,
the
molecular
mechanisms
responsible
for
remain
poorly
understood.
Here,
we
develop
genome-wide
map
of
accessible
chromatin
regions
(ACRs)
cultivated
strawberry
(2
n
=
8
x
56,
with
A,
B,
C,
D
subgenomes).
Each
ACR
is
identified
as
an
MNase
hypersensitive
site
(MHS).
We
discover
that
dominant
A
contains
a
greater
number
total
MHSs
MHS
per
gene
submissive
B/C/D
subgenomes.
suffers
fewer
losses
MHS-related
DNA
sequences
fragmentations
caused
by
insertions
transposable
elements.
also
related
to
stress
response
have
A.
conclude
preservation
their
cognate
ACRs,
especially
responses,
play
major
role
establishment
octoploid
strawberry.
Nature Genetics,
Год журнала:
2024,
Номер
56(11), С. 2538 - 2550
Опубликована: Ноя. 1, 2024
Although
individual
genomic
structural
variants
(SVs)
are
known
to
influence
gene
expression
and
trait
variation,
the
extent
scale
of
SV
impact
across
a
species
remain
unknown.
In
present
study,
we
constructed
reference
library
334,461
SVs
from
genome
assemblies
16
representative
morphotypes
neopolyploid
Brassica
napus
accessions
detected
258,865
in
2,105
resequenced
genomes.
Coupling
with
5
tissue
population
transcriptomes,
uncovered
285,976
SV-expression
quantitative
loci
(eQTLs)
that
associate
altered
73,580
genes.
We
developed
pipeline
for
high-throughput
joint
analyses
SV-genome-wide
association
studies
(SV-GWASs)
transcriptome-wide
phenomic
data,
eQTLs
eQTL-GWAS
colocalization,
identified
726
SV-gene
expression-trait
variation
associations,
some
which
were
verified
by
transgenics.
The
pervasive
on
how
reshapes
was
demonstrated
glucosinolate
biosynthesis
transport
pathway.
study
highlighting
genome-wide
species-scale
provides
powerful
methodological
strategy
valuable
resources
studying
evolution,
discovery
breeding.
Nature Genetics,
Год журнала:
2024,
Номер
56(9), С. 1975 - 1984
Опубликована: Авг. 13, 2024
Abstract
Cultivated
peanut
(
Arachis
hypogaea
L.)
is
a
widely
grown
oilseed
crop
worldwide;
however,
the
events
leading
to
its
origin
and
diversification
are
not
fully
understood.
Here
by
combining
chloroplast
whole-genome
sequence
data
from
large
germplasm
collection,
we
show
that
two
subspecies
of
A.
fastigiata
)
likely
arose
distinct
allopolyploidization
domestication
events.
Peanut
genetic
clusters
were
then
differentiated
in
relation
dissemination
routes
breeding
efforts.
A
combination
linkage
mapping
genome-wide
association
studies
allowed
us
characterize
genes
genomic
regions
related
main
morpho-agronomic
traits,
namely
flowering
pattern,
inner
tegument
color,
growth
habit,
pod/seed
weight
oil
content.
Together,
our
findings
shed
light
on
evolutionary
history
phenotypic
peanuts
might
be
broad
interest
plant
breeders.
Poa
annua
(annual
bluegrass)
is
an
allotetraploid
turfgrass,
agronomically
significant
weed,
and
one
of
the
most
widely
dispersed
plant
species
on
earth.
Here,
we
report
chromosome-scale
genome
assemblies
P.
annua's
diploid
progenitors,
infirma
supina,
use
multi-omic
analyses
spanning
all
three
to
better
understand
evolutionary
novelty.We
find
that
diploids
diverged
from
their
common
ancestor
5.5
-
6.3
million
years
ago
hybridized
form
≤
50,000
ago.
The
genomes
are
similar
in
chromosome
structure
notably
distinguished
by
divergent
histories
transposable
elements,
leading
a
1.7
×
difference
size.
In
annua,
biased
movement
retrotransposons
larger
(A)
subgenome
smaller
(B)
subgenome.
We
show
B
preferentially
accumulating
genes
its
more
highly
expressed.
Whole-genome
resequencing
several
additional
accessions
revealed
large-scale
chromosomal
rearrangements
characterized
extensive
TE-downsizing
evidence
support
Genome
Balance
Hypothesis.The
evolutions
progenitors
played
central
role
conferring
onto
remarkable
phenotypic
plasticity.
(guided
selection
drift)
elements
(mostly
guided
host
immunity)
each
respond
polyploidy
unique
ways
uses
whole-genome
duplication
purge
parasitized
heterochromatic
sequences.
findings
genomic
resources
presented
here
will
enable
development
homoeolog-specific
markers
for
accelerated
weed
science
turfgrass
breeding.
Molecular Biology and Evolution,
Год журнала:
2024,
Номер
41(3)
Опубликована: Фев. 29, 2024
Abstract
Polyploidy,
a
significant
catalyst
for
speciation
and
evolutionary
processes
in
both
plant
animal
kingdoms,
has
been
recognized
long
time.
However,
the
exact
molecular
mechanism
that
leads
to
polyploid
formation,
especially
vertebrates,
is
not
fully
understood.
Our
study
aimed
elucidate
this
phenomenon
using
zebrafish
model.
We
successfully
achieved
an
effective
knockout
of
cyclin
N-terminal
domain
containing
1
(cntd1)
CRISPR/Cas9
technology.
This
resulted
impaired
formation
meiotic
crossovers,
leading
cell-cycle
arrest
during
metaphase
triggering
apoptosis
spermatocytes
testes.
Despite
these
defects,
mutant
(cntd1−/−)
males
were
still
able
produce
limited
amount
sperm
with
normal
ploidy
function.
Interestingly,
females,
it
was
capacity
egg
production
altered.
haploid,
aneuploid,
unreduced
gametes.
alteration
enabled
us
obtain
triploid
tetraploid
from
cntd1−/−
cntd1−/−/−
respectively.
Furthermore,
tetraploid-heterozygous
produced
reduced-diploid
gametes
yielded
all-triploid
or
all-tetraploid
offspring
when
crossed
wild-type
(WT)
zebrafish,
Collectively,
our
findings
provide
direct
evidence
supporting
crucial
role
crossover
defects
process
polyploidization.
particularly
evident
generation
eggs
fish
and,
potentially,
other
vertebrate
species.
Polyploidy
is
widely
recognized
as
a
significant
evolutionary
force
in
the
plant
kingdom,
contributing
to
diversification
of
plants.
One
notable
features
allopolyploidy
occurrence
homoeologous
exchange
(HE)
events
between
subgenomes,
causing
changes
genomic
composition,
gene
expression,
and
phenotypic
variations.
However,
role
HE
adaptation
domestication
remains
unclear.
Here
we
analyze
whole-genome
resequencing
data
from
Brassica
napus
accessions
representing
different
morphotypes
ecotypes,
investigate
domestication.
Our
findings
demonstrate
frequent
HEs
napus,
with
substantial
patterns
shared
across
populations,
indicating
their
potential
promoting
crop
are
asymmetric,
A
genome
more
frequently
replacing
C
segments.
These
show
preference
for
specific
regions
vary
among
populations.
We
also
identify
candidate
genes
certain
which
likely
contribute
flowering-time
diverse
ecotypes.
In
addition,
assemble
new
swede
accession,
confirming
signals
on
involvement
root
tuber
development.
By
analyzing
another
allopolyploid
species,
juncea,
characterize
broader
results
provide
novel
insights
into
polyploid
species
highlight
crucial
mechanism
generating
variations
that
selected
improvement
species.
Applications in Plant Sciences,
Год журнала:
2024,
Номер
12(4)
Опубликована: Апрель 22, 2024
Phylogenetic
inference
of
polyploid
species
is
the
first
step
towards
understanding
their
patterns
diversification.
In
this
paper,
we
review
challenges
and
limitations
inferring
relationships
plants
using
traditional
phylogenetic
sequencing
approaches,
as
well
mischaracterization
tree
from
single
or
multiple
gene
trees.
We
provide
a
roadmap
to
infer
interspecific
among
lineages
by
comparing
evaluating
application
current
phylogenetic,
phylogenomic,
transcriptomic,
whole-genome
approaches
different
platforms.
For
reconstruction,
assess
following
criteria:
(1)
amount
prior
information
tools
required
capture
genetic
region(s)
interest;
(2)
probability
recovering
homeologs
for
species;
(3)
time
efficiency
downstream
data
analysis.
Moreover,
discuss
bioinformatic
pipelines
that
can
reconstruct
networks
relationships.
summary,
although
phylogenomic
have
improved
our
reticulate
in
polyploid-rich
genera,
difficulties
reliable
orthologous
genes
sorting
all
homeologous
copies
allopolyploids
remain
challenge.
future,
assembled
long-read
will
assist
recovery
identification
copies,
which
be
particularly
useful
reconstructing
independent
origins
polyploids.
American Journal of Botany,
Год журнала:
2024,
Номер
111(8)
Опубликована: Авг. 1, 2024
A
complicating
factor
in
analyzing
allopolyploid
genomes
is
the
possibility
of
physical
interactions
between
homoeologous
chromosomes
during
meiosis,
resulting
either
crossover
(homoeologous
exchanges)
or
non-crossover
products
gene
conversion).
Homoeologous
conversion
was
first
described
cotton
by
comparing
SNP
patterns
sequences
from
two
diploid
progenitors
with
those
subgenomes.
These
analyses,
however,
did
not
explicitly
consider
other
evolutionary
scenarios
that
may
give
rise
to
similar
as
conversion,
creating
uncertainties
about
reality
inferred
events.
