The Plant Journal,
Год журнала:
2023,
Номер
116(4), С. 1003 - 1017
Опубликована: Сен. 7, 2023
Populus
species
play
a
foundational
role
in
diverse
ecosystems
and
are
important
renewable
feedstocks
for
bioenergy
bioproducts.
Hybrid
aspen
tremula
×
P.
alba
INRA
717-1B4
is
widely
used
transformation
model
tree
functional
genomics
biotechnology
research.
As
an
outcrossing
interspecific
hybrid,
its
genome
riddled
with
sequence
polymorphisms
which
present
challenge
sequence-sensitive
analyses.
Here
we
report
telomere-to-telomere
this
hybrid
two
chromosome-scale,
haplotype-resolved
assemblies.
We
performed
comprehensive
analysis
of
the
repetitive
landscape
identified
both
tandem
repeat
array-based
array-less
centromeres.
Unexpectedly,
most
abundant
satellite
repeats
haplotypes
lie
outside
centromeres,
consist
147
bp
monomer
PtaM147,
frequently
span
>1
megabases,
form
heterochromatic
knobs.
PtaM147
detected
exclusively
aspens
(section
Populus)
but
PtaM147-like
sequences
occur
LTR-retrotransposons
closely
related
species,
suggesting
their
origin
from
retrotransposons.
The
genomic
resource
generated
genotype
has
greatly
improved
design
editing
experiments
that
highly
sensitive
to
polymorphisms.
work
should
motivate
future
hypothesis-driven
research
probe
into
function
aspen-specific
DNA.
Abstract
Summary
Large-scale
comparative
genomic
studies
have
provided
important
insights
into
species
evolution
and
diversity,
but
also
lead
to
a
great
challenge
visualize.
Quick
catching
or
presenting
key
information
hidden
in
the
vast
amount
of
data
relationships
among
multiple
genomes
requires
an
efficient
visualization
tool.
However,
current
tools
for
such
remain
inflexible
layout
and/or
require
advanced
computation
skills,
especially
genome-based
synteny.
Here,
we
developed
easy-to-use
flexible
tool,
NGenomeSyn
[multiple
(N)
Genome
Synteny],
publication-ready
syntenic
whole
genome
local
region
features
(e.g.
repeats,
structural
variations,
genes)
across
with
high
customization.
provides
easy
way
its
users
visualize
large
rich
by
simply
adjusting
options
moving,
scaling,
rotation
target
genomes.
Moreover,
could
be
applied
on
non-genomic
similar
input
formats.
Availability
implementation
is
freely
available
at
GitHub
(https://github.com/hewm2008/NGenomeSyn)
Zenodo
(https://doi.org/10.5281/zenodo.7645148).
Nature Plants,
Год журнала:
2024,
Номер
10(3), С. 423 - 438
Опубликована: Фев. 9, 2024
Abstract
Centromeres
strongly
affect
(epi)genomic
architecture
and
meiotic
recombination
dynamics,
influencing
the
overall
distribution
frequency
of
crossovers.
Here
we
show
how
is
regulated
distributed
in
holocentric
plant
Rhynchospora
breviuscula
,
a
species
with
diffused
centromeres.
Combining
immunocytochemistry,
chromatin
analysis
high-throughput
single-pollen
sequencing,
discovered
that
crossover
distally
biased,
sharp
contrast
to
hundreds
centromeric
units
features.
Remarkably,
found
crossovers
were
abolished
inside
but
not
their
proximity,
indicating
absence
canonical
centromere
effect.
We
further
propose
telomere-led
synapsis
homologues
feature
best
explains
observed
landscape.
Our
results
hint
at
primary
influence
mechanistic
features
pairing
rather
than
organization
determining
biased
R.
whereas
centromeres
(epi)genetic
properties
only
positioning
locally.
Abstract
A
pan-transcriptome
describes
the
transcriptional
and
post-transcriptional
consequences
of
genome
diversity
from
multiple
individuals
within
a
species.
We
developed
barley
using
20
inbred
genotypes
representing
domesticated
by
generating
analyzing
short-
long-read
RNA-sequencing
datasets
tissues.
To
overcome
single
reference
bias
in
transcript
quantification,
we
constructed
genotype-specific
(RTDs)
integrated
these
into
linear
pan-genome
framework
to
create
pan-RTD,
allowing
categorization
as
core,
shell
or
cloud.
Focusing
on
core
(expressed
all
genotypes),
observed
significant
abundance
variation
among
tissues
between
driven
partly
RNA
processing,
gene
copy
number,
structural
rearrangements
conservation
promotor
motifs.
Network
analyses
revealed
conserved
co-expression
module::tissue
correlations
frequent
functional
diversification.
complement
pan-transcriptome,
comprehensive
cultivar
(cv.)
Morex
gene-expression
atlas
illustrate
how
combined
can
be
used
guide
biological
inquiry.
Abstract
Cowpea,
Vigna
unguiculata
L
.
Walp.,
is
a
diploid
warm‐season
legume
of
critical
importance
as
both
food
and
fodder
in
sub‐Saharan
Africa.
This
species
also
grown
Northern
Africa,
Europe,
Latin
America,
North
East
to
Southeast
Asia.
To
capture
the
genomic
diversity
domesticates
this
important
legume,
de
novo
genome
assemblies
were
produced
for
representatives
six
subpopulations
cultivated
cowpea
identified
previously
from
genotyping
several
hundred
diverse
accessions.
In
most
complete
assembly
(IT97K‐499‐35),
26,026
core
4963
noncore
genes
identified,
with
35,436
pan
when
considering
all
seven
GO
terms
associated
response
stress
defense
highly
enriched
among
genes,
while
related
transcription
factor
activity,
transport
metabolic
processes.
Over
5
million
single
nucleotide
polymorphisms
(SNPs)
relative
each
over
40
structural
variants
>1
Mb
size
by
comparing
genomes.
Vu10
was
chromosome
highest
frequency
SNPs,
Vu04
had
variants.
Noncore
harbor
larger
proportion
potentially
disruptive
than
including
missense,
stop
gain,
frameshift
mutations;
suggests
that
substantially
contribute
within
domesticated
cowpea.
Grapevine
breeding
is
hindered
by
a
limited
understanding
of
the
genetic
basis
complex
agronomic
traits.
This
study
constructs
graph-based
pangenome
reference
(Grapepan
v.1.0)
from
18
newly
generated
phased
telomere-to-telomere
assemblies
and
11
published
assemblies.
Using
Grapepan
v.1.0,
we
build
variation
map
with
9,105,787
short
variations
236,449
structural
(SVs)
resequencing
data
466
grapevine
cultivars.
Integrating
SVs
into
genome-wide
association
study,
148
quantitative
trait
loci
for
29
traits
(50.7%
identified),
12
significantly
contributed
SVs.
The
estimated
heritability
improves
22.78%
on
average
when
including
We
discovered
locus
regions
under
divergent
artificial
selection
in
metabolism
berry
development
between
wine
table
grapes,
respectively.
Moreover,
significant
correlations
were
detected
among
Under
polygenic
model,
conducted
genomic
predictions
each
trait.
In
general,
our
facilitates
superior
cultivars
via
multiple
By
constructing
incorporating
phenotypic
maps,
investigates
traits,
empowering
breeding.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Май 24, 2024
Cannabis
sativa
is
a
globally
significant
seed-oil,
fiber,
and
drug-producing
plant
species.
However,
century
of
prohibition
has
severely
restricted
legal
breeding
germplasm
resource
development,
leaving
potential
hemp-based
nutritional
fiber
applications
unrealized.
Existing
cultivars
are
highly
heterozygous
lack
competitiveness
in
the
overall
grain
markets,
relegating
hemp
to
less
than
200,000
hectares
globally1.
The
relaxation
drug
laws
recent
decades
generated
widespread
interest
expanding
reincorporating
cannabis
into
agricultural
systems,
but
progress
been
impeded
by
limited
understanding
genomics
potential.
No
studies
date
have
examined
genomic
diversity
evolution
populations
using
haplotype-resolved,
chromosome-scale
assemblies
from
publicly
available
germplasm.
Here
we
present
pangenome,
constructed
with
181
new
12
previously
released
genomes
total
156
biological
samples
both
male
(XY)
female
(XX)
plants,
including
42
trio
phased
36
assemblies.
We
discovered
regions
pangenome
that
surprisingly
diverse
for
single
species,
high
levels
genetic
structural
variation,
propose
novel
population
structure
hybridization
history.
Conversely,
cannabinoid
synthase
genes
contain
very
low
diversity,
despite
being
embedded
within
variable
region
containing
multiple
pseudogenized
paralogs
distinct
transposable
element
arrangements.
Additionally,
identified
variants
acyl-lipid
thioesterase
(ALT)
associated
fatty
acid
chain
length
variation
production
rare
cannabinoids,
tetrahydrocannabinol
varin
(THCV)
cannabidiol
(CBDV).
conclude
gene
pool
only
partially
characterized,
existence
wild
relatives
Asia
remains
likely,
while
its
as
crop
species
largely
Journal of Integrative Plant Biology,
Год журнала:
2024,
Номер
66(7), С. 1408 - 1426
Опубликована: Апрель 5, 2024
ABSTRACT
Structural
variations
(SVs)
are
a
feature
of
plant
genomes
that
has
been
largely
unexplored
despite
their
significant
impact
on
phenotypic
traits
and
local
adaptation
to
abiotic
biotic
stress.
In
this
study,
we
employed
woolly
grape
(
Vitis
retordii
),
species
native
the
tropical
subtropical
regions
East
Asia
with
both
coastal
inland
habitats,
as
valuable
model
for
examining
SVs
adaptation.
We
assembled
haplotype‐resolved
chromosomal
reference
genome
grape,
conducted
population
genetic
analyses
based
whole‐genome
sequencing
(WGS)
data
from
populations.
The
demographic
revealed
recent
bottlenecks
in
all
populations
asymmetric
gene
flow
population.
total,
1,035
genes
associated
adaptive
regulation
salt
stress,
radiation,
environmental
were
detected
underlying
selection
by
SNPs
population,
which
37.29%
65.26%
SNPs,
respectively.
Candidate
such
FSD2
,
RGA1
AAP8
tolerance
found
be
highly
differentiated
selected
during
process
habitats
SV
regions.
Our
study
highlights
importance
adaptation;
candidate
related
stress
climatic
environments
important
genomic
resources
future
breeding
programs
grapevine
its
rootstocks.
Current Biology,
Год журнала:
2024,
Номер
34(16), С. 3763 - 3777.e5
Опубликована: Авг. 1, 2024
Seedlessness
is
a
crucial
quality
trait
in
table
grape
(Vitis
vinifera
L.)
breeding.
However,
the
development
of
seeds
involved
intricate
regulations,
and
polygenic
basis
seed
abortion
remains
unclear.
Here,
we
combine
comparative
genomics,
population
genetics,
quantitative
integrative
genomics
to
unravel
evolution
seedlessness
grapes.
We
generated
haplotype-resolved
genomes
for
two
seedless
cultivars,
"Thompson
Seedless"
(TS,
syn.
"Sultania")
"Black
Monukka"
(BM).
Comparative
identified
∼4.25
Mb
hemizygous
inversion
on
Chr10
specific
with
seedless-associated
genes
VvTT16
VvSUS2
located
at
breakpoints.
Population
genomic
analyses
548
grapevine
accessions
revealed
distinct
clusters
identity-by-descent
(IBD)
results
indicated
that
origin
could
be
traced
back
"Sultania."
Introgression,
rather
than
convergent
selection,
shaped
evolutionary
history
improvement.
Genome-wide
association
study
(GWAS)
analysis
110
loci
(QTLs)
associated
634
candidate
genes,
including
previously
unidentified
such
as
three
11S
GLOBULIN
SEED
STORAGE
PROTEIN
CYTOCHROME
P450
well-known
like
VviAGL11.
Integrative
resulted
339
core
categorized
into
13
functional
categories
related
development.
Machine
learning-based
selection
achieved
remarkable
prediction
accuracy
97%
grapevines.
Our
findings
highlight
nature
provide
molecular
genetics
an
effective