Transposable
elements
(TEs)
are
major
contributors
to
structural
genomic
variation
by
creating
interspersed
duplications
of
themselves.
In
return,
variants
(SVs)
can
affect
the
distribution
TE
copies
and
shape
their
load.
One
long-standing
hypothesis
states
that
hybridization
could
trigger
mobilization
thus
increase
load
in
hybrids.
We
previously
tested
this
performing
a
large-scale
evolution
experiment
mutation
accumulation
(MA)
on
multiple
hybrid
genotypes
within
between
wild
populations
yeasts
Saccharomyces
paradoxus
cerevisiae
.
Using
aggregate
measures
with
short-read
sequencing,
we
found
no
evidence
for
MA
lines.
Here,
resolve
genomes
lines
long-read
phasing
assembly
precisely
characterize
role
SVs
shaping
landscape.
Highly
contiguous
phased
assemblies
127
revealed
SV
types
like
polyploidy,
aneuploidy
loss
heterozygosity
have
large
impacts
characterized
18
de
novo
insertions,
indicating
transposition
only
has
minor
landscape
Because
scarcity
provided
insufficient
resolution
confidently
dissect
rate
hybrids,
adapted
an
vivo
assay
measure
rates
various
S.
backgrounds.
not
increased
hybridization,
but
modulated
many
genotype-specific
factors
including
initial
load,
sequence
mitochondrial
DNA
inheritance.
Our
results
show
scales
at
which
is
shaped
genomes,
being
highly
impacted
dynamics
finely
rates.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 27, 2023
Background
Multidrug
resistance
has
been
identified
in
the
fungal
pathogen
responsible
for
Septoria
leaf
blotch,
Zymoseptoria
tritici
,
since
2011.
It
linked
to
overexpression
of
gene
encoding
MFS1
transporter
due
inserts
promoter
region
(P
),
namely
types
I-III.
Recently,
two
new
were
discovered
P
that
not
MDR,
interrogating
about
whether
are
only
drivers
MDR
Z.
.
The
goal
our
study
was
gain
a
more
complete
view
by
examining
genotypic
diversity
associated
with
phenotype
large
sample
modern
population.
Results
We
isolated
384
potential
strains
between
2020
and
2021
northern
Europe
genotype
assessment.
six
bringing
total
count
13
including
one
insertion-deletion
5’
UTR
region.
Of
these,
11
display
similarities
transposable
elements,
3
MDR.
Some
field
significantly
resistant
than
their
respective
reference
same
some
without
insert
displayed
phenotype.
Conclusion
described
landscape
population
postulate
is
hot-spot
insertions
involving
transposition
events.
Our
shows
cannot
be
solely
explained
found
additional
mechanisms
might
at
work.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Июль 15, 2023
Abstract
Genomic
instability
caused
by
chromosomal
rearrangements
has
severe
consequences
for
organismal
fitness
and
progression
of
cancerous
cell
lines.
The
triggers
destabilized
chromosomes
remain
poorly
understood
but
are
often
assumed
to
be
associated
with
fragile
sites.
Here,
we
retrace
a
runaway
degeneration
process
observed
in
fungal
pathogen
using
telomere-to-telomere
assemblies
across
an
experimental
pedigree.
We
show
that
the
same
sites
triggered
reproducible,
large-scale
through
non-allelic
recombination.
Across
four-generation
pedigree,
were
accompanied
non-disjunction
events
aneuploid
progeny
carry
up
four
copies.
identify
specific
transposable
element
as
most
likely
trigger
repeated
degeneration.
is
higher
virulence
undergone
burst
increasing
copy
numbers
genome.
Chromosome
sequences
also
targeted
genome
defense
mechanism
active
on
duplicated
sequences,
which
may
contribute
decay.
Our
work
identifies
exact
sequence
initiating
chromosome
perpetuating
degenerative
cycles.
Dissecting
proximate
causes
leading
run-away
expands
our
understanding
evolution
beyond
cancer
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Июль 16, 2023
Abstract
Background
In
agricultural
ecosystems,
outbreaks
of
diseases
are
frequent
and
pose
a
significant
threat
to
food
security.
A
successful
pathogen
undergoes
complex
well-timed
sequence
regulatory
changes
avoid
detection
by
the
host
immune
system,
hence
well-tuned
gene
regulation
is
essential
for
survival.
However,
extent
which
polymorphisms
in
population
provide
an
adaptive
advantage
poorly
understood.
Results
We
used
Zymoseptoria
tritici
,
one
most
important
pathogens
wheat,
generate
genome-wide
map
polymorphism
governing
expression.
investigated
transcription
levels
146
strains
grown
under
nutrient
starvation
performed
expression
quantitative
trait
loci
(eQTL)
mapping.
identified
cis
-eQTLs
65.3%
all
genes
majority
eQTL
within
2kb
upstream
downstream
start
site
(TSS).
also
show
that
different
elements
contributes
disproportionally
variation.
Investigating
categories,
we
found
enrichment
variants
predicted
be
fungal
pathogenesis
but
with
comparatively
low
effect
size,
suggesting
separate
layer
involving
epigenetics.
previously
reported
trait-associated
SNPs
populations
frequently
-regulatory
neighboring
implications
architecture.
Conclusions
Overall,
our
study
provides
extensive
evidence
single
segregate
large-scale
variation
likely
fuel
rapid
adaptation
resistant
hosts
environmental
change.
Abstract
Background
The
genome
of
the
filamentous
ascomycete
Podospora
anserina
shows
a
relatively
high
abundance
retrotransposons
compared
to
other
interspersed
repeats.
LTR-retrotransposon
family
crapaud
is
particularly
abundant
in
genome,
and
consists
multiple
diverged
sequence
variations
specifically
localized
5’
half
both
long
terminal
repeats
(LTRs).
P.
part
recently
species-complex,
which
makes
system
ideal
classify
based
on
observed
LTR
variation
study
evolutionary
dynamics,
such
as
diversification
bursts
elements
over
recent
time.
Results
We
developed
similarity
network
approach
seven
genomes
representing
species
complex
into
14
subfamilies.
This
method
does
not
utilize
consensus
sequence,
but
instead
it
connects
any
copies
that
share
enough
set
coverage.
Based
phylogenetic
analyses,
we
found
likely
diversified
ancestor
have
had
activity
at
different
time
points
for
Furthermore,
while
hypothesized
evolution
subfamilies
could
been
direct
effect
escaping
defense
repeat
induced
point
mutations,
this
be
case.
Conclusions
Our
contributes
development
methods
transposable
fungi,
also
highlights
intricate
patterns
retrotransposon
short
timescales
under
mutational
load
caused
by
nucleotide-altering
defense.
Transposable
elements
(TEs)
are
major
contributors
to
structural
genomic
variation
by
creating
interspersed
duplications
of
themselves.
In
return,
variants
(SVs)
can
affect
the
distribution
TE
copies
and
shape
their
load.
One
long-standing
hypothesis
states
that
hybridization
could
trigger
mobilization
thus
increase
load
in
hybrids.
We
previously
tested
this
performing
a
large-scale
evolution
experiment
mutation
accumulation
(MA)
on
multiple
hybrid
genotypes
within
between
wild
populations
yeasts
Saccharomyces
paradoxus
cerevisiae
.
Using
aggregate
measures
with
short-read
sequencing,
we
found
no
evidence
for
MA
lines.
Here,
resolve
genomes
lines
long-read
phasing
assembly
precisely
characterize
role
SVs
shaping
landscape.
Highly
contiguous
phased
assemblies
127
revealed
SV
types
like
polyploidy,
aneuploidy
loss
heterozygosity
have
large
impacts
characterized
18
de
novo
insertions,
indicating
transposition
only
has
minor
landscape
Because
scarcity
provided
insufficient
resolution
confidently
dissect
rate
hybrids,
adapted
an
vivo
assay
measure
rates
various
S.
backgrounds.
not
increased
hybridization,
but
modulated
many
genotype-specific
factors
including
initial
load,
sequence
mitochondrial
DNA
inheritance.
Our
results
show
scales
at
which
is
shaped
genomes,
being
highly
impacted
dynamics
finely
rates.