The role of centromeric transposable elements in shaping chromosome evolution
Research Square (Research Square),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 3, 2025
Abstract
Transposable
elements
(TEs)
play
pivotal
roles
in
genome
evolution,
yet
their
impact
on
pericentromeric
regions
of
chromosomes,
characterized
by
high
sequence
turnover
and
TE
abundance,
remains
largely
unclear.
This
gap
knowledge
limits
our
understanding
TEs
biology
role
within
host
genomes.
In
this
study,
we
address
analysing
chromosome-scale
assemblies
to
explore
the
content
dynamics
four
closely
related
Biscutella
species.
Although
they
share
substantial
synteny,
observe
significant
variability
non-coding
genome,
especially
species
affected
strongest
genetic
drift
due
smallest
population
size.
By
comparing
from
CRM
clade,
which
specifically
target
centromeric
regions,
with
those
Athila
identify
specialized
CRMs
that
follow
centromeres
after
recent
repositioning,
alongside
an
invasion
copies
exhibit
less
insertion
bias.
Additionally,
find
migration
towards
distal
nucleolus
organizer
correlates
increased
DNA
methylation
decreased
gene
expression.
These
results
highlight
how
rapid
evolution
driven
bursts
activity
can
significantly
functionality
stability.
Our
findings
offer
new
insights
into
evolutionary
mechanisms
shaping
organization
underscore
broader
implications
for
adaptation.
Язык: Английский
Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 15, 2025
Abstract
Genetic
variation
underpins
evolutionary
change,
but
accumulation
of
slightly
deleterious
mutations
also
increases
mutation
load.
There
are
multiple
factors
affecting
the
extent
load
such
as
population
size
and
breeding
system,
yet
other
potential
determinants
remain
unexplored.
A
common
macromutation,
whole-genome
duplication
(WGD)
occurs
broadly
across
Eukaryotes,
we
lack
a
clear
understanding
how
WGD
impacts
neutral
selective
processes
within
population.
Using
forward
simulations
empirical
analysis
632
short-
16
long-read
sequenced
individuals
Arabidopsis
arenosa
(23
diploid
42
natural
autotetraploid
populations),
test
for
effects
on
genome-wide
diversity
Our
show
genetic
gradually
rises
in
autotetraploids
due
to
increase
mutational
target
size.
Moreover,
relaxed
purifying
selection
when
masked
by
additional
chromosome
copies.
Empirical
data
confirm
these
patterns,
showing
significant
nucleotide
diversity,
ratios
non-synonymous
synonymous
SNPs,
number
indels
large
structural
variants
A.
autotetraploids.
However,
rather
modest
proxies
together
with
broad
distribution
niche
suggests
has
not
(yet)
limited
their
successful
expansion.
Overall,
demonstrate
complex
interplay
between
shaping
following
highlight
ploidy
an
important
determinant
populations.
Язык: Английский
Post-polyploid chromosomal diploidization in plants is affected by clade divergence and constrained by shared genomic features
Research Square (Research Square),
Год журнала:
2025,
Номер
unknown
Опубликована: Май 12, 2025
Abstract
Genomic
redundancy
resulting
from
whole-genome
duplication
creates
opportunities
for
double-strand
misrepair
that
can
lead
to
chromosomal
rearrangements
and
a
reduction
in
chromosome
number,
known
as
descending
dysploidy.
Although
flowering
plants
often
undergo
post-polyploid
rediploidization,
the
pathways
consequences
of
dysploidy
are
still
poorly
understood.
In
this
study,
we
sequenced
assembled
genomes
eight
Biscutella
species
varying
size
0.6
1.1
Gb
exhibiting
numbers
n
=
6,
8
9.
Our
analysis
revealed
an
estimated
12
million
years
diploidization
allotetraploid
ancestral
genome
(
n
=
14)
characterized
by
independent
dysploidy,
of
n
9,
8,
6.
We
identified
clades
early-diverging
(n
8/6)
late-diverging
(n=
9)
exhibited
both
convergent
divergent
features.
While
showed
similar
levels
subgenome
fractionation
preferential
retention
polyploidy-derived
genes,
higher
removal
ratio
LTR
retrotransposons
greater
variability
topologically
associated
domains
(TADs).
addition,
breakage
hotspots
enriched
frequently
located
at
TAD
boundaries.
breakpoint
This
suggests
although
descendig
dysploid
appears
be
superficially
random
process,
some
shared
genomic
features
may
favor
occurrence
recurrent
breakpoints
different
species.
Язык: Английский
Co-occurring Luzula species (Juncaceae) of different ploidies exhibit weak ecological differentiation at local scale in alpine grasslands of the Eastern Alps
Alpine Botany,
Год журнала:
2025,
Номер
unknown
Опубликована: Май 20, 2025
Язык: Английский