Abstract
Peppermint,
Mentha
×
piperita
L.,
is
a
hexaploid
(2n
=
6x
72)
and
the
predominant
cultivar
of
commercial
mint
oil
production
in
US.
This
threatened
because
high
susceptibility
to
fungal
disease
verticillium
wilt,
caused
by
Verticillium
dahliae.
report
details
first
draft
polyploid
chromosome-level
genome
assembly
for
this
species.
The
“Mitcham”
resource
will
broaden
comparative
studies
resistance,
essential
biosynthesis,
hybridization
events
within
genus
Mentha.
It
also
be
valuable
contribution
body
phylogenetic
involving
other
genera
that
contain
species
with
varying
ploidy
levels.
Plant Biology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 29, 2025
Abstract
Transposable
elements
(TEs)
constitute
a
significant
part
of
plant
genomes
and
shape
their
genomic
landscape.
While
some
TEs
are
ubiquitously
dispersed,
other
specifically
occupy
discrete
loci.
The
evolutionary
forces
behind
the
chromosomal
localization
poorly
understood.
Therefore,
we
first
review
specific
niches
where
often
localized
including
(i)
centromeres,
(ii)
(sub)telomeres,
(iii)
genes,
(iv)
sex
chromosomes.
In
second
this
review,
focus
on
processes
standing
non‐equal
distribution
various
in
purifying
selection,
insertion
site
preference
or
targeting
TEs,
post‐insertion
ectopic
recombination
between
spatiotemporal
regulation
TE
jumping.
Using
combination
above
processes,
explain
We
also
describe
phenomena
mutual
nesting
epigenetic
mark
silencing
interactions
3D
interphase
nucleus
concerning
localization.
summarize
functional
consequences
relate
them
to
cell
functioning
genome
evolution.
PLoS ONE,
Journal Year:
2025,
Volume and Issue:
20(6), P. e0325165 - e0325165
Published: June 2, 2025
Eukaryotic
genomes
are
often
rich
in
DNA
repetitive
elements,
involving
both
transposable
elements
(TE)
and
tandemly
repeated
satellite
DNA.
Grasshopper
species,
known
for
their
large
genome
sizes,
comprising
relatively
a
high
proportion
of
genomic
repeats.
This
study
aimed
to
identify
perform
comparative
analysis
content
eight
grasshopper
species
from
the
Pyrgomorphidae
Acrididae
families.
We
utilized
unassembled
low-coverage
Illumina
paired-end
short
reads
RepeatExplorer2
pipeline
repeats,
RepeatMasker
estimate
abundance
divergence
activity.
Flow
cytometry
estimated
ranging
1C
=
7.670
pg
18.612
pg,
with
Aularches
miliaris
(18.612
pg)
being
second
largest
insect
reported
date.
The
repeat
ranged
51%
74%,
mean
value
64.26%
total
genome.
major
identified
included
LINE,
Ty3_Gypsy,
Penelope,
Ty1-copia,
Helitron,
Maverick,
LINE
most
abundant,
constituting
24%
54%
Apalacris
varicornis
A.
,
respectively.
positive
correlation
TEs
size
suggests
that
expansion
has
contributed
sizes
observed.
Satellite
65
satDNA
families
across
species.
Additionally,
phylogenetic
TE
protein
domains
revealed
consensus
sequences
same
domain
cluster
together,
suggesting
domain-specific
evolutionary
pathways
reveals
new
dynamics
into
role
gigantism
as
well
other
mechanisms
Orthoptera.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: April 13, 2024
Abstract
This
study
presents
the
first
genome
and
transcriptome
analyses
for
Fusarium
oxysporum
f.sp.
lactucae
(Fola)
which
causes
wilt
disease
of
lettuce.
Long-read
sequencing
three
race
1
(Fola1)
4
(Fola4)
isolates
revealed
key
differences
in
putative
effector
complement
between
races
with
other
F.
f.spp.
following
mimp
-based
bioinformatic
analyses.
Notably,
homologues
Secreted
Xylem
(
SIX
)
genes,
also
present
many
f.spp,
were
identified
Fola,
both
SIX9
SIX14
(multiple
copies
sequence
variants)
Fola1
Fola4.
All
Fola4
contained
an
additional
single
copy
SIX8
.
RNAseq
lettuce
infection
highly
expressed
effectors,
some
those
reported
including
several
apii
Although
,
all
Fola4,
two
genes
Fola1,
only
was
as
further
analysis
that
gene
disrupted
by
insertion
a
transposable
element.
Two
variants
based
on
different
effector-based
included
divergently
transcribed
from
shared
promoter
either
PSE1
or
PSL1
respectively.
In
addition
there
evidence
independent
instances
HCT
variants.
The
involvement
helitrons
Fola
rearrangement
expression
is
discussed.
BMC Genomics,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: Sept. 30, 2024
Abstract
Background
Plant-virus
interaction
models
propose
that
a
virus’s
ability
to
infect
host
genotype
depends
on
the
compatibility
between
virulence
and
resistance
genes.
Recently,
we
conducted
an
evolution
experiment
in
which
lineages
of
turnip
mosaic
virus
(TuMV)
were
passaged
Arabidopsis
thaliana
genotypes
carrying
mutations
components
DNA
methylation
histone
demethylation
epigenetic
pathways.
All
evolved
increased
infectivity,
viral
load
genotype-dependent
manner.
Results
To
better
understand
underlying
reasons
for
these
relationships,
delved
into
transcriptomic
responses
mutant
WT
plant
mock
conditions
infected
with
either
ancestral
or
viruses.
Such
comparison
allowed
us
classify
every
gene
nine
basic
expression
profiles.
Regarding
targets
adaptation,
our
analyses
identification
common
as
well
genotype-specific
genes
categories
biological
processes.
As
expected,
immune
response-related
found
be
altered
upon
infection.
However,
also
noticed
pervasive
over-representation
other
functional
groups,
suggesting
adaptation
was
not
solely
driven
by
level
In
addition,
significant
association
presence
transposable
elements
within
upstream
differentially
expressed
observed.
Finally,
integration
data
virus-host
protein-protein
network
highlighted
most
impactful
interactions.
Conclusions
These
findings
shed
extra
light
complex
dynamics
plants
viruses,
indicating
infectivity
various
factors
beyond
just
plant’s
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: March 16, 2024
Abstract
Structural
variants
(SVs,
eg.
insertions
and
deletions)
are
genomic
variations
>
50
bp
that
known
to
be
associated
with
a
range
of
crop
traits,
from
yield
flowering
behaviour
stress
responses.
Recently,
pangenome
graphs
have
emerged
as
powerful
framework
for
analysing
data
by
encoding
population-
or
species-level
diversity
in
one
structure.
Pangenome
the
potential
serve
unbiased
references
downstream
applications,
including
SV
genotyping
pan-transcriptomic
analyses.
In
this
work,
we
hypothesized
extensive
variation
affects
transcript
quantification
expression
quantitative
trait
locus
(eQTL)
analysis
when
relying
on
single
reference,
using
can
mitigate
reference
sequence
bias.
We
combined
long
short
read
whole
genome
sequencing
profiling
Brassica
napus
(oilseed
rape)
assess
impact
SVs
gene
regulation
explored
utility
eQTL
analysis.
demonstrate
provides
superior
eliminating
bias
quantification.
Combined
graph-based
SVs,
identified
240
eQTL-SVs
found
close
proximity
target
loci.
These
affect
genes
related
important
often
not
linkage
SNPs
represent
unaccounted
classical
SNP-based
This
study
highlights
multiple
advantages
approaches
population-scale
studies
novel
insight
into
an
crop.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: March 16, 2024
Peppermint,
Mentha
xpiperita
L.,
is
a
hexaploid
(2n
=
6x
72)
and
the
predominant
cultivar
of
commercial
mint
oil
production
in
US.
This
threatened
because
high
susceptibility
to
fungal
disease
Verticillium
wilt,
caused
by
dahliae
.
report
details
first
draft
polyploid
chromosome-level
genome
assembly
for
this
species.
The
Black
Mitcham
resource
will
broaden
comparative
studies
resistance,
essential
biosynthesis,
hybridization
events
within
genus
It
also
be
valuable
contribution
body
phylogenetic
involving
other
genera
that
contain
species
with
varying
ploidy
levels.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: June 22, 2024
Abstract
Plant-virus
interaction
models
propose
that
a
virus’s
ability
to
infect
host
genotype
depends
on
the
compatibility
between
virulence
and
resistance
genes.
Recently,
we
conducted
an
evolution
experiment
in
which
lineages
of
turnip
mosaic
virus
(TuMV)
were
passaged
Arabidopsis
thaliana
genotypes
carrying
mutations
components
DNA
methylation
histone
demethylation
epigenetic
pathways.
All
evolved
increased
infectivity,
viral
load
genotype-dependent
manner.
To
better
understand
underlying
reasons
for
these
relationships,
delved
into
transcriptomic
responses
mutant
WT
plant
mock
conditions
infected
with
either
ancestral
or
viruses.
Such
comparison
allowed
us
classify
every
gene
nine
basic
expression
profiles.
Regarding
targets
adaptation,
our
analyses
identification
common
as
well
genotype-specific
genes
categories
biological
processes.
As
expected,
immune
response-related
found
be
altered
upon
infection.
However,
also
noticed
pervasive
over-representation
other
functional
groups,
suggesting
adaptation
was
not
solely
driven
by
level
In
addition,
significant
association
presence
transposable
elements
within
upstream
differentially
expressed
observed.
Finally,
integration
data
virus-host
protein-protein
network
highlighted
most
impactful
interactions.
These
findings
shed
extra
light
complex
dynamics
plants
viruses,
indicating
infectivity
various
factors
beyond
just
plant’s
Abstract
Understanding
the
role
of
repetitive
elements
(REs)
in
cancer
development
is
crucial
for
identifying
novel
biomarkers
and
therapeutic
targets.
This
study
investigated
locus-specific
dysregulation
REs,
including
differential
expression
methylation
across
12
TCGA
types
stratified
by
their
genomic
context
(
i.e.
,
genic
intergenic
REs).
We
found
uniquely
dysregulated
REs
co-regulated
with
corresponding
transcripts
associated
distinct
biological
functions
different
types.
Uniquely
were
identified
each
type
used
to
cluster
sample
Recurrently
several
types,
genes
up-regulated
involved
cell
cycle
processes
those
down-regulated
extracellular
matrix.
Interestingly,
4
out
5
consistently
all
located
intronic
region
TMEM252,
a
recently
discovered
tumor
suppressor
gene.
TMEM252
was
also
10
suggesting
its
potential
importance
wide
range
With
DNA
array
data,
we
higher
prevalence
hypo-methylated
most
(10
12).
Despite
slight
overlaps
between
differentially
expressed
methylated
showed
that
negatively
correlates
some