The
big-data
analysis
of
multi-omics
data
associated
with
maize
genomes
is
increasingly
utilized
to
accelerate
genetic
research
and
improve
agronomic
traits.
As
a
result,
efforts
have
increased
integrate
diverse
datasets
extract
meaning
from
these
measurements.
For
my
Ph.D.
dissertation,
I
evaluated
the
current
pitfalls
integration
built
platforms
that
automatically
analyze
omics'
datasets.
One
such
platform
qTeller,
now
designed
handle
pan-genome
level
transcriptomics
proteomics
meaningful
interpretation
them
by
providing
an
interactive
user
interface.
Although
genomics
been
more
extensively
used,
other
omics
technologies,
as
epigenomics,
variomics,
proteomics,
are
often
incorporated
into
standard
methodologies.
Therefore,
fully
automated
platform,
called
Maize
Feature
Store
(MFS),
allows
complex
construct
models
can
be
used
predict
gene
traits
or
annotations.
To
demonstrate
utility
MFS,
critically
discussed
application
MFS
in
using
only
single
genome
(B73v5)
case
study.
also
aim
utilize
large-scale
solve
several
biological
problems
phenome.
continue
improving
tools
assisting
users
implementing
them.
Journal of Experimental Botany,
Год журнала:
2024,
Номер
75(18), С. 5568 - 5584
Опубликована: Июнь 18, 2024
Abstract
In
the
last
20
years,
several
techniques
have
been
developed
for
quantifying
DNA
methylation,
most
studied
epigenetic
marks
in
eukaryotes,
including
gold
standard
method,
whole-genome
bisulfite
sequencing
(WGBS).
WGBS
quantifies
genome-wide
methylation
but
has
inconveniences
rendering
it
less
suitable
population-scale
studies.
The
high
cost
of
deep
and
large
amounts
data
generated
prompted
us
to
seek
an
alternative
approach.
Restricting
studies
parts
genome
would
be
a
satisfactory
had
there
not
major
limitation:
need
select
upstream
targets
corresponding
differentially
methylated
regions
as
targets.
Given
study
numbers
samples,
we
propose
strategy
investigating
variation
natural
populations,
taking
into
account
structural
complexity
genomes,
their
size,
content
unique
coding
versus
repeated
transposable
elements.
We
first
identified
highly
variable
subset
genotypes
representative
biological
diversity
population
by
WGBS.
then
analysed
variations
these
targeted
at
level
capture
(SeqCapBis).
entire
was
validated
applying
another
species.
Our
proof
concept
on
populations
two
forest
species:
Populus
nigra
Quercus
petraea.
PLANT PHYSIOLOGY,
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 7, 2024
Abstract
Embryogenesis
is
a
brief
but
potentially
critical
phase
in
the
life
cycle
of
tree
for
adaptive
phenotypic
plasticity.
Using
somatic
embryogenesis
maritime
pine
(Pinus
pinaster
Ait.),
we
found
that
temperature
during
maturation
affects
embryo
development
and
postembryonic
growth
up
to
3
yr.
We
examined
whether
this
stress
memory
could
stem
from
temperature-
and/or
development-induced
changes
DNA
methylation.
For
this,
developed
200
mb
custom
sequence
capture
bisulfite
analysis
genes
promoters
identify
differentially
methylated
cytosines
(DMCs)
between
treatments
(18,
23,
28
°C)
developmental
stages
(immature
cotyledonary
embryos,
shoot
apical
meristem
2-yr-old
plants)
investigate
if
these
differences
can
be
mitotically
transmitted
embryonic
(epigenetic
memory).
revealed
high
prevalence
temperature-induced
DMCs
(8%
14%)
compared
(<1%)
all
cytosine
contexts.
Developmental
showed
comparable
pattern
only
CG
context
with
strong
trend
toward
hypomethylation,
particularly
promoters.
A
percentage
induced
by
transitions
were
memorized
(up
45%–50%)
90%).
By
contrast,
was
lower
confined
after
both
8%).
stringent
criteria,
identified
10
involved
defense
responses
adaptation,
development,
chromatin
regulation
are
candidates
establishment
persistent
epigenetic
sensed
pine.
Here,
provide
evidence
methylation
marks
established
plant
phase.
European Journal of Forest Research,
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 18, 2024
Abstract
Understanding
adaptive
genetic
responses
to
climate
change
is
an
issue
of
utmost
importance
improve
conservation
policies
and
management.
This
study
deeps
on
it,
focusing
rear-edge
silver
fir
(
Abies
alba
)
forests,
where
decline
has
been
reported
linked
climatic
stressors,
such
as
warming
recurrent
drought
events.
Hotspots
coldspots
forest
mortality
were
defined.
Different
sets
single
nucleotide
polymorphisms
(SNPs),
namely
genome-wide
adaptive,
used
their
characteristics,
aiming
identify
differences
in
diversity
between
vigor
classes
(declining
non-declining
trees)
age
cohorts
(adult
trees
saplings).
Global
DNA
methylation
levels
assessed
investigate
a
possible
role
epigenetic
processes
adaptation
stressful
environments.
Parentage
relatedness
analysis
conducted
track
the
lineage
from
each
site.
Our
findings
indicate
that,
even
though
SNPs
seem
provide
more
insightful
information
than
set,
optimal
approach
for
evolutionary
studies
combination
both.
Changes
genomic
observed
classes,
revealing
existence
molecular
basis
behind
ongoing
events
forests.
Besides,
trees’
relatives
display
higher
mixture
origins
coldspots,
which
could
temporary
refuge
species’
potential.
All
all,
both
characteristics
should
be
considered
order
comprehend
how
respond
stress
achieve
change.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Март 15, 2023
Abstract
Long
non-coding
RNAs
(lncRNAs)
are
understudied
and
underannotated
in
plants.
In
mammals,
lncRNA
loci
nearly
as
ubiquitous
protein-coding
genes,
their
expression
is
highly
variable
between
individuals
of
the
same
species.
Using
Arabidopsis
thaliana
a
model,
we
aimed
to
understand
true
scope
transcription
across
plants
from
different
regions
study
its
natural
variation.
We
used
transcriptome
deep
sequencing
datasets
spanning
hundreds
accessions
several
developmental
stages
create
population-wide
annotation
lncRNAs,
revealing
thousands
previously
unannotated
loci.
While
genome,
most
appear
be
actively
silenced
extremely
accessions.
This
high
variability
largely
caused
by
repressive
chromatin
levels
at
High
was
particularly
common
for
intergenic
lncRNAs
(lincRNAs),
where
pieces
transposable
elements
(TEs)
present
50%
these
lincRNA
associated
with
increased
silencing
variation,
such
tend
targeted
TE
machinery.
A.
improve
our
understanding
plant
genome
biology,
raising
fundamental
questions
about
what
causes
genome.
One-sentence
summary
plentiful
but
repressed,
enriched
aiding
silencing.
Applied Ecology and Environmental Research,
Год журнала:
2023,
Номер
21(2), С. 1389 - 1407
Опубликована: Янв. 1, 2023
Potamogeton
crispus
is
an
important
species
in
purifying
water
and
maintaining
a
healthy
aquatic
ecosystem.To
find
the
effect
of
UV-B
radiation
on
life
history
P.
crispus,
seeding
plants
were
exposed
to
different
doses
for
7
h
within
81
days.Plant
growth
status,
morphological
indexes,
turion
morphology,
germination
indexes
monitored.The
results
showed
that
can
promote
branch,
did
not
branch
absence
radiation.P.
had
most
branches
when
intensity
was
100
µW/cm
2
.UV-B
accelerated
plant
decline
exposure
dose
exceeded
.Plant
height,
internode
length,
leaf
area,
dry
weight
per
all
decreased
with
increasing
doses.UV-B
could
stimulate
form
turions
increase
number
but
reduced
turions,
it
also
led
low
rate
index
shoots
sprouted
from
these
especially
.These
suggest
moderate
plays
role
controlling
branches,
height
formation
crispus.
Plants,
Год журнала:
2023,
Номер
12(17), С. 3056 - 3056
Опубликована: Авг. 25, 2023
Holm
oaks
(Quercus
ilex
L.)
can
suffer
severe
infection
by
the
oomycete
Phytophthora
cinnamomi
Rands;
production
of
more
tolerant
plants
is,
therefore,
required.
Embryo
formation
is
a
key
period
in
establishment
epigenetic
memory.
Somatic
embryos
from
three
holm
oak
genotypes
were
elicited,
either
over
3
days
or
60
days,
with
methyl-jasmonate,
salicylic
acid
(SA),
β-aminobutyric
(BABA),
benzothiadiazole
(all
at
50
μM
and
100
μM),
10%
30%
filtered
extract
(FILT10
FILT30)
to
activate
plant
immune
responses.
The
number
produced
conversion
rate
under
all
conditions
recorded.
Some
elicited
then
exposed
P.
dual
culture,
differential
mycelial
growth
progression
necrosis
measured.
same
was
performed
roots
germinated
embryos.
Within
genotypes,
significant
differences
seen
among
elicitation
treatments
terms
both
variables.
Embryos
60-day
BABA,
SA,
FILT10
inhibited
mycelium
growth.
3-day
BABA
(either
concentration)
induced
greatest
inhibition
necrosis.
Mycelium
compared
those
trees.
Both
inhibitions
might
be
defense
response
maintained
after
primed
embryo
germination,
thus
increasing
likelihood
tolerance
infection.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 30, 2024
Abstract
Embryogenesis
is
a
brief
but
potentially
critical
phase
in
the
tree
life
cycle
for
adaptive
phenotypic
plasticity.
Using
somatic
embryogenesis
maritime
pine,
we
found
that
temperature
during
maturation
affects
embryo
development
and
post-embryonic
growth
up
to
three
years.
We
examined
whether
this
stress
memory
could
stem
from
temperature-
and/or
development-induced
changes
DNA
methylation.
To
do
this,
developed
200
Mb
custom
sequence
capture
bisulfite
analysis
of
genes
promoters
identify
differentially
methylated
cytosines
(DMCs)
between
treatments
(18,
23,
28°C)
developmental
stages
(immature
cotyledonary
embryos,
shoot
apical
meristem
2-year-old
plants)
investigate
if
these
differences
can
be
mitotically
transmitted
embryonic
(epigenetic
memory).
revealed
high
prevalence
temperature-induced
DMCs
(8-14%)
compared
(less
than
1%)
all
3
cytosine
contexts.
Developmental
showed
comparable
pattern
only
CG
context,
with
trend
towards
hypo-methylation,
particularly
promoters.
A
percentage
induced
by
transitions
were
memorized
(up
45-50%)
90%).
In
contrast,
was
lower
confined
after
both
14%)
8%).
stringent
criteria,
identified
ten
involved
defense
responses
adaptation,
chromatin
regulation
are
candidates
establishment
persistent
epigenetic
sensed
pine.
Graphical
abstract
