The Plant Cell,
Journal Year:
2020,
Volume and Issue:
32(5), P. 1434 - 1448
Published: March 17, 2020
Abstract
The
gene
balance
hypothesis
postulates
that
there
is
selection
on
copy
number
(gene
dosage)
to
preserve
the
stoichiometric
among
interacting
proteins.
This
presupposes
product
abundance
governed
by
dosage
and
responses
are
consistent
for
genes
in
a
dosage-balance-sensitive
network
or
complex.
Gene
responses,
however,
have
rarely
been
quantified,
available
data
suggest
they
highly
variable.
We
sequenced
transcriptomes
of
two
synthetic
autopolyploid
accessions
Arabidopsis
(Arabidopsis
thaliana)
their
diploid
progenitors,
as
well
one
natural
tetraploid
its
produced
via
haploid
induction,
estimate
transcriptome
size
immediately
following
ploidy
change.
Similar
what
has
observed
previous
studies,
overall
does
not
exhibit
simple
doubling
response
genome
doubling,
individual
variable
all
three
accessions,
indicating
expression
strictly
coupled
with
dosage.
Nonetheless,
putatively
balance-sensitive
groups
(Gene
Ontology
terms,
metabolic
networks,
families,
predicted
proteins)
smaller
more
coordinated
than
do
dosage-insensitive
groups,
suggesting
constraints
operate
whole-genome
duplication
duplicate
retention
patterns
shaped
balance.
The Plant Cell,
Journal Year:
2020,
Volume and Issue:
33(1), P. 11 - 26
Published: Dec. 1, 2020
Polyploidy
has
been
hypothesized
to
be
both
an
evolutionary
dead-end
and
a
source
for
innovation
species
diversification.
Although
polyploid
organisms,
especially
plants,
abound,
the
apparent
nonrandom
long-term
establishment
of
genome
duplications
suggests
link
with
environmental
conditions.
Whole-genome
seem
correlate
periods
extinction
or
global
change,
while
polyploids
often
thrive
in
harsh
disturbed
environments.
Evidence
is
also
accumulating
that
biotic
interactions,
instance,
pathogens
mutualists,
affect
differently
than
nonpolyploids.
Here,
we
review
recent
findings
insights
on
effect
abiotic
stress
versus
nonpolyploids
propose
response
general
important
even
determining
factor
success
polyploidy.
New Phytologist,
Journal Year:
2022,
Volume and Issue:
235(2), P. 801 - 809
Published: April 23, 2022
Summary
With
advanced
sequencing
technology,
dozens
of
complex
polyploid
plant
genomes
have
been
characterized.
However,
for
many
species,
their
diploid
ancestors
are
unknown
or
extinct,
making
it
impossible
to
unravel
the
subgenomes
and
genome
evolution
directly.
We
developed
a
novel
subgenome‐phasing
algorithm,
S
ub
P
haser
,
specifically
designed
neoallopolyploid
homoploid
hybrid.
first
searches
subgenome‐specific
sequence
(
k
‐mer),
then
assigns
homoeologous
chromosomes
into
subgenomes,
further
provides
tools
annotate
investigate
specific
sequences.
works
well
on
neoallopolyploids
hybrids
containing
sequences
like
wheat,
but
fails
autopolyploids
lacking
alfalfa,
indicating
that
can
phase
neoallopolyploid/homoploid
with
high
accuracy,
sensitivity
performance.
This
highly
accurate,
sensitive,
ancestral
data
free
chromosome
phasing
offers
significant
application
value
subgenome
in
hybrids,
subsequent
exploration
related
genetic/epigenetic
mechanisms.
Frontiers in Plant Science,
Journal Year:
2022,
Volume and Issue:
13
Published: Aug. 22, 2022
Polyploidy,
defined
as
the
coexistence
of
three
or
more
complete
sets
chromosomes
in
an
organism's
cells,
is
considered
a
pivotal
moving
force
evolutionary
history
vascular
plants
and
has
played
major
role
domestication
several
crops.
In
last
decades,
improved
cultivars
economically
important
species
have
been
developed
artificially
by
inducing
autopolyploidy
with
chemical
agents.
Studies
on
diverse
shown
that
anatomical
physiological
changes
generated
either
natural
artificial
polyploidization
can
increase
tolerance
to
abiotic
biotic
stresses
well
disease
resistance,
which
may
positively
impact
plant
growth
net
production.
The
aim
this
work
review
current
literature
regarding
link
between
ploidy
level
stressors,
emphasis
molecular
mechanisms
responsible
for
these
effects,
their
development
both
polyploids,
during
exposure
adverse
environmental
conditions.
We
focused
analysis
those
types
stressors
progress
made
knowledge
putative
morpho-physiological
and/or
involved,
revealing
factors
common,
need
be
addressed
future
research.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Feb. 22, 2024
Abstract
Whole-genome
duplication
(WGD),
or
polyploidy,
events
are
widespread
and
significant
in
the
evolutionary
history
of
angiosperms.
However,
empirical
evidence
for
rediploidization,
major
process
where
polyploids
give
rise
to
diploid
descendants,
is
still
lacking
at
genomic
level.
Here
we
present
chromosome-scale
genomes
mangrove
tree
Sonneratia
alba
related
inland
plant
Lagerstroemia
speciosa
.
Their
common
ancestor
has
experienced
a
whole-genome
triplication
(WGT)
approximately
64
million
years
ago
coinciding
with
period
dramatic
global
climate
change.
,
adapting
habitats,
extensive
chromosome
rearrangements
post-WGT.
We
observe
WGT
retentions
display
sequence
expression
divergence,
suggesting
potential
neo-
sub-functionalization.
Strong
selection
acting
on
three-copy
indicates
adaptive
value
response
new
environments.
To
elucidate
role
ploidy
changes
genome
evolution,
improve
model
polyploidization–rediploidization
based
evidence,
contributing
understanding
evolution
during
Frontiers in Genetics,
Journal Year:
2020,
Volume and Issue:
11
Published: July 28, 2020
It
has
long
been
recognized
that
hybridization
and
polyploidy
are
prominent
processes
in
plant
evolution.
Although
classically
as
significant
speciation
adaptation,
recognition
of
the
importance
interspecific
gene
flow
dramatically
increased
during
genomics
era,
concomitant
with
an
unending
flood
empirical
examples,
or
without
genome
doubling.
Interspecific
is
thus
increasingly
thought
to
lead
evolutionary
innovation
diversification,
via
adaptive
introgression,
homoploid
hybrid
allopolyploid
speciation.
Less
well
understood,
however,
suite
genetic
genomic
mechanisms
set
motion
by
merger
differentiated
genomes,
temporal
scale
over
which
recombinational
complexity
mediated
might
be
expressed
exposed
natural
selection.
We
focus
on
these
issues
here,
considering
types
molecular
saltational
event
between
two
diverged
species,
either
doubling,
how
various
can
contribute
novel
phenotypes.
Genetic
include
infusion
new
alleles
genesis
structural
variation
including
translocations
inversions,
homoeologous
exchanges,
transposable
element
mobilization
insertional
effects,
presence-absence
copy
number
variation.
Polyploidy
generates
massive
transcriptomic
regulatory
alteration,
presumably
disrupted
stoichiometries
factors,
small
RNAs
other
interactions
cascade
from
single-gene
expression
change
up
through
entire
networks
transformed
modules.
highlight
both
combinatorial
possibilities
range
scales
such
generated,
selection
drift.
International Journal of Plant Sciences,
Journal Year:
2019,
Volume and Issue:
181(1), P. 75 - 87
Published: Sept. 30, 2019
A
central
challenge
in
plant
ecology
is
to
define
the
major
axes
of
functional
variation
with
direct
consequences
for
fitness.
Central
three
main
components
fitness
(growth,
survival,
and
reproduction)
rate
metabolic
conversion
CO2
into
carbon
that
can
be
allocated
various
structures
functions.
Here
we
(1)
argue
a
primary
constraint
on
maximum
photosynthesis
per
unit
leaf
area
size
packing
density
cells
(2)
show
genome
strong
predictor
cell
sizes,
densities,
across
terrestrial
vascular
plants.
Regardless
genic
content
associated
size,
simple
biophysical
constraints
encapsulating
lower
limit
upper
as
well
range
possible
sizes
densities.
Genome
therefore,
acts
first-order
gain
predicted
limits
allocation
growth,
reproduction,
defense.
The
effects
metabolism,
have
broad
implications
biogeography
other
theories
suggest
selection
metabolism
may
role
evolution.
Proceedings of the Royal Society B Biological Sciences,
Journal Year:
2020,
Volume and Issue:
287(1939), P. 20202154 - 20202154
Published: Nov. 18, 2020
Whole-genome
duplication
(WGD),
which
leads
to
polyploidy,
is
implicated
in
adaptation
and
speciation.
But
what
are
the
immediate
effects
of
WGD
how
do
newly
polyploid
lineages
adapt
them?
With
many
studies
new
evolved
polyploids
now
available,
along
with
genes
under
selection
polyploids,
we
an
increasingly
good
position
understand
polyploidy
generates
novelty.
Here,
I
will
review
consistent
on
biology
plants,
such
as
increase
cell
size,
increased
stress
tolerance
more.
discuss
a
change
something
fundamental
size
can
challenge
function
some
types
particular.
also
have
learned
about
short-
medium-term
evolutionary
response
WGD.
It
clear
that
this
may
‘lock
in’
traits
happen
be
beneficial,
while
other
cases,
it
might
more
‘emergency
response’
work
around
physiological
changes
either
deleterious,
or
cannot
undone
context.
Yet,
return
rapidly
diploid-like
state.
Polyploids
may,
by
re-jigging
inter-related
processes,
find
new,
conditionally
adaptive,
normal.
Philosophical Transactions of the Royal Society B Biological Sciences,
Journal Year:
2021,
Volume and Issue:
376(1826), P. 20200117 - 20200117
Published: April 17, 2021
Biological
invasions
impose
ecological
and
economic
problems
on
a
global
scale,
but
also
provide
extraordinary
opportunities
for
studying
contemporary
evolution.
It
is
critical
to
understand
the
evolutionary
processes
that
underly
invasion
success
in
order
successfully
manage
existing
invaders,
prevent
future
invasions.
As
successful
invasive
species
sometimes
are
suspected
rapidly
adjust
their
new
environments
spite
of
very
low
genetic
diversity,
we
obliged
re-evaluate
genomic-level
translate
into
phenotypic
diversity.
In
this
paper,
review
work
supports
idea
trait
variation,
within
among
populations,
can
be
created
through
epigenetic
or
other
non-genetic
processes,
particularly
clonal
invaders
where
somatic
changes
persist
indefinitely.
We
consider
several
have
been
implicated
as
adaptive
success,
focusing
various
forms
'genomic
shock'
resulting
from
exposure
environmental
stress,
hybridization
whole-genome
duplication
(polyploidy),
leading
patterns
gene
expression
re-programming
contribute
variation
even
novelty.
These
mechanisms
transgressive
phenotypes,
including
hybrid
vigour
novel
traits,
may
thus
help
huge
successes
some
plant
especially
those
genetically
impoverished.
This
article
part
theme
issue
'How
does
epigenetics
influence
course
evolution?'
The Plant Journal,
Journal Year:
2021,
Volume and Issue:
107(4), P. 1003 - 1015
Published: June 2, 2021
SUMMARY
An
analysis
of
over
10
000
plant
genome
sizes
(GSs)
indicates
that
most
species
have
smaller
genomes
than
expected
given
the
incidence
polyploidy
in
their
ancestries,
suggesting
selection
for
downsizing.
However,
comparing
ancestral
GS
with
suggests
rate
DNA
loss
following
is
likely
to
been
very
low
(4–70
Mb/million
years,
4–482
bp/generation).
This
poses
a
problem.
How
might
such
small
losses
be
visible
selection,
overcome
power
genetic
drift
and
drive
downsizing?
Here
we
explore
problem,
focussing
on
role
double‐strand
break
(DSB)
repair
pathways
(non‐homologous
end
joining
homologous
recombination)
may
played.
We
also
two
hypotheses
could
explain
how
favour
downsizing
polyploidy:
reduce
(i)
nitrogen
(N)
phosphate
(P)
costs
associated
nucleic
acid
synthesis
nucleus
transcriptome
(ii)
impact
scaling
effects
cell
size,
which
influences
CO
2
uptake
water
loss.
hypothesis
must
fastest
early
polyploid
generations.
Alternatively,
if
more
continuous
process
evolutionary
time,
then
propose
it
byproduct
elsewhere,
as
limiting
damaging
activity
repetitive
DNA.
If
so,
photosynthesis,
use
efficiency
and/or
nutrient
at
level
emergent
properties,
advantages,
but
not
ones
selected
generational
timescales.