bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Nov. 5, 2023
ABSTRACT
Premise
Leafless,
heterotrophic
plants
are
prime
examples
of
organismal
modification,
the
genomic
consequences
which
have
received
considerable
interest.
In
particular,
plastid
genomes
(plastomes)
being
sequenced
at
a
high
rate,
allowing
continual
refinement
conceptual
models
reductive
evolution
in
heterotrophs.
Yet,
numerous
sampling
gaps
exist,
hindering
ability
to
conduct
comprehensive
phylogenomic
analyses
these
plants.
Methods
We
and
analyzed
plastome
Degranvillea
dermaptera
,
rarely
collected,
leafless
orchid
species
from
South
America
about
little
is
known,
including
its
phylogenetic
affinities.
Key
Results
revealed
most
reduced
date
among
subfamily
Orchidoideae.
has
lost
majority
genes
found
leafy
autotrophic
species,
structurally
rearranged,
similar
gene
content
plastomes
orchids.
strong
evidence
for
placement
within
subtribe
Spiranthinae
using
that
explicitly
account
heterotachy,
or
lineage-specific
evolutionary
rate
variation
over
time.
further
relaxed
selection
on
several
correlations
substitution
rates
other
“traits”
members
Conclusions
Our
findings
advance
knowledge
relationships
paths
genome
orchids,
experienced
more
independent
transitions
heterotrophy
than
any
plant
family.
This
study
demonstrates
importance
herbarium
collections
comparative
genomics
poorly
known
conservation
concern.
Proceedings of the Royal Society B Biological Sciences,
Journal Year:
2025,
Volume and Issue:
292(2043)
Published: March 1, 2025
The
independent
transition
to
a
heterotrophic
lifestyle
in
plants
drove
remarkably
convergent
evolutionary
trajectories,
characterized
by
morphological
modifications
and
reductions
their
plastomes.
characteristics
of
the
minimum
plastome
required
for
survival,
if
they
exist,
remain
topic
debate.
holoparasitic
family
Balanophoraceae
was
initially
presumed
have
entirely
lost
plastids,
however,
recent
reports
revealed
presence
reduced
aberrant
plastids
with
odd
genomes.
Among
outstanding
features
these
genomes
are
highest
nucleotide
composition
bias
across
tree
life
only
two
genetic
code
changes
ever
recorded
among
plants.
In
this
study,
we
assembled
plastomes
from
five
genera,
four
which
had
never
been
studied.
Major
common
include
extremely
high
AT
content,
lack
typical
quadripartite
structure
extensive
size
reduction
due
gene
elimination
genome
compaction.
exhibits
multiple
intron
losses,
broad
range
scenarios
regarding
evolution
plastid
trnE
,
considered
essential
because
its
dual
function
tetrapyrrole
biosynthesis
translation
within
plastid.
addition,
phylogenetic
analyses
suggest
that
genus
Scybalium
is
not
monophyletic.
An
model
proposed.
Annals of Botany,
Journal Year:
2023,
Volume and Issue:
132(5), P. 909 - 928
Published: July 27, 2023
The
molecular
evolution
of
organellar
genomes
in
angiosperms
has
been
studied
extensively,
with
some
lineages,
such
as
parasitic
ones,
displaying
unique
characteristics.
Parasitism
emerged
12
times
independently
angiosperm
evolution.
Holoparasitism
is
the
most
severe
form
parasitism,
and
found
~10
%
angiosperms.
Although
a
few
holoparasitic
species
have
examined
at
level,
reports
involve
plastomes
instead
mitogenomes.
Parasitic
plants
establish
vascular
connections
their
hosts
through
haustoria
to
obtain
water
nutrients,
which
facilitates
exchange
genetic
information,
making
them
more
susceptible
horizontal
gene
transfer
(HGT).
HGT
prevalent
mitochondria
than
chloroplast
or
nuclear
compartments.
Frontiers in Plant Science,
Journal Year:
2024,
Volume and Issue:
15
Published: June 28, 2024
The
plastid-targeted
transcription
factor
Whirly1
(
WHY1
)
has
been
implicated
in
chloroplast
biogenesis,
plastid
genome
stability,
and
fungal
defense
response,
which
together
represent
characteristics
of
interest
for
the
study
autotrophic
losses
across
angiosperms.
While
gene
loss
nuclear
genomes
well
studied
mycoheterotrophic
plants,
evolution
molecular
mechanisms
impacting
stability
is
completely
unknown.
Here,
we
characterize
four
early
transitional
orchid
species
genus
Corallorhiza
by
synthesizing
results
phylogenetic,
transcriptomic,
comparative
genomic
analyses
with
sequences
sampled
from
21
orders
We
found
an
increased
number
non-canonical
isoforms
assembled
all
but
greenest
species,
including
intron
retention
some
isoforms.
Within
,
phylotranscriptomic
revealed
presence
tissue-specific
differential
expression
only
most
photosynthetically
capable
a
coincident
increase
fully
species.
Gene-
codon-level
tests
selective
regimes
did
not
infer
significant
signal
either
relaxed
selection
or
episodic
diversifying
so
late-stage
full
orchids
Epipogium
aphyllum
Gastrodia
elata
.
Additionally,
nucleotide
substitutions
that
likely
impact
function
such
as
nonsense
mutations,
were
observed
mycoheterotrophs.
propose
our
findings
suggest
splicing
changes
may
precede
shifts
inferred
therefore
does
support
primary
role
transition
to
mycoheterotrophy
Orchidaceae.
Taken
together,
this
provides
comprehensive
view
angiosperms
date.
Annals of Botany,
Journal Year:
2024,
Volume and Issue:
unknown
Published: May 28, 2024
Abstract
Background
and
Aims
Heterotrophic
plants
have
long
been
a
challenge
for
systematists,
exemplified
by
the
base
of
orchid
subfamily
Epidendroideae,
which
contains
numerous
mycoheterotrophic
species.
Methods
Here
we
address
utility
organellar
genomes
in
resolving
relationships
at
epidendroid
base,
specifically
employing
models
heterotachy,
or
lineage-specific
rate
variation
over
time.
We
further
conduct
comparative
analyses
plastid
genome
evolution
heterotrophs
structural
matK.
Key
Results
present
first
complete
(plastomes)
Wullschlaegelia,
sole
genus
tribe
Wullschlaegelieae,
revealing
highly
reduced
37
kb,
retains
fraction
genes
related
autotrophs.
Plastid
phylogenomic
recovered
strongly
supported
clade
composed
exclusively
species
with
branches.
analysed
mitochondrial
gene
sets,
similar
to
those
other
studies
using
nuclear
data,
but
placement
Wullschlaegelia
remains
uncertain.
conducted
plastome
among
heterotrophic
orchids,
suite
correlated
substitutional
changes
relative
autotrophic
Lastly,
investigated
evolutionary
matK,
is
retained
few
‘late
stage’
found
evidence
conservation
despite
rapid
substitution
rates
both
leafless
Gastrodia.
Conclusions
Our
reveal
limits
what
can
tell
us
on
this
part
tree,
even
when
applying
parameter-rich
heterotachy
models.
study
underscores
need
increased
taxon
sampling
across
all
three
illustrates
research
addressing
analyses.
American Journal of Botany,
Journal Year:
2024,
Volume and Issue:
111(7)
Published: July 1, 2024
Abstract
Premise
Leafless,
heterotrophic
plants
are
prime
examples
of
organismal
modification,
the
genomic
consequences
which
have
received
considerable
interest.
In
particular,
plastid
genomes
(plastomes)
being
sequenced
at
a
high
rate,
allowing
continual
refinement
conceptual
models
reductive
evolution
in
heterotrophs.
However,
numerous
sampling
gaps
exist,
hindering
ability
to
conduct
comprehensive
phylogenomic
analyses
these
plants.
Methods
Using
floral
tissue
from
an
herbarium
specimen,
we
and
analyzed
plastome
Degranvillea
dermaptera
,
rarely
collected,
leafless
orchid
species
South
America
about
little
is
known,
including
its
phylogenetic
affinities.
Results
The
most
reduced
those
among
subfamily
Orchidoideae.
it
has
lost
majority
genes
found
leafy
autotrophic
species,
structurally
rearranged,
similar
gene
content
plastomes
orchids.
We
strong
evidence
for
placement
within
subtribe
Spiranthinae
using
that
explicitly
account
heterotachy,
or
lineage‐specific
evolutionary
rate
variation
over
time.
further
relaxed
selection
on
several
correlations
substitution
rates
other
“traits”
members
Conclusions
Our
findings
advance
knowledge
relationships
paths
genome
orchids,
experienced
more
independent
transitions
heterotrophy
than
any
plant
family.
This
study
demonstrates
importance
collections
comparative
genomics
poorly
known
conservation
concern.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 16, 2025
The
altered
life
history
strategies
of
heterotrophic
organisms
often
leave
a
profound
genetic
footprint
on
energy
metabolism
related
functions.
In
parasitic
plants,
the
reliance
host-derived
nutrients
and
loss
photosynthesis
in
holoparasites
have
led
to
highly
degraded
absent
plastid
genomes,
but
its
impact
mitochondrial
genome
(mitogenome)
evolution
has
remained
controversial.
By
examining
mitogenomes
from
45
Orobanchaceae
species
including
three
independent
transitions
holoparasitism
key
evolutionary
intermediates,
we
identified
measurable
predictable
alterations
genomic
shuffling,
RNA
editing,
intracellular
(IGT)
horizontal
gene
transfer
(HGT)
en
route
nonphotosynthetic
lifestyle.
In-depth
comparative
analyses
revealed
DNA
recombination
repair
processes,
especially
RNA-mediated
retroprocessing,
as
significant
drivers
for
structure
evolution.
particular,
novel
IGT
HGT
mechanism,
which
not
been
demonstrated
cross-species
inter-organelle
transfers.
Based
this,
propose
generalized
dosage
effect
mechanism
explain
biased
transferability
mitochondria
across
green
lineages
like
parasites
mycoheterotrophs.
Evolutionary
rates
scaled
with
these
changes,
direction
strength
selection
varied
substantially
among
genes
clades,
resulting
high
contingency
Finally,
describe
universal
roadmap
plants
where
increased
activities,
rather
than
relaxed
alone,
lead
differentiated
compared
free-living
species.
European Journal of Theoretical and Applied Sciences,
Journal Year:
2025,
Volume and Issue:
3(3), P. 3 - 15
Published: April 15, 2025
The
presence
of
parasites
in
host
animals
can
lead
to
changes
various
functions
the
animal,
such
as
disorders
haematopoiesis,
immunosuppression,
digestive
gastrointestinal
tract,
effects
on
food
intake
and
enzymatic
degradation
related
digestion.
modification
animal's
physiological
subsequent
fractal
behaviour
becomes
a
complex
system
that
plays
an
important
role
this
area.
This
work
is
based
model,
which
was
mainly
used
screen
main
modulations
their
inherent
intrinsic
properties
space
using
histological
criteria.
Ultimately,
spatial
conformation
tissues
plastically
adapted
maximise
efficient
distribution
resources
within
animal.
many
attractive
statistics
have
facilitated
developments
field.
To
characterise
these
more
specifically,
shape
model
has
generally
been
derived
from
relationship
hypervolume
surface
high-dimensional
Euclidean
space.
paper
discusses
two
advanced
biophysical
models
offers
inductive
equation
constraints
between
samples
amoebic
infective
amoebiasis
with
mode.
results
reflect
growth
patterns
variations
series.
BMC Plant Biology,
Journal Year:
2024,
Volume and Issue:
24(1)
Published: Oct. 21, 2024
Evidence
shows
that
full
mycoheterotrophs
and
holoparasites
often
have
reduced
plastid
genomes
with
rampant
gene
loss,
elevated
substitution
rates,
deeply
altered
to
conventional
evolution
in
mitochondrial
genomes,
but
mechanisms
of
cytonuclear
is
unknown.
Endoparasitic
Sapria
himalayana
mycoheterotrophic
Gastrodia
Platanthera
guangdongensis
represent
different
heterotrophic
types,
providing
a
basis
illustrate
evolution.
Here,
we
focused
on
nuclear-encoded
/
(N-pt
mt)
-targeting
protein
complexes,
including
caseinolytic
protease
(ClpP),
ribulose-1,5-bisphosphate
carboxylase/oxygenase
(RuBisCo),
oxidative
phosphorylation
system
(OXPHOS),
DNA
recombination,
replication,
repair
(DNA-RRR)
system,
pentatricopeptide
repeat
(PPR)
proteins,
identify
evolutionary
drivers
for
interaction.
The
severity
loss
N-pt
PPR
pt-RRR
genes
was
positively
associated
increased
degree
heterotrophy
S.
himalayana,
while
N-mt
mt-RRR
were
retained.
Substitution
rates
organellar
nuclear
encoding
N-pt/mt
subunits
complexes
evaluated,
coevolution
identified
whereas
disproportionate
observed
the
OXPHOS
complex
mycoheterotrophs,
only
slight
accelerations
mycoheterotrophs.
Nuclear
compensatory
encoded
by
genes.
Selection
shaping
codon
preferences,
functional
constraint,
regulation,
post-transcriptional
regulation
all
facilitate
mito-nuclear
Our
study
enriches
our
understanding
genomic
scenarios
fully
plants.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Aug. 9, 2024
Abstract
Two
key
factors
have
been
implicated
as
major
impediments
to
phylogenomic
inference:
incomplete
lineage
sorting
(ILS)—especially
in
cases
where
clades
are
the
anomaly
zone—and
erroneous
gene
tree
estimation—commonly
manifested
by
long-branch
attraction
Felsenstein
zone.
Seldom
these
analyzed
when
they
occur
simultaneously
involving
ancient
adaptive
radiations.
Rafflesiaceae
(Malpighiales)
is
an
iconic
holoparasitic
plant
clade
growing
west
of
Wallace’s
line
tropical
Southeast
Asia.
This
has
notoriously
difficult
place
phylogenetically
and
nested
within
explosive
radiation
Malpighiales.
To
complicate
matters,
parasitic
plants
like
well-known
exhibit
accelerated
rates
nucleotide
substitution.
Here,
using
2,141
genes
we
identify
for
first
time
that
substitution
a
genome-wide
phenomenon
holoparasites.
We
demonstrate
two
orders
magnitude
increase
compared
its
free-living
relatives,
rendering
nearly
every
prone
attraction.
Our
analyses
rejected
monophyletic
(Rafflesiaceae,
Euphorbiaceae)
proposed
previous
studies
but
favored
earlier
divergence
close
affinity
with
Euphorbiaceae,
Peraceae,
Putranjivaceae,
Pandaceae.
therefore
prey
joint
trap
zones.
Moreover,
owing
massive
loss
Rafflesiaceae,
our
simulation
suggests
this
represents
intractable
phylogenetic
problem
will
never
achieve
single
resolution.
case
study
highlights
seemingly
insurmountable
confluence
factors—a
danger
zone—that
hinders
resolution
demonstrates
need
be
flexible
multiple
placements
equally
likely.
Plant and Cell Physiology,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Oct. 11, 2024
Abstract
Mitochondria
play
a
crucial
role
in
eukaryotic
organisms,
housing
their
own
genome
with
genes
vital
for
oxidative
phosphorylation.
Coordination
between
nuclear
and
mitochondrial
genomes
is
pivotal
organelle
gene
expression.
Splicing,
editing
processing
of
transcripts
are
regulated
by
nuclear-encoded
factors.
Splicing
efficiency
(SEf)
the
many
group
II
introns
present
plant
critical
function
since
splicing
defect
or
deficiency
can
severely
impact
growth
development.
This
study
investigates
SEf
free-living
holoparasitic
plants,
focusing
on
25
from
15
angiosperm
species.
Our
comparative
analyses
reveal
distinctive
patterns
holoparasites
exhibiting
significantly
lower
SEf,
potentially
linked
to
unique
evolutionary
trajectory.
Given
preponderance
horizontal
transfer
(HGT)
parasitic
we
investigated
effect
HGT
such
as
presence
foreign
Contrary
expectations,
reductions
do
not
correlate
events,
suggesting
that
other
factors
at
play,
loss
photosynthesis
transition
lifestyle.
The
findings
this
broaden
our
understanding
molecular
evolution
plants
shed
light
multifaceted
influencing