bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Июль 7, 2023
Genetic
elements
encoded
in
nuclear
DNA
determine
the
sex
of
an
individual
many
animals.
In
bivalves,
however,
mitochondrial
(mtDNA)
has
been
hypothesized
to
contribute
determination
lineages
that
possess
doubly
uniparental
inheritance
(DUI).
these
cases,
females
transmit
a
female
mtDNA
(F
mtDNA)
all
offspring,
while
male
(M
is
transmitted
only
from
fathers
sons.
Because
M
inherited
same
way
as
Y
chromosomes,
it
may
be
responsible
for
determination.
However,
role
and
genes
yet
validated
DUI
bivalves.
this
study,
we
used
DNA,
RNA,
short
non-coding
RNA
(sncRNA)
sequencing
explore
sexual
development
pathway
freshwater
mussel
Abstract
Animal
and
plant
species
exhibit
an
astonishing
diversity
of
sexual
systems,
including
environmental
genetic
determinants
sex,
with
the
latter
material
in
mitochondrial
genome.
In
several
hermaphroditic
plants
for
example,
sex
is
determined
by
interaction
between
cytoplasmic
male
sterility
(CMS)
genes
nuclear
restorer
genes.
Specifically,
CMS
involves
aberrant
that
prevent
pollen
development
specific
restore
it,
leading
to
a
mixture
female
(male‐sterile)
individuals
population
(gynodioecy).
Such
mitochondrial‐nuclear
determination
system
thought
be
rare
outside
plants.
Here,
we
present
one
possible
case
animals.
We
hypothesize
only
exception
strict
maternal
mtDNA
inheritance
animals,
doubly
uniparental
(DUI)
bivalves,
might
have
originated
as
sex‐determination
system.
document
explore
similarities
exist
DUI
CMS,
propose
various
ways
test
our
hypothesis.
Journal of Heredity,
Год журнала:
2023,
Номер
114(3), С. 199 - 206
Опубликована: Март 10, 2023
In
most
animals,
mitochondrial
DNA
is
strictly
maternally
inherited
and
non-recombining.
One
exception
to
this
pattern
called
doubly
uniparental
inheritance
(DUI),
a
phenomenon
involving
the
independent
transmission
of
female
male
genomes.
DUI
known
only
from
molluskan
class
Bivalvia.
The
phylogenetic
distribution
male-transmitted
(M
mtDNA)
in
bivalves
consistent
with
several
evolutionary
scenarios,
including
multiple
gains,
losses,
varying
degrees
recombination
female-transmitted
(F
mtDNA).
study,
we
use
methods
test
M
mtDNA
origination
hypotheses
infer
prevalence
DUI.
Phylogenetic
modeling
using
site
concordance
factors
supported
single
origin
coupled
acting
over
long
timescales.
Ongoing
present
Mytilida
Venerida,
which
results
concerted
evolution
F
mtDNA.
Mitochondrial
could
be
favored
offset
deleterious
effects
asexual
maintain
mitonuclear
compatibility
across
tissues.
Cardiida
Unionida
have
gone
without
recent
recombination,
possibly
due
an
extension
COX2
gene
DNA.
loss
connected
role
sex
determination
or
sexual
development.
Our
support
that
events
may
occur
throughout
genomes
species.
Future
investigations
reveal
more
complex
patterns
recombinants,
explain
retention
signal
for
protein-coding
genes.
Genome Biology and Evolution,
Год журнала:
2022,
Номер
14(12)
Опубликована: Дек. 1, 2022
The
molecular
factors
and
gene
regulation
involved
in
sex
determination
gonad
differentiation
bivalve
molluscs
are
unknown.
It
has
been
suggested
that
doubly
uniparental
inheritance
(DUI)
of
mitochondria
may
be
these
processes
species
such
as
the
ubiquitous
commercially
relevant
Manila
clam,
Ruditapes
philippinarum.
We
present
first
long-read-based
de
novo
genome
assembly
a
RNA-Seq
multi-tissue
analysis
15
females
males.
highly
contiguous
was
used
reference
to
investigate
expression,
alternative
splicing,
sequence
evolution,
tissue-specific
co-expression
networks,
sexual
contrasting
SNPs.
Differential
expression
(DE)
differential
splicing
(DS)
analyses
revealed
sex-specific
transcriptional
gonads,
but
not
somatic
tissues.
Co-expression
networks
complex
genes
gonad-associated
modules
showed
high
tissue
specificity.
However,
male
patterns
evolution
One
set
related
structural
organization
gametes
presented
slow
pleiotropy,
whereas
another
enriched
reproduction-related
characterized
by
fast
Sexual
SNPs
were
found
overrepresented
mitochondrial-related
functions,
providing
new
candidates
for
investigating
relationship
between
DUI
species.
Together,
results
increase
our
understanding
role
DE,
DS,
an
understudied
taxon.
also
provide
resourceful
genomic
data
studies
regarding
diagnosis
breeding
bivalves.
Molecular Biology and Evolution,
Год журнала:
2023,
Номер
40(11)
Опубликована: Ноя. 1, 2023
Genetic
elements
encoded
in
nuclear
DNA
determine
the
sex
of
an
individual
many
animals.
In
certain
bivalve
lineages
that
possess
doubly
uniparental
inheritance
(DUI),
mitochondrial
(mtDNA)
has
been
hypothesized
to
contribute
determination.
these
cases,
females
transmit
a
female
mtDNA
all
offspring,
while
male
(M
mtDNA)
is
transmitted
only
from
fathers
sons.
Because
M
inherited
same
way
as
Y
chromosomes,
it
may
be
responsible
for
However,
role
and
genes
determination
yet
validated
DUI
bivalves.
this
study,
we
used
DNA,
RNA,
short
noncoding
RNA
(sncRNA)
sequencing
explore
sexual
development
pathway
freshwater
mussel
Potamilus
streckersoni
(Bivalvia:
Unionida).
We
found
sheds
sncRNA
partially
within
male-specific
gene
targets
involved
mitophagy.
RNA-seq
confirmed
target
was
significantly
upregulated
females,
supporting
direct
sncRNAs
silencing.
These
findings
support
hypothesis
inhibits
development.
Genome-wide
patterns
genetic
differentiation
heterozygosity
did
not
sex-determining
region,
although
cannot
reject
factors
are
with
Our
results
provide
further
evidence
loci
diverse,
nonrespiratory
functions
additional
insights
into
unorthodox
system.
Evolution,
Год журнала:
2024,
Номер
78(11), С. 1790 - 1803
Опубликована: Июль 11, 2024
Abstract
Mitonuclear
coevolution
is
common
in
eukaryotes,
but
bivalve
lineages
that
have
doubly
uniparental
inheritance
(DUI)
of
mitochondria
may
be
an
interesting
example.
In
this
system,
females
transmit
mtDNA
(F
mtDNA)
to
all
offspring,
while
males
a
different
(M
solely
their
sons.
Molecular
evolution
and
functional
data
suggest
oxidative
phosphorylation
(OXPHOS)
genes
encoded
M
evolve
under
relaxed
selection
due
function
being
limited
sperm
only
(vs.
other
tissues
for
F
mtDNA).
This
has
led
the
hypothesis
mitonuclear
less
important
mtDNA.
Here,
we
use
comparative
phylogenetics,
transcriptomics,
proteomics
understand
interactions
DUI
bivalves.
We
found
nuclear
OXPHOS
proteins
coevolve
maintain
compatibility
similarly
with
both
proteins.
Mitochondrial
recombination
did
not
influence
nuclear-encoded
were
upregulated
offset
dysfunction.
Our
results
support
maintains
despite
on
Strict
transmission,
lower
effective
population
size,
higher
mutation
rates
explain
study
highlights
broad
features
eukaryotes.
动物学研究,
Год журнала:
2021,
Номер
43(1), С. 111 - 128
Опубликована: Дек. 10, 2021
In
most
eukaryotes,
oxidative
phosphorylation
(OXPHOS)
is
the
main
energy
production
process
and
it
involves
both
mitochondrial
nuclear
genomes.
The
close
interaction
between
two
genomes
critical
for
coordinated
function
of
OXPHOS
process.
Some
bivalves
show
doubly
uniparental
inheritance
(DUI)
mitochondria,
where
highly
divergent
genomes,
one
inherited
through
eggs
(F-type)
other
sperm
(M-type),
coexist
in
same
individual.
However,
remains
a
puzzle
how
genes
coordinate
with
DUI
species.
this
study,
we
compared
transcription,
polymorphism,
synonymous
codon
usage
species
Ruditapes
philippinarum
using
sex-
tissue-specific
transcriptomes.
Mitochondrial
showed
different
transcription
profiles.
Strong
co-transcription
signal
was
observed
within
(separate
F-
M-type)
but
weak
or
absent
genes,
suggesting
that
coordination
subunits
not
achieved
transcriptionally.
McDonald-Kreitman
frequency-spectrum
based
tests
indicated
M-type
deviated
significantly
from
neutrality,
F-type
undergo
selection
patterns.
Codon
analysis
revealed
mutation
bias
translational
were
major
factors
affecting
nevertheless,
appears
to
be
less
efficient
than
genes.
Therefore,
speculate
may
involve
post-transcriptional/translational
regulation.在大多数真核生物中，氧化磷酸化
(Oxidative
phosphorylation,
OXPHOS)
是主要的能量产生过程，它同时涉及线粒体基因组与核基因组。两个基因组之间密切的相互作用对于OXPHOS过程的功能协调至关重要。一些双壳类动物表现出线粒体的双单亲遗传（Doubly
,
DUI），其中两个遗传差异极大的线粒体基因组——一个通过卵细胞遗传（F型），另一个通过精子遗传（M型）——在同一个体中共存。然而，在DUI
物种中，核OXPHOS基因如何与两个遗传差异极大的线粒体基因组协调仍然未知。在该研究中，我们利用性别和组织特异性转录组比较了DUI
物种菲律宾蛤仔（
philippinarum）的线粒体与核OXPHOS基因的转录、遗传多态性和密码子使用偏好。线粒体和核OXPHOS基因显示出不同的转录模式。在F型、M型线粒体基因和核
基因内分别存在较强的共转录信号，但线粒体和核
基因之间的信号很弱或不存在，这表明线粒体和核
亚基之间的协调可能不在转录水平实现。McDonald-Kreitman检验和基于等位基因频谱的检验表明M型
基因显著偏离中性，且F型和M型
基因经历了不同的选择压力。对密码子的使用偏好分析表明，突变偏倚和翻译选择是影响不同OXPHOS
基因密码子使用偏好的主要因素；然而，线粒体OXPHOS基因受到的翻译选择低于核
基因。综上，我们推测OXPHOS基因之间的协调可能涉及转录后/翻译调节。.
Genes,
Год журнала:
2022,
Номер
13(11), С. 2151 - 2151
Опубликована: Ноя. 18, 2022
The
mitochondrion
was
characterized
for
years
as
the
energy
factory
of
cell,
but
now
its
role
in
many
more
cellular
processes
is
recognized.
and
mitochondrial
DNA
(mtDNA)
also
possess
a
set
distinct
properties,
including
maternal
inheritance,
that
creates
Mother’s
Curse
phenomenon.
As
mtDNA
inherited
from
females
to
all
offspring,
mutations
are
harmful
males
tend
accumulate
easily.
associated
with
various
diseases,
has
significant
effect
on
males,
cases
even
affecting
their
reproductive
ability.
Sometimes,
it
leads
isolation,
crosses
between
different
populations,
genome
cannot
cooperate
effectively
nuclear
one
resulting
mito-nuclear
incompatibility
reduce
fitness
hybrids.
This
phenomenon
observed
both
laboratory
natural
have
potential
influence
evolution
speciation.
Therefore,
turns
out
study
mitochondria
an
exciting
field
finds
applications,
pest
control,
can
shed
light
molecular
mechanism
several
improving
successful
diagnosis
therapeutics.
Finally,
co-adaptation,
paternal
leakage,
kin
selection
some
mechanisms
mitigate
impact
Curse.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Окт. 6, 2022
Abstract
Disentangling
different
types
of
selection
is
a
common
goal
in
molecular
evolution.
Elevated
d
N
/
S
ratios
(the
ratio
nonsynonymous
to
synonymous
substitution
rates)
focal
lineages
are
often
interpreted
as
signs
positive
selection.
Paradoxically,
relaxed
purifying
can
also
result
elevated
ratios,
but
tests
distinguish
these
two
causes
seldomly
implemented.
Here,
we
reevaluated
seven
case
studies
describing
animal
mtDNA
and
their
accompanying
hypotheses
regarding
They
included
flightless
vs.
flighted
birds,
bats,
insects,
physiological
adaptations
snakes,
groups
electric
fishes,
primates.
We
found
that
were
not
caused
by
the
predicted
mechanism,
sometimes
strong
support
for
opposite
mechanism.
discuss
reasons
why
energetic
may
be
confounded
other
selective
forces
acting
on
caution
against
overinterpreting
“spandrels”,
including
ratios.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Окт. 24, 2022
Abstract
In
most
animals,
mitochondrial
DNA
is
strictly
maternally
inherited
and
non-recombining.
One
exception
to
these
assumptions
called
doubly
uniparental
inheritance
(DUI):
a
phenomenon
involving
the
independent
transmission
of
female
male
genomes.
DUI
known
only
from
molluscan
class
Bivalvia.
The
phylogenetic
distribution
in
bivalves
consistent
with
several
evolutionary
scenarios,
including
multiple
gains,
losses,
varying
degrees
recombination
DNA.
this
study,
we
use
methods
test
origination
hypotheses
infer
prevalence
DUI.
Phylogenetic
modeling
using
site
concordance
factors
supported
single
origin
coupled
acting
over
long
timescales.
Ongoing
present
Mytilida
Venerida,
which
results
pattern
concerted
evolution
Mitochondrial
could
be
favored
offset
deleterious
effects
asexual
maintain
mitonuclear
compatibility
across
tissues.
Cardiida
Unionida
have
gone
without
recent
recombination,
possibly
due
an
extension
COX2
gene
loss
may
neutral
but
connected
role
M
mtDNA
sex
determination
or
sexual
development.
Our
support
events
species
occur
throughout
their
Future
investigations
reveal
more
complex
patterns
recombinants,
explain
retention
signal
for
protein
coding
genes.
