Conserved gene content and unique phylogenetic history characterize the 'bloopergene' underlying Triturus' balanced lethal system
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 25, 2024
Abstract
In
a
balanced
lethal
system,
half
the
reproductive
output
succumbs.
Triturus
newts
are
best-known
example.
Their
chromosome
1
comes
in
two
distinct
versions
and
embryos
carrying
same
version
twice
experience
developmental
arrest.
Those
possessing
different
survive,
suggesting
that
each
carries
something
uniquely
vital.
With
target
capture
we
obtain
over
7,000
nuclear
DNA
markers
across
genus
all
main
lineages
of
Salamandridae
(the
family
to
which
belongs)
investigate
evolutionary
history
Triturus’
versus
other
chromosomes.
Dozens
genes
completely
missing
from
either
one
or
.
Furthermore,
unique
gene
content
1A
1B
is
remarkably
similar
species,
system
evolved
before
radiated.
The
tree
topology
differs
rest
genome,
presumably
due
pervasive,
ancient
hybridization
between
ancestor
newt
lineages.
Our
findings
accentuate
complex
nature
–
‘bloopergene’
driving
evolutionarily
enigmatic
system.
Язык: Английский
Genomic evidence suggests the balanced lethal system inTriturusnewts originated in an instantaneous speciation event.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 1, 2024
Abstract
The
balanced
lethal
system
found
in
crested
and
marbled
newts
of
the
genus
Triturus
presents
an
intriguing
mystery.
All
adults
possess
two
distinct
forms
their
largest
chromosome,
resulting
50%
offspring
inheriting
copies
one
these
forms.
These
homomorphic
individuals
undergo
fatal
developmental
arrest
during
embryogenesis.
How
could
such
obviously
maladaptive
trait,
destroying
half
organism’s
reproductive
output,
evolve?
We
construct
a
high-density
linkage
maps
for
its
sister
Lissotriton
,
identifying
genes
involved
system.
find
that
each
chromosome
1
is
characterized
by
single
massive
deletion.
Ploidy
analysis
shows
deletion
compensated
duplication
same
region
on
opposite
chromosome.
This
suggests
was
created
suddenly,
as
result
unequal
exchange
between
chromosomes
individual.
simulate
consequences
mutation,
finding
that,
if
rearranged
exert
fitness
penalty
when
combined
with
ancestral
version,
stable
can
become
fixed
within
population.
Counterintuitively,
deleterious
nature
causes
isolation
protects
them
from
invasion
fitter
ancestor.
conclude
origin
effectively
instantaneous
speciation
event,
which
resulted
fixation
Язык: Английский
Genome-wide patterns of diversity in the European midwife toad complex: phylogeographic and conservation prospects
Conservation Genetics,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 6, 2025
Язык: Английский
Determining zygosity with multiplex Kompetitive Allele-Specific PCR (mxKASP) genotyping
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 25, 2024
Abstract
We
introduce
multiplex
Kompetitive
Allele-Specific
PCR
(mxKASP):
a
modification
of
‘classical’
KASP
genotyping
that
allows
zygosity
to
be
determined
in
diploid
organisms.
Rather
than
targeting
SNP
associated
with
single
marker,
mxKASP
targets
two
non-homologous
markers.
show
proof
concept
by
applying
the
balanced
lethal
system
Triturus
newts,
which
individuals
are
known
possess
either:
(1)
zero
copies
1A
version
chromosome
1
and
1B
version;
(2)
one
copy
1B;
or
(3)
1B.
is
successful
amplifying
both
marker
reaction
(if
present),
allowing
inferred.
independently
confirm
our
results
approach.
argue
can
applied
rapidly
economically
determine
zygostity
organisms,
for
large
number
samples
at
once.
Язык: Английский
PAV-spotter: using signal cross-correlations to identify Presence/Absence Variation in target capture data
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 29, 2024
Abstract
High
throughput
sequencing
technologies
have
become
essential
in
the
fields
of
evolutionary
biology
and
genomics.
When
dealing
with
non-model
organisms
or
genomic
gigantism,
whole
genomes
is
still
relatively
costly
therefore
reduced-genome
representations
are
frequently
obtained,
for
instance
by
‘target
capture’
approaches.
While
computational
tools
exist
that
can
handle
target
capture
data
identify
small-scale
variants
such
as
single
nucleotide
polymorphisms
micro-indels,
options
to
large
scale
structural
limited.
To
meet
this
need,
we
introduce
PAV-spotter:
a
tool
presence/absence
variation
(PAV)
data.
PAV-spotter
conducts
signal
cross-correlation
calculation,
which
distribution
read
counts
per
between
samples
different
priori
defined
classes
–
e.g.
male
versus
female,
diseased
healthy
compared.
We
apply
test
our
methodology
studying
Triturus
newts:
salamanders
gigantic
currently
lack
an
annotated
reference
genome.
newts
suffer
from
hereditary
disease
kills
half
their
offspring
during
embryogenesis.
compare
two
types
embryos,
characterized
unique
deletions,
those
embryos.
Our
findings
show
helps
expose
variants,
even
face
medium
low
coverage
levels,
sample
sizes,
background
noise
due
mis-mapped
reads.
be
used
study
underlying
supergene
systems
absence
genome
assemblies.
The
code,
including
further
explanation
on
how
use
customize
it,
available
through
GitHub
repository:
https://github.com/Wielstra-Lab/PAVspotter
.
Язык: Английский
Phylogenomics yields new systematic and taxonomical insights for Lissotriton newts, a genus with a strong legacy of introgressive hybridization
Molecular Phylogenetics and Evolution,
Год журнала:
2024,
Номер
unknown, С. 108282 - 108282
Опубликована: Дек. 1, 2024
Язык: Английский