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
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
Identification of Y-chromosome turnover in newts fails to support a sex chromosome origin for theTriturusbalanced lethal system
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 5, 2024
Abstract
Non-recombining
regions
of
the
genome
often
have
profound
effects
on
evolution,
resulting
in
phenomena
such
as
sex
chromosomes
and
supergenes.
Amongst
strangest
examples
are
balanced
lethal
systems,
that
found
newts
genus
Triturus
.
These
systems
halve
reproductive
output,
evolution
a
deleterious
trait
is
difficult
to
explain.
For
an
intriguing
model
proposes
system
evolved
from
ancestral
Y-chromosome.
To
test
this
hypothesis,
we
identify
Y-chromosome
verify
whether
it,
or
system,
homologous
its
sister
Lissotriton
,
which
does
not
possess
system.
We
set
candidate
Y-linked
markers
T.
ivanbureschi
place
them
high-density
linkage
map
construct
with
7,233
RADseq
markers.
validate
male
specificity
across
genus,
then
both
within
previously
constructed
target
capture
maps
include
genes
linked
observe
neither
nor
This
first
molecular
evidence
transition
between
salamanders.
However,
unless
additional
chromosome
turnover
events
involved,
our
data
support
origin
Язык: Английский