Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities
Journal of Molecular Evolution,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 17, 2025
Language: Английский
Klumpy: A tool to evaluate the integrity of long‐read genome assemblies and illusive sequence motifs
Molecular Ecology Resources,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: May 27, 2024
Abstract
The
improvement
and
decreasing
costs
of
third‐generation
sequencing
technologies
has
widened
the
scope
biological
questions
researchers
can
address
with
de
novo
genome
assemblies.
With
increasing
number
reference
genomes,
validating
their
integrity
minimal
overhead
is
vital
for
establishing
confident
results
in
applications.
Here,
we
present
Klumpy,
a
tool
detecting
visualizing
both
misassembled
regions
assembly
genetic
elements
(e.g.
genes)
interest
set
sequences.
By
leveraging
initial
raw
reads
combination
respective
assembly,
illustrate
Klumpy's
utility
by
investigating
antifreeze
glycoprotein
(
afgp
)
loci
across
two
icefishes,
searching
reported
absent
gene
northern
snakehead
fish,
scanning
genomes
mudskipper
bumblebee
regions.
In
former
cases,
were
able
to
provide
support
noncanonical
placement
an
locus
icefishes
locate
missing
gene.
Furthermore,
our
scans
identify
unmappable
putative
repetitive
element
shared
among
several
species
bees.
Language: Английский
Detecting Assembly Errors With Klumpy: Building Confidence in Your Daily Genomic Analysis
Molecular Ecology Resources,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Oct. 23, 2024
In
the
realm
of
genome
assembly,
even
minor
errors
can
send
researchers
down
to
rabbit
holes
unintended
misinterpretation.
Enter
Klumpy—a
tool
designed
help
detecting
these
elusive
mistakes
before
they
cause
significant
problems.
By
providing
detailed,
region‐specific
assessments
and
an
intuitive
visualisation
platform,
Klumpy
(Madrigal,
et
al.
2024)
empowers
pinpoint
resolve
potential
issues
with
precision,
paving
way
for
more
reliable
downstream
analyses
discoveries.
Language: Английский
Common Ancestry of the Id Locus: Genetic Clues and Polygenic Possibilities
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Dec. 29, 2023
Abstract
The
diversity
in
dermal
pigmentation
and
plumage
color
among
domestic
chickens
is
striking,
with
Black
Bone
Chickens
(BBC)
particularly
notable
for
their
intense
melanin
hyperpigmentation.
This
unique
trait
driven
by
a
complex
chromosomal
rearrangement
on
chromosome
20
at
the
Fm
locus,
resulting
overexpression
of
EDN3
(a
gene
central
to
melanocyte
regulation).
In
contrast,
inhibition
regulated
Id
locus.
Although
prior
studies
using
genetic
crosses,
GWAS,
expression
analysis
have
investigated
underpinnings
its
precise
location
functional
details
remain
elusive.
Our
study
aims
precisely
locate
identify
associated
rearrangements
candidate
genes
influencing
pigmentation,
examine
ancestral
status
locus
BBC
breeds.
Using
public
genomic
data
from
non-BBC
breeds,
we
refined
∼1.6
Mb
region
that
co-localizes
Z
amplicon
repeat
units
distal
end
q-arm
within
10.36
inversion
Silkie
BBC.
Phylogenetic
population
structure
analyses
reveal
shares
common
ancestry
across
all
much
like
Selection
signatures
highly
differentiated
BBC-specific
SNPs
MTAP
position
it
as
prime
CCDC112
additional
genes,
suggesting
possible
polygenic
nature.
results
suggest
shared
breeds
may
function
supergene
cluster
shank
variation.
Language: Английский