Research Square (Research Square),
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 8, 2025
Abstract
The
cattle
genome
is
crucial
for
understanding
ruminant
biology,
but
it
remains
incomplete.
first
telomere-to-telomere
haplotype-resolved
X
chromosome
and
four
autosomes
of
are
presented
in
a
near-complete
assembly
that
431
Mb
(16%)
longer
than
the
current
reference
genome.
UOA_Wagyu_1
identified
738
new
protein-coding
genes
supported
characterization
centromeric
repeats
transposable
elements
while
revealing
49,610
structural
variants.
centromere
natural
neocentromere
with
highly
identical
inverted
repeats,
no
bovine
satellite
low
CENP-A
signal,
methylation,
CpG
content,
contrast
to
autosomal
centromeres
comprised
typical
epigenetic
features.
It
likely
formed
from
element
expansion
deamination,
suggesting
dynamic
evolution.
Eighteen
X-pseudoautosomal
region
have
conserved
testes
expression
between
apes.
All
expressed
testes,
which
suggest
they
potentially
play
role
reproduction.
Nature,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 9, 2025
Abstract
The
most
dynamic
and
repetitive
regions
of
great
ape
genomes
have
traditionally
been
excluded
from
comparative
studies
1–3
.
Consequently,
our
understanding
the
evolution
species
is
incomplete.
Here
we
present
haplotype-resolved
reference
analyses
six
species:
chimpanzee,
bonobo,
gorilla,
Bornean
orangutan,
Sumatran
orangutan
siamang.
We
achieve
chromosome-level
contiguity
with
substantial
sequence
accuracy
(<1
error
in
2.7
megabases)
completely
215
gapless
chromosomes
telomere-to-telomere.
resolve
challenging
regions,
such
as
major
histocompatibility
complex
immunoglobulin
loci,
to
provide
in-depth
evolutionary
insights.
Comparative
enabled
investigations
diversity
previously
uncharacterized
or
incompletely
studied
without
bias
mapping
human
genome.
Such
include
newly
minted
gene
families
lineage-specific
segmental
duplications,
centromeric
DNA,
acrocentric
subterminal
heterochromatin.
This
resource
serves
a
comprehensive
baseline
for
future
humans
closest
living
relatives.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: July 31, 2024
We
present
haplotype-resolved
reference
genomes
and
comparative
analyses
of
six
ape
species,
namely:
chimpanzee,
bonobo,
gorilla,
Bornean
orangutan,
Sumatran
siamang.
achieve
chromosome-level
contiguity
with
unparalleled
sequence
accuracy
(<1
error
in
500,000
base
pairs),
completely
sequencing
215
gapless
chromosomes
telomere-to-telomere.
resolve
challenging
regions,
such
as
the
major
histocompatibility
complex
immunoglobulin
loci,
providing
more
in-depth
evolutionary
insights.
Comparative
analyses,
including
human,
allow
us
to
investigate
evolution
diversity
regions
previously
uncharacterized
or
incompletely
studied
without
bias
from
mapping
human
reference.
This
includes
newly
minted
gene
families
within
lineage-specific
segmental
duplications,
centromeric
DNA,
acrocentric
chromosomes,
subterminal
heterochromatin.
resource
should
serve
a
definitive
baseline
for
all
future
studies
humans
our
closest
living
relatives.
Genome Research,
Journal Year:
2024,
Volume and Issue:
34(11), P. 1919 - 1930
Published: Nov. 1, 2024
The
combination
of
ultra-long
(UL)
Oxford
Nanopore
Technologies
(ONT)
sequencing
reads
with
long,
accurate
Pacific
Bioscience
(PacBio)
High
Fidelity
(HiFi)
has
enabled
the
completion
a
human
genome
and
spurred
similar
efforts
to
complete
genomes
many
other
species.
However,
this
approach
for
complete,
“telomere-to-telomere”
assembly
relies
on
multiple
platforms,
limiting
its
accessibility.
ONT
“Duplex”
reads,
where
both
strands
DNA
are
read
improve
quality,
promise
high
per-base
accuracy.
To
evaluate
new
data
type,
we
generated
Duplex
three
widely
studied
genomes:
HG002,
Solanum
lycopersicum
Heinz
1706
(tomato),
Zea
mays
B73
(maize).
For
diploid,
heterozygous
HG002
genome,
also
used
“Pore-C”
chromatin
contact
mapping
completely
phase
haplotypes.
We
found
accuracy
be
HiFi
sequencing,
but
lengths
tens
kilobases
longer,
Pore-C
compatible
existing
diploid
algorithms.
This
length
enables
construction
high-quality
initial
assembly,
which
can
then
further
resolved
using
UL
finally
phased
into
chromosome-scale
haplotypes
Pore-C.
resulting
assemblies
have
base
exceeding
99.999%
(Q50)
near-perfect
continuity,
most
chromosomes
assembled
as
single
contigs.
conclude
that
is
viable
alternative
de
novo
provides
multirun
single-instrument
solution
reconstruction
genomes.
Nucleic Acids Research,
Journal Year:
2024,
Volume and Issue:
53(D1), P. D243 - D257
Published: Nov. 11, 2024
Reference
sequences
and
annotations
serve
as
the
foundation
for
many
lines
of
research
today,
from
organism
sequence
identification
to
providing
a
core
description
genes,
transcripts
proteins
found
in
an
organism's
genome.
Interpretation
data
including
transcriptomics,
proteomics,
variation
comparative
analyses
based
on
reference
gene
informs
our
understanding
function
possible
disease
mechanisms,
leading
new
biomedical
discoveries.
The
Sequence
(RefSeq)
resource
created
at
National
Center
Biotechnology
Information
(NCBI)
leverages
both
automatic
processes
expert
curation
create
robust
set
genomic,
transcript
protein
spanning
tree
life.
RefSeq
continues
refine
its
annotation
quality
control
utilize
better
genomes
resulting
advances
sequencing
technologies
well
RNA-Seq
produce
high-quality
annotated
genomes,
ortholog
predictions
across
more
organisms
other
products
that
are
easily
accessible
through
multiple
NCBI
resources.
This
report
summarizes
current
status
eukaryotic,
prokaryotic
viral
resources,
with
focus
eukaryotic
annotation,
increase
taxonomic
representation
effect
it
will
have
genomics.
is
publicly
https://www.ncbi.nlm.nih.gov/refseq.
NAR Genomics and Bioinformatics,
Journal Year:
2025,
Volume and Issue:
7(1)
Published: Jan. 7, 2025
Repetitive
DNA
sequences
can
form
noncanonical
structures
such
as
H-DNA.
The
new
telomere-to-telomere
genome
assembly
for
the
human
has
eliminated
gaps,
enabling
examination
of
highly
repetitive
regions
including
centromeric
and
pericentromeric
repeats
ribosomal
arrays.
We
find
that
H-DNA
appears
once
every
25
000
base
pairs
in
genome.
Its
distribution
is
inhomogeneous
with
motif
hotspots
being
detectable
acrocentric
chromosomes.
Ribosomal
arrays
are
genomic
element
a
40.94-fold
enrichment.
Across
chromosomes,
we
report
54.82%
motifs
found
these
chromosomes
rDNA
array
loci.
discover
binding
sites
PRDM9-B
allele,
variant
PRDM9
protein,
enriched
motifs.
further
investigate
findings
through
an
analysis
PRDM-9
ChIP-seq
data
across
various
alleles,
observing
enrichment
A-like
alleles
(including
A,
B,
N
alleles),
but
not
C-like
C
L4
alleles).
at
consistent
nonhuman
great
ape
genomes.
conclude
most
loci
other
