Nature,
Год журнала:
2024,
Номер
630(8016), С. 401 - 411
Опубликована: Май 29, 2024
Abstract
Apes
possess
two
sex
chromosomes—the
male-specific
Y
chromosome
and
the
X
chromosome,
which
is
present
in
both
males
females.
The
crucial
for
male
reproduction,
with
deletions
being
linked
to
infertility
1
.
vital
reproduction
cognition
2
Variation
mating
patterns
brain
function
among
apes
suggests
corresponding
differences
their
chromosomes.
However,
owing
repetitive
nature
incomplete
reference
assemblies,
ape
chromosomes
have
been
challenging
study.
Here,
using
methodology
developed
telomere-to-telomere
(T2T)
human
genome,
we
produced
gapless
assemblies
of
five
great
(bonobo
(
Pan
paniscus
),
chimpanzee
troglodytes
western
lowland
gorilla
Gorilla
Bornean
orangutan
Pongo
pygmaeus
)
Sumatran
abelii
))
a
lesser
(the
siamang
gibbon
Symphalangus
syndactylus
)),
untangled
intricacies
evolution.
Compared
chromosomes,
vary
greatly
size
low
alignability
high
levels
structural
rearrangements—owing
accumulation
lineage-specific
ampliconic
regions,
palindromes,
transposable
elements
satellites.
Many
genes
expand
multi-copy
families
some
evolve
under
purifying
selection.
Thus,
exhibits
dynamic
evolution,
whereas
more
stable.
Mapping
short-read
sequencing
data
these
revealed
diversity
selection
on
than
100
individual
apes.
These
are
expected
inform
evolution
conservation
genetics
non-human
apes,
all
endangered
species.
Proceedings of the National Academy of Sciences,
Год журнала:
2023,
Номер
120(8)
Опубликована: Фев. 13, 2023
Microchromosomes
are
prevalent
in
nonmammalian
vertebrates
[P.
D.
Waters
et
al.
,
Proc.
Natl.
Acad.
Sci.
U.S.A.
118
(2021)],
but
a
few
of
them
missing
bird
genome
assemblies.
Here,
we
present
new
chicken
reference
containing
all
autosomes,
Z
and
W
chromosome,
with
gaps
closed
except
for
the
W.
We
identified
ten
small
microchromosomes
(termed
dot
chromosomes)
distinct
sequence
epigenetic
features,
among
which
six
were
newly
assembled.
Those
chromosomes
exhibit
extremely
high
GC
content
level
DNA
methylation
enriched
housekeeping
genes.
The
pericentromeric
heterochromatin
is
disproportionately
large
continues
to
expand
proliferation
satellite
testis-expressed
Our
analyses
revealed
that
41-bp
CNM
repeat
frequently
forms
higher-order
repeats
(HORs)
at
centromeres
acrocentric
chromosomes.
centromere
core
regions
where
kinetochore
attaches
often
encompass
telomeric
(TTAGGG)n,
one
chromosomes,
recruits
an
endogenous
retrovirus
(ERV).
further
demonstrate
chromosome
shares
some
common
features
having
arrays
hypermethylated
tandem
repeats.
Finally,
using
complete
models,
reconstructed
fine
picture
chordate
karyotype
evolution,
revealing
frequent
chromosomal
fusions
before
after
vertebrate
whole-genome
duplications.
characterization
shed
insights
into
understanding
evolution
biology.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Июль 9, 2022
Abstract
The
Human
Pangenome
Reference
Consortium
(HPRC)
presents
a
first
draft
human
pangenome
reference.
contains
47
phased,
diploid
assemblies
from
cohort
of
genetically
diverse
individuals.
These
cover
more
than
99%
the
expected
sequence
and
are
accurate
at
structural
base-pair
levels.
Based
on
alignments
assemblies,
we
generated
that
captures
known
variants
haplotypes,
reveals
novel
alleles
structurally
complex
loci,
adds
119
million
base
pairs
euchromatic
polymorphic
1,529
gene
duplications
relative
to
existing
reference,
GRCh38.
Roughly
90
additional
derive
variation.
Using
our
analyze
short-read
data
reduces
errors
when
discovering
small
by
34%
boosts
detected
per
haplotype
104%
compared
GRCh38-based
workflows,
using
previous
diversity
sets
genome
assemblies.
Nature,
Год журнала:
2024,
Номер
629(8010), С. 136 - 145
Опубликована: Апрель 3, 2024
Abstract
Human
centromeres
have
been
traditionally
very
difficult
to
sequence
and
assemble
owing
their
repetitive
nature
large
size
1
.
As
a
result,
patterns
of
human
centromeric
variation
models
for
evolution
function
remain
incomplete,
despite
being
among
the
most
rapidly
mutating
regions
2,3
Here,
using
long-read
sequencing,
we
completely
sequenced
assembled
all
from
second
genome
compared
it
finished
reference
4,5
We
find
that
two
sets
show
at
least
4.1-fold
increase
in
single-nucleotide
when
with
unique
flanks
vary
up
3-fold
size.
Moreover,
45.8%
cannot
be
reliably
aligned
standard
methods
emergence
new
α-satellite
higher-order
repeats
(HORs).
DNA
methylation
CENP-A
chromatin
immunoprecipitation
experiments
26%
differ
kinetochore
position
by
>500
kb.
To
understand
evolutionary
change,
selected
six
chromosomes
31
orthologous
common
chimpanzee,
orangutan
macaque
genomes.
Comparative
analyses
reveal
nearly
complete
turnover
HORs,
characteristic
idiosyncratic
changes
HORs
each
species.
Phylogenetic
reconstruction
haplotypes
supports
limited
no
recombination
between
short
(p)
long
(q)
arms
across
reveals
novel
share
monophyletic
origin,
providing
strategy
estimate
rate
saltatory
amplification
mutation
DNA.
