Efficient and Highly Continuous Chromosome-Level Genome Assembly of the First Chameleon Genome
Genome Biology and Evolution,
Journal Year:
2023,
Volume and Issue:
15(8)
Published: July 22, 2023
Abstract
Most
amniote
genomes
are
diploid
and
moderate
in
size
(∼1–6
Gbp)
contain
a
large
proportion
of
repetitive
sequences.
The
development
next-generation
sequencing
technology,
especially
the
emergence
high-fidelity
(HiFi)
long-read
data,
has
made
it
feasible
to
resolve
high-quality
genome
assembly
for
nonmodel
species
efficiently.
However,
reference
squamate
reptiles
have
lagged
behind
other
lineages.
Here,
we
de
novo
assembled
first
from
Chameleonidae
family,
panther
chameleon
(Furcifer
pardalis).
We
obtained
telomere-to-telomere
contigs
using
only
HiFi
reaching
contig
N50
158.72
Mbp.
final
chromosome-level
is
1.61
Gbp
size,
100%
primary
were
placed
pseudochromosomes
Hi-C
interaction
data.
also
found
that
depth
>
30
folds
can
ensure
both
integrity
accuracy
genome,
whereas
insufficient
led
false
increase
duplicated
genes.
provide
valuable
evolutionary
ecological
studies
chameleons
as
well
comparative
genomic
resources
reptiles.
Language: Английский
Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean
Scientific Data,
Journal Year:
2023,
Volume and Issue:
10(1)
Published: Dec. 8, 2023
Chub
mackerels
(Scomber
japonicus)
are
a
migratory
marine
fish
widely
distributed
in
the
Indo-Pacific
Ocean.
They
globally
consumed
for
their
high
Omega-3
content,
but
population
is
declining
due
to
global
warming.
Here,
we
generated
first
chromosome-level
genome
assembly
of
chub
mackerel
(fScoJap1)
using
Vertebrate
Genomes
Project
pipeline
with
PacBio
HiFi
genomic
sequencing
and
Arima
Hi-C
chromosome
contact
data.
The
final
828.68
Mb
24
chromosomes,
nearly
all
containing
telomeric
repeats
at
ends.
We
annotated
31,656
genes
discovered
that
approximately
2.19%
contained
DNA
transposon
elements
repressed
within
duplicated
genes.
Analyzing
5-methylcytosine
(5mC)
modifications
reads,
observed
open/close
chromatin
patterns
gene
promoters,
including
FADS2
involved
production.
This
reference
provides
unprecedented
opportunities
advancing
our
knowledge
biology,
industry,
conservation.
Language: Английский