Genome biology,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: April 26, 2024
Long-read
sequencing
data,
particularly
those
derived
from
the
Oxford
Nanopore
platform,
tend
to
exhibit
high
error
rates.
Here,
we
present
NextDenovo,
an
efficient
correction
and
assembly
tool
for
noisy
long
reads,
which
achieves
a
level
of
accuracy
in
genome
assembly.
We
apply
NextDenovo
assemble
35
diverse
human
genomes
around
world
using
long-read
data.
These
allow
us
identify
landscape
segmental
duplication
gene
copy
number
variation
modern
populations.
The
use
should
pave
way
population-scale
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: March 12, 2023
Abstract
Long
read
sequencing
data,
particularly
those
derived
from
the
Oxford
Nanopore
(ONT)
platform,
tend
to
exhibit
a
high
error
rate.
Here,
we
present
NextDenovo,
highly
efficient
correction
and
assembly
tool
for
noisy
long
reads,
which
achieves
level
of
accuracy
in
genome
assembly.
NextDenovo
can
rapidly
correct
reads;
these
corrected
reads
contain
fewer
errors
than
other
comparable
tools
are
characterized
by
chimeric
alignments.
We
applied
quality
reference
genomes
35
diverse
humans
across
world
using
ONT
data.
Based
on
de
novo
assemblies,
were
able
identify
landscape
segmental
duplications
gene
copy
number
variation
modern
human
population.
The
use
program
should
pave
way
population-scale
long-read
assembly,
thereby
facilitating
construction
pan-genomes,
Nature Genetics,
Journal Year:
2023,
Volume and Issue:
55(8), P. 1390 - 1399
Published: July 31, 2023
Pangenomes
provide
access
to
an
accurate
representation
of
the
genetic
diversity
species,
both
in
terms
sequence
polymorphisms
and
structural
variants
(SVs).
Here
we
generated
Saccharomyces
cerevisiae
Reference
Assembly
Panel
(ScRAP)
comprising
reference-quality
genomes
for
142
strains
representing
species'
phylogenetic
ecological
diversity.
The
ScRAP
includes
phased
haplotype
assemblies
several
heterozygous
diploid
polyploid
isolates.
We
identified
circa
(ca.)
4,800
nonredundant
SVs
that
a
broad
view
genomic
diversity,
including
dynamics
telomere
length
transposable
elements.
uncovered
frequent
cases
complex
aneuploidies
where
large
chromosomes
underwent
deletions
translocations.
found
can
impact
gene
expression
near
breakpoints
substantially
contribute
repertoire
evolution.
also
discovered
horizontally
acquired
regions
insert
at
chromosome
ends
generate
new
telomeres.
Overall,
demonstrates
benefit
pangenome
understanding
genome
evolution
population
scale.
Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: May 5, 2023
Abstract
As
large-scale
genomic
studies
have
progressed,
it
has
been
revealed
that
a
single
reference
genome
pattern
cannot
represent
genetic
diversity
at
the
species
level.
While
domestic
animals
tend
to
complex
routes
of
origin
and
migration,
suggesting
possible
omission
some
population-specific
sequences
in
current
genome.
Conversely,
pangenome
is
collection
all
DNA
contains
shared
by
individuals
(core
genome)
also
able
display
sequence
information
unique
each
individual
(variable
genome).
The
progress
research
humans,
plants
proved
missing
components
identification
large
structural
variants
(SVs)
can
be
explored
through
pangenomic
studies.
Many
specific
shown
related
biological
adaptability,
phenotype
important
economic
traits.
maturity
technologies
methods
such
as
third-generation
sequencing,
Telomere-to-telomere
genomes,
graphic
reference-free
assembly
will
further
promote
development
pangenome.
In
future,
combined
with
long-read
data
multi-omics
help
resolve
SVs
their
relationship
main
traits
interest
domesticated
animals,
providing
better
insights
into
animal
domestication,
evolution
breeding.
this
review,
we
mainly
discuss
how
analysis
reveals
variations
(sheep,
cattle,
pigs,
chickens)
impacts
on
phenotypes
contribute
understanding
diversity.
Additionally,
go
potential
issues
future
perspectives
livestock
poultry.
Nature Genetics,
Journal Year:
2024,
Volume and Issue:
56(5), P. 982 - 991
Published: April 11, 2024
Abstract
Although
originally
primarily
a
system
for
functional
biology,
Arabidopsis
thaliana
has,
owing
to
its
broad
geographical
distribution
and
adaptation
diverse
environments,
developed
into
powerful
model
in
population
genomics.
Here
we
present
chromosome-level
genome
assemblies
of
69
accessions
from
global
species
range.
We
found
that
genomic
colinearity
is
very
conserved,
even
among
geographically
genetically
distant
accessions.
Along
chromosome
arms,
megabase-scale
rearrangements
are
rare
typically
only
single
accession.
This
indicates
the
karyotype
quasi-fixed
arms
counter-selected.
Centromeric
regions
display
higher
structural
dynamics,
divergences
core
centromeres
account
most
size
variations.
Pan-genome
analyses
uncovered
32,986
distinct
gene
families,
60%
being
all
40%
appearing
be
dispensable,
including
18%
private
accession,
indicating
unexplored
genic
diversity.
These
new
will
empower
future
genetic
research.
Nature Communications,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: Sept. 19, 2023
Yak
has
been
subject
to
natural
selection,
human
domestication
and
interspecific
introgression
during
its
evolution.
However,
genetic
variants
favored
by
each
of
these
processes
have
not
distinguished
previously.
We
constructed
a
graph-genome
for
47
genomes
7
cross-fertile
bovine
species.
This
allowed
detection
57,432
high-resolution
structural
(SVs)
within
across
the
species,
which
were
genotyped
in
386
individuals.
evolutionary
origins
diverse
SVs
domestic
yaks
phylogenetic
analyses.
further
identified
334
genes
overlapping
with
that
bore
potential
signals
selection
from
wild
yaks,
plus
an
additional
686
introgressed
cattle.
Nearly
90%
Introgression
SV
spanning
KIT
gene
triggered
breeding
white
yaks.
validated
significant
association
selected
stratified
expression,
contributes
phenotypic
variations.
Our
results
highlight
different
contribute
diversity
Microbiome,
Journal Year:
2024,
Volume and Issue:
12(1)
Published: Feb. 26, 2024
Abstract
Background
Bacterial
transfers
from
plants
to
insect
herbivore
guts
have
been
well
investigated.
However,
bacterial
exchanges
between
plant
phyllospheres
and
cuticles
remain
unclear,
as
does
their
related
biological
function.
Results
Here,
we
report
that
the
cuticular
loads
of
silkworm
larvae
quickly
increased
after
molting
feeding
on
white
mulberry
(
Morus
alba
)
leaves.
The
isolation
examination
bacteria
identified
one
bacterium
Mammaliicoccus
sciuri
could
completely
inhibit
spore
germination
fungal
entomopathogens
Metarhizium
robertsii
Beauveria
bassiana
.
Interestingly,
Ma.
was
evident
originally
leaves,
which
produce
a
secreted
chitinolytic
lysozyme
(termed
Msp1)
damage
cell
walls.
In
consistency,
deletion
Msp1
substantially
impaired
antifungal
activity.
Pretreating
with
cells
followed
by
topical
infections
revealed
this
help
defend
silkworms
against
infections.
Unsurprisingly,
protective
efficacy
Δ
considerably
reduced
when
compared
wild-type
bacterium.
Administration
bacterium-treated
diets
had
no
negative
effect
development;
instead,
supplementation
protect
artificial
diet
Aspergillus
contamination.
Conclusions
results
study
evidence
cross-kingdom
transfer
can
insects
parasite
attacks.
ACS Biomaterials Science & Engineering,
Journal Year:
2023,
Volume and Issue:
10(1), P. 12 - 28
Published: Jan. 27, 2023
Medical
silks
have
captured
global
interest.
While
silk
sutures
a
long
track
record
in
humans,
bioconjugates
are
still
preclinical
development.
This
perspective
examines
key
advances
bioconjugation,
including
the
fabrication
of
silk–protein
conjugates,
bioconjugated
particles,
and
substrates
to
enhance
cell–material
interactions
two
three
dimensions.
Many
these
systems
rely
on
chemical
modification
biopolymer,
often
using
carbodiimide
reactive
ester
chemistries.
However,
recent
progress
enzyme-mediated
click
chemistries
has
expanded
molecular
toolbox
enable
biorthogonal,
site-specific
conjugation
single
step
when
combined
with
recombinant
fibroin
tagged
noncanonical
amino
acids.
outlines
strategies
available
for
modification,
compares
resulting
conjugates
clinical
benchmarks,
open
questions
areas
that
require
more
work.
Overall,
this
assessment
highlights
domain
new
sunrise
capabilities
development
opportunities
may
ultimately
offer
ways
delivering
improved
healthcare.
