Genome assembly and population analysis of tetraploid marama bean reveal two distinct genome types
Scientific Reports,
Год журнала:
2025,
Номер
15(1)
Опубликована: Янв. 21, 2025
Tylosema
esculentum
(marama
bean),
an
underutilized
orphan
legume
native
to
southern
Africa,
holds
significant
potential
for
domestication
as
a
rescue
crop
enhance
local
food
security.
Well-adapted
harsh
desert
environments,
it
offers
valuable
insights
into
plant
resilience
extreme
drought
and
high
temperatures.
In
this
study,
k-mer
analysis
indicated
marama
ancient
allotetraploid
legume.
Using
21.5
Gb
of
PacBio
HiFi
data,
the
genome
was
assembled
with
two
assemblers,
HiCanu
Hifiasm,
followed
by
scaffolding
Omni-C
data
from
Dovetail
Genomics
(Cantata
Bio)
using
HiRise,
resulting
in
558.78
Mb
assembly
near
chromosome-level
continuity
(N50
=
22.68
Mb,
L50
8).
Repeats
accounted
58.43%
genome.
Phylogenetic
close
relationship
Bauhinia
variegata
Cercis
canadensis,
diverging
approximately
27.22
31.68
million
years
ago
(Ma),
respectively.
Whole-genome
duplication
(WGD)
revealed
event
marama.
Gene
family
expanded
families
enriched
pathways
related
stress
adaptation,
energy
metabolism,
environmental
signaling,
including
spliceosome,
citrate
cycle,
carbon
fixation
pathways.
These
findings
highlight
marama's
arid
environments.
contrast,
contracted
gene
associated
secondary
metabolite
biosynthesis
defense
suggest
trade-off,
potentially
due
reduced
pathogen
pressure.
Marama-specific
genes
were
amino
acid
catabolism
pathways,
playing
roles
signaling
regulation.
Core
shared
other
legumes
conserved
such
photosynthesis
hormone
which
are
fundamental
growth
survival.
Population
geographically
diverse
samples
distinct
clusters,
though
phenotypic
differences
remain
unclear.
Overall,
study
presents
first
high-quality
bean,
offering
genomic
reference
understanding
its
unique
biology
highlighting
improvement
challenging
Язык: Английский
Non-coding RNAs in the pathogenesis of Alzheimer’s disease: β-amyloid aggregation, Tau phosphorylation and neuroinflammation
Molecular Biology Reports,
Год журнала:
2025,
Номер
52(1)
Опубликована: Янв. 31, 2025
Язык: Английский
Proteogenomic analysis reveals Arp 2/3 complex as a common molecular mechanism in high risk pancreatic cysts and pancreatic cancer
Scientific Reports,
Год журнала:
2025,
Номер
15(1)
Опубликована: Янв. 31, 2025
Pancreatic
cysts,
particularly
intraductal
papillary
mucinous
neoplasms
(IPMNs),
pose
a
potential
risk
for
progressing
to
pancreatic
cancer
(PC).
This
study
investigates
the
genetic
architecture
of
benign
cysts
and
its
connection
PC
using
genome-wide
association
studies
(GWAS).
The
discovery
GWAS
identified
significant
variants
associated
with
specifically
rs142409042
variant
near
OPCML
gene.
A
pairwise
comparing
revealed
rs7190458
BCAR1
CTRB1
genes.
Further
analysis
genes
highlighted
Actin
Related
Protein
(Arp)
2/3
complex
as
potentially
important
molecular
mechanism
connecting
PC.
Arp2/3
complex-associated
were
significantly
upregulated
in
PC,
suggesting
their
role
malignant
transformation
cysts.
Differential
expression
these
was
observed
across
various
cell
types
indicating
involvement
tumor
microenvironment.
These
findings
suggest
that
can
serve
biomarkers
predicting
opening
new
avenues
targeted
therapies
early
detection
strategies.
Язык: Английский
A single-cell transcriptomic atlas of developing inhibitory neurons reveals expanding and contracting modes of diversification.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 19, 2025
Abstract
The
cerebral
cortex
relies
on
vastly
different
types
of
inhibitory
neurons
to
compute.
How
this
diversity
emerges
during
development
remains
an
open
question.
rarity
individual
neuron
often
leads
their
underrepresentation
in
single-cell
RNA
sequencing
(scRNAseq)
datasets,
limiting
insights
into
developmental
trajectories.
To
address
problem,
we
developed
a
computational
pipeline
enrich
and
integrate
rare
cell
across
multiple
datasets.
Applying
approach
somatostatin-expressing
(SST+)
neurons—the
most
diverse
class
the
cortex—we
constructed
Dev-SST-Atlas,
comprehensive
resource
containing
mouse
transcriptomic
data
over
51,000
SST+
neurons.
We
identify
three
principal
groups—Martinotti
cells
(MCs),
non-Martinotti
(nMCs),
long-range
projecting
(LRPs)—each
following
distinct
diversification
MCs
commit
early,
with
embryonic
neonatal
clusters
that
map
directly
adult
counterparts.
In
contrast,
nMCs
diversify
gradually,
each
cluster
giving
rise
types.
LRPs
follow
unique
‘contracting’
mode.
Initially,
two
are
present
until
postnatal
day
5
(P5),
but
by
P7,
one
type
is
eliminated
through
programmed
death,
leaving
single
surviving
population.
This
transient
LRP
also
found
fetal
human
cortex,
revealing
evolutionarily
conserved
feature
cortical
development.
Together,
these
findings
highlight
modes
diversification—invariant,
expanding,
contracting—offering
new
framework
understand
how
large
repertoire
Язык: Английский