DNA Research,
Journal Year:
2022,
Volume and Issue:
29(6)
Published: Sept. 12, 2022
Homologous
chromosomes
in
the
diploid
genome
are
thought
to
contain
equivalent
genetic
information,
but
this
common
concept
has
not
been
fully
verified
animal
genomes
with
high
heterozygosity.
Here
we
report
a
near-complete,
haplotype-phased,
assembly
of
pearl
oyster,
Pinctada
fucata,
using
hi-fidelity
(HiFi)
long
reads
and
chromosome
conformation
capture
data.
This
includes
14
pairs
scaffolds
(>38
Mb)
corresponding
(2n
=
28).
The
accuracy
assembly,
as
measured
by
an
analysis
k-mers,
is
estimated
be
99.99997%.
Moreover,
haplotypes
95.2%
95.9%,
respectively,
complete
single-copy
BUSCO
genes,
demonstrating
quality
assembly.
Transposons
comprise
53.3%
major
contributor
structural
variations.
Despite
overall
collinearity
between
haplotypes,
one
chromosomal
contains
megabase-scale
non-syntenic
regions,
which
necessarily
have
never
detected
resolved
conventional
haplotype-merged
assemblies.
These
regions
encode
expanded
gene
families
NACHT,
DZIP3/hRUL138-like
HEPN,
immunoglobulin
domains,
multiplying
immunity
repertoire,
hypothesize
important
for
innate
immune
capability
oysters.
oyster
provides
insight
into
remarkable
haplotype
diversity
animals.
Reviews in Aquaculture,
Journal Year:
2024,
Volume and Issue:
16(4), P. 1472 - 1498
Published: April 30, 2024
Abstract
Recent
evidence
has
demonstrated
the
unique
properties
of
innate
immune
system,
known
as
memory,
priming,
or
trained
immunity.
These
have
been
described
ability
system
to
learn
from
previous
microbial
experiences,
which
improves
survival
after
subsequent
infection.
In
this
review,
we
present
state
knowledge
on
immunity
in
invertebrates
and
provide
a
comprehensive
overview
these
capabilities
cultured
marine
molluscs,
are
currently
threatened
by
recurrent
diseases.
Studies
shown
that
exposure
environmental
microbiota,
pathogens,
derived
elements,
can
stronger
response
protection
against
future
infections.
studies
highlight
common
distinct
features
protection,
mechanisms,
specificity,
duration
vary
with
markers,
methods
stimulation.
While
cellular
molecular
basis
responses
is
only
partially
understood,
effects
phagocytosis,
haemocyte
populations,
apoptosis,
oxidative
stress,
gene
expression
suggested.
Finally,
propose
framework
for
research
go
beyond
current
address
potential
limitations
implementation
immunity‐based
strategies
control
disease.
Immune
training
may
opportunity
promote
sustainable
development
mollusc
aquaculture.
Development,
Journal Year:
2024,
Volume and Issue:
151(4)
Published: Jan. 25, 2024
ABSTRACT
A
model
organism
in
developmental
biology
is
defined
by
its
experimental
amenability
and
resources
created
for
the
system
scientific
community.
For
most
powerful
invertebrate
models,
combination
of
both
has
already
yielded
a
thorough
understanding
processes.
However,
number
systems
still
limited,
their
phylogenetic
distribution
heavily
biased.
Members
one
largest
animal
lineages,
Spiralia,
example,
have
long
been
neglected.
In
order
to
remedy
this
shortcoming,
we
produced
detailed
transcriptome
bivalve
mollusk
Mytilus
galloprovincialis,
expanded
list
protocols
available
species.
Our
high-quality
allowed
us
identify
transcriptomic
signatures
progression
perform
first
comparison
with
another
mollusk:
Pacific
oyster
Crassostrea
gigas.
To
allow
co-labelling
studies,
optimized
combined
immunohistochemistry
hybridization
chain
reaction
create
high-resolution
co-expression
maps
genes.
The
described
here
represent
an
enormous
boost
establishment
galloprovincialis
as
alternative
biology.
Frontiers in Immunology,
Journal Year:
2021,
Volume and Issue:
12
Published: June 30, 2021
The
scopes
related
to
the
interplay
between
stem
cells
and
immune
system
are
broad
range
from
basic
understanding
of
organism's
physiology
ecology
translational
studies,
further
contributing
(eco)toxicology,
biotechnology,
medicine
as
well
regulatory
ethical
aspects.
Stem
originate
through
hematopoiesis,
two
cell
types
is
required
in
processes
like
regeneration.
In
addition,
anomalies
directly
affect
functions,
its
ability
cope
with
environmental
changes
and,
indirectly,
role
ecosystem
services.
However,
continue
be
considered
parts
branches
biological
research
few
interconnections
them.
This
review
aims
bridge
these
seemingly
disparate
disciplines
towards
much
more
integrative
transformative
approaches
examples
deriving
mainly
aquatic
invertebrates.
We
discuss
current
cross-disciplinary
collaborative
emerging
issues,
raising
novel
hypotheses
comments.
also
problems
perspectives
how
integrate
their
conceptual
frameworks
address
equations
biology
a
new,
innovative
way.
Evolutionary Applications,
Journal Year:
2022,
Volume and Issue:
15(11), P. 1713 - 1729
Published: Aug. 4, 2022
Abstract
The
European
flat
oyster
(
Ostrea
edulis
L.)
is
a
bivalve
naturally
distributed
across
Europe,
which
was
an
integral
part
of
human
diets
for
centuries,
until
anthropogenic
activities
and
disease
outbreaks
severely
reduced
wild
populations.
Despite
growing
interest
in
genetic
applications
to
support
population
management
aquaculture,
reference
genome
this
species
lacking
date.
Here,
we
report
chromosome‐level
assembly
annotation
the
Flat
genome,
generated
using
Oxford
Nanopore,
Illumina,
Dovetail
OmniC™
proximity
ligation
RNA
sequencing.
A
contig
(N50:
2.38
Mb)
scaffolded
into
expected
karyotype
10
pseudochromosomes.
final
935.13
Mb,
with
scaffold‐N50
95.56
predicted
repeat
landscape
dominated
by
unclassified
elements
specific
O.
.
verified
accuracy
completeness
multiple
approaches,
including
novel
linkage
map
built
ddRAD‐Seq
technology,
comprising
4016
SNPs
from
four
full‐sib
families
(eight
parents
163
F1
offspring).
Annotation
integrating
multitissue
transcriptome
data,
comparative
protein
evidence
ab‐initio
gene
prediction
identified
35,699
protein‐coding
genes.
Chromosome‐level
synteny
demonstrated
against
high‐quality
assemblies,
independently
French
individual.
Comparative
genomics
used
characterize
family
expansions
during
evolution
that
potentially
facilitated
adaptation.
This
new
will
enable
high‐resolution
conservation
aquaculture
initiatives,
improves
our
understanding
evolution.
DNA Research,
Journal Year:
2022,
Volume and Issue:
29(6)
Published: Sept. 12, 2022
Homologous
chromosomes
in
the
diploid
genome
are
thought
to
contain
equivalent
genetic
information,
but
this
common
concept
has
not
been
fully
verified
animal
genomes
with
high
heterozygosity.
Here
we
report
a
near-complete,
haplotype-phased,
assembly
of
pearl
oyster,
Pinctada
fucata,
using
hi-fidelity
(HiFi)
long
reads
and
chromosome
conformation
capture
data.
This
includes
14
pairs
scaffolds
(>38
Mb)
corresponding
(2n
=
28).
The
accuracy
assembly,
as
measured
by
an
analysis
k-mers,
is
estimated
be
99.99997%.
Moreover,
haplotypes
95.2%
95.9%,
respectively,
complete
single-copy
BUSCO
genes,
demonstrating
quality
assembly.
Transposons
comprise
53.3%
major
contributor
structural
variations.
Despite
overall
collinearity
between
haplotypes,
one
chromosomal
contains
megabase-scale
non-syntenic
regions,
which
necessarily
have
never
detected
resolved
conventional
haplotype-merged
assemblies.
These
regions
encode
expanded
gene
families
NACHT,
DZIP3/hRUL138-like
HEPN,
immunoglobulin
domains,
multiplying
immunity
repertoire,
hypothesize
important
for
innate
immune
capability
oysters.
oyster
provides
insight
into
remarkable
haplotype
diversity
animals.
