Nucleic Acids Research,
Год журнала:
2022,
Номер
51(D1), С. D913 - D923
Опубликована: Ноя. 1, 2022
Evolutionary
developmental
biology
(evo-devo)
has
been
among
the
most
fascinating
interdisciplinary
fields
for
decades,
which
aims
to
elucidate
origin
and
evolution
of
diverse
processes.
The
rapid
accumulation
omics
data
provides
unprecedented
opportunities
answer
many
interesting
but
unresolved
evo-devo
questions.
However,
access
utilization
these
resources
are
hindered
by
challenges
particularly
in
non-model
animals.
Here,
we
establish
a
comparative
multi-omics
database
animal
(EDomics,
http://edomics.qnlm.ac)
containing
comprehensive
genomes,
bulk
transcriptomes,
single-cell
across
40
representative
species,
generally
used
as
model
organisms
study.
EDomics
systematic
view
genomic/transcriptomic
information
from
various
aspects,
including
genome
assembly
statistics,
gene
features
families,
transcription
factors,
transposable
elements,
expressional
profiles/networks.
It
also
exhibits
spatiotemporal
expression
profiles
at
level,
such
cell
atlas,
markers,
spatial-map
information.
Moreover,
highly
valuable,
customized
datasets/resources
research,
family
expansion/contraction,
inferred
core
repertoires,
macrosynteny
analysis
karyotype
evolution,
type
analysis.
presents
platform
community
decipher
whole
history
tree
life.
Abstract
Echinobase
(www.echinobase.org)
is
a
model
organism
knowledgebase
serving
as
resource
for
the
community
that
studies
echinoderms,
phylum
of
marine
invertebrates
includes
sea
urchins
and
stars.
Echinoderms
have
been
important
experimental
models
over
100
years
continue
to
make
contributions
environmental,
evolutionary,
developmental
studies,
including
research
on
gene
regulatory
networks.
As
centralized
resource,
hosts
genomes
collects
functional
genomic
data,
reagents,
literature,
other
information
community.
This
third-generation
site
based
Xenbase
design
utilizes
gene-centric
pages
minimize
time
effort
required
access
information.
Summary
display
symbols
names,
links
JBrowse
genome
browser,
orthology
organisms
tabs
from
page
contain
more
detailed
concerning
mRNAs,
proteins,
diseases,
protein–protein
interactions.
The
also
1:1
orthologs
between
fully
supported
species
Strongylocentrotus
purpuratus
(purple
urchin),
Lytechinus
variegatus
(green
Patiria
miniata
(bat
star),
Acanthaster
planci
(crown-of-thorns
star).
tracks
are
available
visualization
data
both
partially
Anneissia
japonica
(feather
Asterias
rubens
(sugar
L.
pictus
(painted
urchin).
serves
vital
role
by
providing
researchers
with
annotated
orthology,
aligned
genomes,
curated
reagents
data.
Echinoderm
Anatomical
Ontology
provides
framework
standardizing
across
phylum,
content
formatted
be
findable,
accessible,
interoperable,
reusable
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Май 9, 2023
Abstract
A
fundamental
goal
in
the
organogenesis
field
is
to
understand
how
cells
organize
into
tubular
shapes.
Toward
this
aim,
we
have
established
hydro-vascular
organ
sea
star
Patiria
miniata
as
a
model
for
tubulogenesis.
In
animal,
bilateral
tubes
grow
out
from
tip
of
developing
gut,
and
precisely
extend
specific
sites
larva.
This
growth
involves
cell
migration
coupled
with
mitosis
distinct
zones.
Cell
proliferation
requires
FGF
signaling,
whereas
three-dimensional
orientation
depends
on
Wnt
signaling.
Specification
maintenance
tube
fate
Delta/Notch
Moreover,
identify
target
genes
pathway
that
contribute
morphology,
revealing
molecular
mechanisms
outgrowth.
Finally,
report
activates
Six1/2
transcription
factor,
which
serves
an
evolutionarily
ancient
regulator
branching
morphogenesis.
study
uncovers
tubulogenesis
vivo
propose
cellular
dynamics
represents
key
comparison
understanding
evolution
vertebrate
organs.
Cell
types
are
the
building
blocks
of
metazoan
biodiversity
and
offer
a
powerful
perspective
for
inferring
evolutionary
phenomena.
With
development
single-cell
transcriptomic
techniques,
new
definitions
cell
emerging.
This
allows
conceptual
reassessment
traditional
novel
their
evolution.
Research
in
echinoderms,
particularly
sea
star
urchin
embryos
has
contributed
significantly
to
understanding
evolution
types,
through
examination
skeletogenic
mesenchyme
pigment
cells,
which
found
larvae,
but
not
larvae.
paper
outlines
gene
expression
atlas
bat
star,
Patiria
miniata,
using
single
nuclear
RNA
sequencing
(snRNA-seq)
embryonic
stages.
The
revealed
23
clusters
covering
all
expected
from
endoderm,
mesoderm,
ectoderm
germ
layers.
In
particular,
four
distinct
neural
clusters,
an
immune-like
cluster,
right
left
coelom
were
as
states.
A
comparison
with
Strongylocentrotus
purpuratus
embryo
transcriptomes
was
performed
1:1
orthologs
anchor
then
compare
patterns.
equivalent
S.
piwil3+
Cells
detected
P.
while
Left
Coelom
miniata
no
cluster
purpuratus.
These
differences
may
reflect
changes
developmental
timing
between
these
species.
While
considered
morphologically,
Pigment
map
containing
Immune-like
Mesenchyme
Neural
cells
Skeletogenic
orthologous
Right
miniata.
results
suggest
interpretation
well-studied
reflection
on
definition
types.
PLoS Biology,
Год журнала:
2024,
Номер
22(6), С. e3002661 - e3002661
Опубликована: Июнь 3, 2024
Deuterostomes
are
a
monophyletic
group
of
animals
that
includes
Hemichordata,
Echinodermata
(together
called
Ambulacraria),
and
Chordata.
The
diversity
deuterostome
body
plans
has
made
it
challenging
to
reconstruct
their
ancestral
condition
decipher
the
genetic
changes
drove
diversification
lineages.
Here,
we
generate
chromosome-level
genome
assemblies
2
hemichordate
species,
Ptychodera
flava
Schizocardium
californicum
,
use
comparative
genomic
approaches
infer
chromosomal
architecture
common
ancestor
delineate
lineage-specific
modifications.
We
show
chromosomes
(1
N
=
23)
exhibit
remarkable
chromosome-scale
macrosynteny
when
compared
other
deuterostomes
can
be
derived
from
24
linkage
groups
(ALGs).
These
ALGs
in
turn
match
previously
inferred
bilaterian
ALGs,
consistent
with
relatively
short
transition
last
origin
deuterostomes.
Based
on
this
ALG
complement,
deduced
rearrangement
events
occurred
different
For
example,
fusion-with-mixing
event
produced
an
Ambulacraria-specific
subsequently
split
into
extant
hemichordates,
while
homologous
further
fused
another
chromosome
sea
urchins.
Orthologous
genes
distributed
these
rearranged
enriched
for
functions
various
developmental
processes.
found
deeply
conserved
Hox
clusters
located
highly
maintenance
likely
due
lower
densities
transposable
elements
within
clusters.
also
provide
evidence
deuterostome-specific
pharyngeal
gene
cluster
was
established
via
combination
3
pre-assembled
microsyntenic
blocks.
suggest
since
formation
new
may
change
regulatory
controls
genes,
have
contributed
evolution
diverse
among
ABSTRACT
Stable
transgenesis
is
a
transformative
tool
in
model
organism
biology.
Although
the
sea
urchin
one
of
oldest
animal
models
cell
and
developmental
biology,
studies
this
have
largely
relied
on
transient
manipulation
wild
animals,
without
strategy
for
stable
transgenesis.
Here,
we
build
recent
progress
to
develop
more
genetically
tractable
species,
Lytechinus
pictus,
establish
robust
transgene
integration
method.
Three
commonly
used
transposons
(Minos,
Tol2
piggyBac)
were
tested
non-autonomous
transposition,
using
plasmids
containing
polyubiquitin
promoter
upstream
H2B-mCerulean
nuclear
marker.
Minos
was
only
transposable
element
that
resulted
significant
expression
beyond
metamorphosis.
F0
animals
raised
sexual
maturity,
spawned
determine
germline
inheritance
frequency,
characterize
patterns
F1
progeny.
The
results
demonstrate
transmission
through
germline,
first
example
transgenic
and,
indeed,
any
echinoderm.
This
milestone
paves
way
generation
diverse
resources
will
dramatically
enhance
utility,
reproducibility
efficiency
research.
The Science of The Total Environment,
Год журнала:
2022,
Номер
864, С. 160901 - 160901
Опубликована: Дек. 13, 2022
Microplastics
are
now
polluting
all
seas
and,
while
studies
have
found
numerous
negative
interactions
between
plastic
pollution
and
marine
animals,
the
effects
on
embryonic
development
poorly
understood.
A
potentially
important
source
of
developmental
ecotoxicity
comes
from
chemicals
leached
particles
to
environment.
Here
we
investigate
leachates
new
beach-collected
pellets
larval
sea
urchin
Strongylocentrotus
purpuratus
demonstrate
that
exposure
developing
embryos
these
elicits
severe,
consistent
treatment-specific
abnormalities
including
radialisation
embryo
malformation
skeleton,
neural
immune
cells.
Using
a
multi-omics
approach
define
pathways
disturbed
upon
PVC
provide
mechanistic
view
pinpoints
cellular
redox
stress
energy
production
as
drivers
phenotypic
following
leachates.
Analysis
identified
high
concentrations
zinc
likely
cause
observed
defects.
Our
findings
point
clear
specific
detrimental
echinoderms,
demonstrating
into
water
can
produce
strong
via
pathways,
therefore
potential
impact
wide
range
organisms.
Communications Biology,
Год журнала:
2022,
Номер
5(1)
Опубликована: Март 10, 2022
Cold
seeps
and
hydrothermal
vents
are
deep-sea
reducing
environments
that
characterized
by
lacking
oxygen
photosynthesis-derived
nutrients.
Most
animals
acquire
nutrition
in
cold
or
maintaining
epi-
endosymbiotic
relationship
with
chemoautotrophic
microorganisms.
Although
several
seep-
vent-dwelling
hosting
symbiotic
microbes
have
been
well-studied,
the
genomic
basis
of
adaptation
to
environment
nonsymbiotic
is
still
lacking.
Here,
we
report
a
high-quality
genome
Chiridota
heheva
Pawson
&
Vance,
2004,
which
thrives
extracting
organic
components
from
sediment
detritus
suspended
material,
as
reference
for
animal's
environments.
The
expansion
aerolysin-like
protein
family
C.
compared
other
echinoderms
might
be
involved
disintegration
during
digestion.
Moreover,
hypoxia-related
genes
(Pyruvate
Kinase
M2,
PKM2;
Phospholysine
Phosphohistidine
Inorganic
Pyrophosphate
Phosphatase,
LHPP;
Poly(A)-specific
Ribonuclease
Subunit
PAN2,
PAN2;
Ribosomal
RNA
Processing
9,
RRP9)
were
subject
positive
selection
heheva,
contributes
their
hypoxic
