Genomics,
Год журнала:
2022,
Номер
114(4), С. 110431 - 110431
Опубликована: Июль 1, 2022
Despite
recent
studies
discussing
the
evolutionary
impacts
of
gene
duplications
and
losses
among
metazoans,
genomic
basis
for
evolution
phyla
remains
enigmatic.
Here,
we
employ
phylogenomic
approaches
to
search
orthologous
genes
without
known
functions
echinoderms,
subsequently
use
them
guide
identification
their
homologs
across
other
metazoans.
Our
final
set
14
was
obtained
via
a
suite
homology
prediction
tools,
expression
data,
ontology,
generating
Strongylocentrotus
purpuratus
phylome.
The
subjected
selection
pressure
analyses,
which
indicated
that
they
are
highly
conserved
under
negative
selection.
Their
presence
broad
taxonomic
depths
suggests
required
form
phylum
ancestral
phylum.
Therefore,
rather
than
de
novo
genesis,
posit
forces
such
as
on
existing
elements
over
large
timescales
may
drive
divergence
contribute
emergence
phyla.
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.
Frontiers in Neuroscience,
Год журнала:
2024,
Номер
18
Опубликована: Апрель 10, 2024
Most
sea
urchin
species
are
indirect
developers,
going
through
a
larval
stage
called
pluteus.
The
pluteus
possesses
its
own
nervous
system,
consisting
mainly
of
the
apical
organ
neurons
(controlling
metamorphosis
and
settlement)
ciliary
band
swimming
behavior
food
collection).
Additional
located
in
various
areas
gut.
In
recent
years,
molecular
complexity
this
apparently
"simple"
system
has
become
apparent,
with
at
least
12
neuronal
populations
identified
scRNA-sequencing
Cells,
Год журнала:
2022,
Номер
11(17), С. 2636 - 2636
Опубликована: Авг. 24, 2022
Molecular
research
on
the
evolution
of
extraocular
photoreception
has
drawn
attention
to
photosensitive
animals
lacking
proper
eye
organs.
Outside
vertebrates,
little
is
known
about
this
type
sensory
system
in
any
other
deuterostome.
In
study,
we
investigate
such
an
photoreceptor
cell
(PRC)
developmental
stages
sea
urchin
In
holothurians,
the
regenerative
process
following
evisceration
involves
development
of
a
“rudiment”
or
“anlage”
at
injured
end
mesentery.
This
regenerating
anlage
plays
pivotal
role
in
formation
new
intestine.
Despite
its
significance,
our
understanding
molecular
characteristics
inherent
to
constituent
cells
this
structure
has
remained
limited.
To
address
gap,
we
employed
state-of-the-art
scRNA-seq
and
HCR-FISH
analyses
discern
distinct
cellular
populations
associated
with
regeneration
anlage.
Through
approach,
successfully
identified
thirteen
cell
clusters.
Among
these,
two
clusters
exhibit
consistent
putative
mesenchymal
cells,
while
another
four
show
features
akin
coelomocyte
populations.
The
remaining
seven
collectively
form
large
group
encompassing
coelomic
epithelium
Within
clusters,
recognized
previously
documented
such
as
muscle
precursors,
neuroepithelial
actively
proliferating
cells.
Strikingly,
analysis
provides
data
for
identifying
least
other
that
define
precursor
growing
Consequently,
findings
strengthen
hypothesis
is
pluripotent
tissue
gives
rise
diverse
types
intestinal
organ.
Moreover,
results
provide
initial
view
into
transcriptomic
responsible
amazing
capabilities
echinoderms.
In
holothurians,
the
regenerative
process
following
evisceration
involves
development
of
a
‘rudiment’
or
‘anlage’
at
injured
end
mesentery.
This
regenerating
anlage
plays
pivotal
role
in
formation
new
intestine.
Despite
its
significance,
our
understanding
molecular
characteristics
inherent
to
constituent
cells
this
structure
has
remained
limited.
To
address
gap,
we
employed
state-of-the-art
scRNA-seq
and
hybridization
chain
reaction
fluorescent
situ
analyses
discern
distinct
cellular
populations
associated
with
regeneration
anlage.
Through
approach,
successfully
identified
13
cell
clusters.
Among
these,
two
clusters
exhibit
consistent
putative
mesenchymal
cells,
while
another
four
show
features
akin
coelomocyte
populations.
The
remaining
seven
collectively
form
large
group
encompassing
coelomic
epithelium
Within
clusters,
recognized
previously
documented
such
as
muscle
precursors,
neuroepithelial
actively
proliferating
cells.
Strikingly,
analysis
provides
data
for
identifying
least
other
that
define
precursor
growing
Consequently,
findings
strengthen
hypothesis
is
pluripotent
tissue
gives
rise
diverse
types
intestinal
organ.
Moreover,
results
provide
initial
view
into
transcriptomic
responsible
amazing
capabilities
echinoderms.
Integrative and Comparative Biology,
Год журнала:
2023,
Номер
63(5), С. 999 - 1009
Опубликована: Май 15, 2023
Synopsis
Over
the
past
decade,
single-cell
RNA-sequencing
(scRNA-seq)
has
made
it
possible
to
study
cellular
diversity
of
a
broad
range
organisms.
Technological
advances
in
isolation
and
sequencing
have
expanded
rapidly,
allowing
transcriptomic
profile
individual
cells
be
captured.
As
result,
there
been
an
explosion
cell
type
atlases
created
for
many
different
marine
invertebrate
species
from
across
tree
life.
Our
focus
this
review
is
synthesize
current
literature
on
scRNA-seq.
Specifically,
we
provide
perspectives
key
insights
scRNA-seq
studies,
including
descriptive
studies
composition,
how
respond
dynamic
processes
such
as
development
regeneration,
evolution
new
types.
Despite
these
tremendous
advances,
also
lie
several
challenges
ahead.
We
discuss
important
considerations
that
are
essential
when
making
comparisons
between
experiments,
or
datasets
species.
Finally,
address
future
analyses
invertebrates,
combining
data
with
other
‘omics
methods
get
fuller
understanding
complexities.
The
full
types
invertebrates
remains
unknown
will
rich
areas
study.
International Journal of Molecular Sciences,
Год журнала:
2024,
Номер
25(3), С. 1685 - 1685
Опубликована: Янв. 30, 2024
The
Mediterranean
purple
sea
urchin
Paracentrotus
lividus
(Lamarck
1816)
is
a
remarkable
model
system
for
molecular,
evolutionary
and
cell
biology
studies,
particularly
in
the
field
of
developmental
biology.
We
sequenced
genome,
performed
de
novo
assembly,
analysed
assembly
content.
genome
P.
was
using
Illumina
NextSeq
500
System
(Illumina)
2
×
150
paired-end
format.
More
than
30,000
open
reading
frames
(ORFs),
(more
8000
are
unique),
were
identified
to
provide
molecular
tools
accessible
scientific
community.
In
particular,
several
genes
involved
complex
innate
immune
responses,
oxidative
metabolism,
signal
transduction,
kinome,
as
well
regulating
membrane
receptors,
genome.
this
way,
employment
investigations
comparative
analyses
empowered,
leading
explanation
cis-regulatory
networks
their
evolution
key
occupying
an
important
position
with
respect
vertebrates
humans.
