The application of irreversible genomic states to define and trace ancient cell type homologies
EvoDevo,
Journal Year:
2025,
Volume and Issue:
16(1)
Published: May 3, 2025
Homology,
or
relationship
among
characters
by
common
descent,
has
been
notoriously
difficult
to
assess
for
many
morphological
features,
and
cell
types
in
particular.
The
ontogenetic
origin
of
traits
means
that
the
only
physically
inherited
information
is
encoded
genomes.
However,
complexity
underlying
gene
regulatory
network
often
miniscule
changes
can
impact
expression,
make
it
practically
impossible
postulate
a
clear
demarcation
line
what
molecular
signature
should
"define"
homologous
type
between
two
deeply
branching
animals.
In
this
Hypothesis
article,
we
propose
use
recently
characterized
irreversible
genomic
states,
occur
after
chromosomal
sub-chromosomal
mixing
genes
elements,
dissect
signatures
each
into
reversible
configurations.
While
such
states
will
be
non-functional,
some
may
permanently
expression
given
type.
Our
proposal
evolutionarily
irreversible,
thus
synapomorphic,
functional
constitute
criterion
timing
deep
evolutionary
homologies.
aims
close
gap
clearly
defined
homology
individual
their
at
phenotypic
level
through
identification
linked
states.
Language: Английский
Topological mixing and irreversibility in animal chromosome evolution
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: July 30, 2024
Abstract/Summary
Paragraph
Animal
chromosomes
can
persist
with
recognizable
homology
over
hundreds
of
millions
years,
in
spite
homology-obfuscating
processes
such
as
chromosomal
fusion
and
translocation.
The
frequency
pace
these
major
genome
structural
changes
are
unknown,
it
remains
unclear
whether
or
how
they
impact
long-term
evolution.
Here,
we
compare
whole
sequences
3,631
genomes
from
2,291
species
spanning
all
animal
clades
show
that
karyotypes
evolve
primarily
via
karyotype
contraction,
associated
increased
rates
fusion-with-mixing
dispersion
largely
obey
algebra
1
,
expansion,
which
breaks
up
ancestral
linkage
groups
forms
new
elements
non-algebraic
changes.
We
be
extinction
events.
Using
a
multi-scale
encoding
pan-animal
manifold
representation
genomic
changes,
find
evolution
is
not
only
driven
by
at
the
level,
but
subchromosomal
mixing
irreversibility
define
clade-specific
this
‘evolutionary
topology’
approach,
calculate
extrema
irreversible
configurations
identify
occupy
intermediate
positions,
providing
evidence
for
distinct
macro-evolutionary
trajectories.
propose
investigation
mixed
state
accumulation
around
important
gene
loci
(such
Hox)
will
crucial
capturing
further
study
regulatory
innovations.
Language: Английский
Emerging trends in functional genomics in Spiralia
Briefings in Functional Genomics,
Journal Year:
2023,
Volume and Issue:
22(6), P. 485 - 486
Published: Nov. 1, 2023
Journal
Article
Emerging
trends
in
functional
genomics
Spiralia
Get
access
José
M
Martín-Durán
Corresponding
author:
M.
Martín-Durán,
Queen
Mary
University
of
London,
School
Biological
and
Behavioural
Sciences.
E-mail:
[email protected]
https://orcid.org/0000-0002-2572-1061
Search
for
other
works
by
this
author
on:
Oxford
Academic
PubMed
Google
Scholar
Briefings
Functional
Genomics,
Volume
22,
Issue
6,
November
2023,
Pages
485–486,
https://doi.org/10.1093/bfgp/elad048
Published:
17
2023
history
Received:
20
October
Accepted:
23
Language: Английский