Ecology Of Freshwater Fish,
Год журнала:
2023,
Номер
32(4), С. 677 - 702
Опубликована: Март 16, 2023
Abstract
Eurasian
perch
Perca
fluviatilis
has
been
a
popular
model
species
for
decades
in
the
fields
of
aquatic
ecology,
community
dynamics,
behaviour,
physiology
and
ecotoxicology.
Yet,
despite
extensive
research,
progress
integrating
genomic
perspective
into
existing
ecological
knowledge
relatively
modest.
Meanwhile,
emergence
high‐throughput
sequencing
technologies
completely
changed
methods
genetic
variation
assessment
conducting
biodiversity
evolutionary
research.
During
last
5
years,
three
genome
assemblies
P.
have
generated,
allowing
substantial
advancement
our
understanding
interactions
between
processes
at
whole‐genome
level.
We
review
past
progress,
current
status
potential
future
impact
resources
tools
research
focusing
on
utility
recent
assemblies.
Furthermore,
we
demonstrate
power
genome‐wide
approaches
newly
developed
outline
cases
where
genomics
contributed
to
new
knowledge.
explore
how
availability
reference
assembly
enables
efficient
application
various
statistical
tools,
can
provide
novel
insights
resource
polymorphism,
host–parasite
phenotypic
changes
associated
with
climate
change
harvesting‐induced
evolution.
In
summary,
call
increased
integration
perch,
as
well
other
fish
species,
which
is
likely
yield
linking
adaptation
plasticity
ecosystem
functioning
environmental
change.
Proceedings of the Royal Society B Biological Sciences,
Год журнала:
2022,
Номер
289(1989)
Опубликована: Дек. 21, 2022
We
organized
this
special
issue
to
highlight
new
work
and
review
recent
advances
at
the
cutting
edge
of
'wild
quantitative
genomics'.
In
editorial,
we
will
present
some
history
wild
genetic
genomic
studies,
before
discussing
main
themes
in
papers
published
highlighting
future
outlook
dynamic
field.
G3 Genes Genomes Genetics,
Год журнала:
2024,
Номер
14(8)
Опубликована: Июнь 7, 2024
We
present
a
reference
genome
for
the
federally
endangered
Gaviota
tarplant,
Deinandra
increscens
subsp.
villosa
(Madiinae,
Asteraceae),
an
annual
herb
endemic
to
Central
California
coast.
Generating
PacBio
HiFi,
Oxford
Nanopore
Technologies,
and
Dovetail
Omni-C
data,
we
assembled
haploid
consensus
of
1.67
Gb
as
28.7
K
scaffolds
with
scaffold
N50
74.9
Mb.
annotated
repeat
content
in
74.8%
genome.
Long
terminal
repeats
(LTRs)
covered
44.0%
Copia
families
predominant
at
22.9%
followed
by
Gypsy
14.2%.
Both
elements
were
common
ancestral
peaks
LTRs,
most
abundant
element
was
containing
nested
Copia/Angela
sequence
similarity,
reflecting
complex
evolutionary
history
activity.
Gene
annotation
produced
33,257
genes
68,942
transcripts,
which
99%
functionally
annotated.
BUSCO
scores
proteins
96.0%
complete
77.6%
single
copy
18.4%
duplicates.
Whole
duplication
synonymous
mutation
rates
tarplant
sunflower
(Helianthus
annuus)
shared
that
correspond
last
Asteraceae
polyploidization
event
subsequent
divergence
from
ancestor
∼27
MYA.
Regions
high-density
tandem
identified,
pointing
potentially
important
loci
environmental
adaptation
this
species.
The
last
known
red
wolves
were
captured
in
southwestern
Louisiana
and
eastern
Texas
1980
to
establish
a
captive
breeding
population.
Before
their
extirpation,
gene
flow
with
coyotes
resulted
the
persistence
of
endangered
wolf
genetic
variation
local
coyote
populations.
We
assessed
genomic
ancestry
morphology
Louisiana.
detected
that
38
62%
genomes
contained
acquired
past
30
years
have
an
admixture
profile
similar
canids
before
extirpation
wolves.
further
documented
positive
correlation
between
weight.
Our
findings
highlight
importance
hybrids
admixed
as
reservoir
species
for
innovative
conservation
efforts.
Together,
this
work
presents
unprecedented
system
can
leverage
enrich
recovery
program
species.
Ecology Of Freshwater Fish,
Год журнала:
2023,
Номер
32(4), С. 677 - 702
Опубликована: Март 16, 2023
Abstract
Eurasian
perch
Perca
fluviatilis
has
been
a
popular
model
species
for
decades
in
the
fields
of
aquatic
ecology,
community
dynamics,
behaviour,
physiology
and
ecotoxicology.
Yet,
despite
extensive
research,
progress
integrating
genomic
perspective
into
existing
ecological
knowledge
relatively
modest.
Meanwhile,
emergence
high‐throughput
sequencing
technologies
completely
changed
methods
genetic
variation
assessment
conducting
biodiversity
evolutionary
research.
During
last
5
years,
three
genome
assemblies
P.
have
generated,
allowing
substantial
advancement
our
understanding
interactions
between
processes
at
whole‐genome
level.
We
review
past
progress,
current
status
potential
future
impact
resources
tools
research
focusing
on
utility
recent
assemblies.
Furthermore,
we
demonstrate
power
genome‐wide
approaches
newly
developed
outline
cases
where
genomics
contributed
to
new
knowledge.
explore
how
availability
reference
assembly
enables
efficient
application
various
statistical
tools,
can
provide
novel
insights
resource
polymorphism,
host–parasite
phenotypic
changes
associated
with
climate
change
harvesting‐induced
evolution.
In
summary,
call
increased
integration
perch,
as
well
other
fish
species,
which
is
likely
yield
linking
adaptation
plasticity
ecosystem
functioning
environmental
change.
