Frontiers in Genetics,
Journal Year:
2021,
Volume and Issue:
12
Published: Aug. 30, 2021
Cycads
represent
one
of
the
most
ancestral
living
seed
plants
as
well
threatened
plant
groups
in
world.
South
China
is
a
major
center
and
potential
origin
Cycas
,
rapidly
diversified
lineage
cycads.
However,
genomic-wide
diversity
remains
poorly
understood
due
to
challenge
generating
genomic
markers
associated
with
their
inherent
large
genomes.
Here,
we
perform
comprehensive
conservation
study
based
on
restriction-site
DNA
sequencing
(RADseq)
data
six
representative
species
China.
Consistently
low
genetic
strong
differentiation
were
detected
across
species.
Both
phylogenetic
inference
structure
analysis
via
several
methods
revealed
generally
congruent
among
The
ADMIXTURE
showed
mixing
composition
species,
while
individuals
C.
dolichophylla
exhibited
substantial
admixture
bifida
changjiangensis
balansae
.
Furthermore,
results
from
Treemix,
f
4
-statistic,
ABBA-BABA
test
consistent
complex
patterns
interspecific
gene
flow.
Relatively
signals
hybridization
between
szechuanensis
ancestor
taiwaniana
Distinct
demographic
history
inferred
for
these
by
Stairway
Plot,
our
suggested
that
both
climate
fluctuation
frequent
geological
activities
during
late
Pleistocene
exerted
deep
impacts
population
dynamics
Finally,
explore
practical
implications
findings
development
strategies
present
demonstrates
efficiency
RADseq
studies
non-model
Given
great
significance
cycads
radical
transition
evolution
biodiversity,
provides
important
insights
into
mechanisms
diversification
such
recently
radiated
fossil
taxa.
BMC Biology,
Journal Year:
2021,
Volume and Issue:
19(1)
Published: April 13, 2021
Abstract
Background
Dinoflagellates
in
the
family
Symbiodiniaceae
are
important
photosynthetic
symbionts
cnidarians
(such
as
corals)
and
other
coral
reef
organisms.
Breakdown
of
coral-dinoflagellate
symbiosis
due
to
environmental
stress
(i.e.
bleaching)
can
lead
death
potential
collapse
ecosystems.
However,
evolution
genomes,
its
implications
for
coral,
is
little
understood.
Genome
sequences
remain
scarce
part
their
large
genome
sizes
(1–5
Gbp)
idiosyncratic
features.
Results
Here,
we
present
de
novo
assemblies
seven
members
genus
Symbiodinium
,
which
two
free-living,
one
an
opportunistic
symbiont,
remainder
mutualistic
symbionts.
Integrating
available
data,
compare
15
dinoflagellate
genomes
revealing
high
sequence
structural
divergence.
Divergence
among
some
isolates
comparable
that
distinct
genera
Symbiodiniaceae.
We
also
recovered
hundreds
gene
families
specific
each
lineage,
many
encode
unknown
functions.
An
in-depth
comparison
between
symbiotic
tridacnidorum
(isolated
from
a
coral)
free-living
natans
reveals
greater
prevalence
transposable
elements,
genetic
duplication,
rearrangements,
pseudogenisation
species.
Conclusions
Our
results
underscore
impact
lifestyle
on
lineage-specific
gene-function
innovation,
divergence,
diversification
The
divergent
features
report,
putative
causes,
may
apply
microbial
eukaryotes
have
undergone
phases
evolutionary
history.
Ecological Solutions and Evidence,
Journal Year:
2020,
Volume and Issue:
1(2)
Published: Nov. 8, 2020
Abstract
1.
Despite
aspirations
for
conservation
impact,
mismatches
between
research
and
implementation
have
limited
progress
towards
this
goal.
There
is,
therefore,
an
urgent
need
to
identify
how
we
can
more
effectively
navigate
the
spaces
practice.
2.
In
2014,
ran
a
workshop
with
researchers
practitioners
that
needed
be
overcome
deliver
evidence‐informed
action.
Five
were
highlighted:
spatial,
temporal,
priority,
communication,
institutional.
3.
Since
thinking
around
‘research–implementation
gap’
has
progressed.
The
term
‘gap’
been
replaced
by
language
dynamic
‘spaces’
action,
representing
shift
in
what
it
takes
better
align
4.
2019,
follow‐up
reflecting
on
shift,
whether
five
identified
2014
still
present
conservation,
had
made
these
during
past
5
years.
We
found
while
there
progress,
some
way
go
across
all
dimensions.
5.
Here,
report
outcomes
of
2019
workshop,
reflect
changed
over
years,
offer
10
recommendations
strengthening
alignment
Molecular Ecology,
Journal Year:
2021,
Volume and Issue:
30(23), P. 5949 - 5965
Published: Aug. 23, 2021
Structural
variants
(SVs)
are
large
rearrangements
(>50
bp)
within
the
genome
that
impact
gene
function
and
content
structure
of
chromosomes.
As
a
result,
SVs
significant
source
functional
genomic
variation,
is,
variation
at
regions
underpinning
phenotype
differences,
can
have
effects
on
individual
population
fitness.
While
there
increasing
opportunities
to
investigate
in
threatened
species
via
single
nucleotide
polymorphism
(SNP)
data
sets,
remain
understudied
despite
their
potential
influence
fitness
traits
conservation
interest.
In
this
future-focused
Opinion,
we
contend
characterizing
offers
genomics
community
an
exciting
opportunity
complement
SNP-based
approaches
enhance
recovery.
We
also
leverage
existing
literature-predominantly
human
health,
agriculture
ecoevolutionary
biology-to
identify
for
readily
consider
how
integrating
these
into
toolbox
may
transform
way
manage
some
world's
most
species.
BMC Bioinformatics,
Journal Year:
2022,
Volume and Issue:
23(1)
Published: June 13, 2022
Many
wild
species
have
suffered
drastic
population
size
declines
over
the
past
centuries,
which
led
to
'genomic
erosion'
processes
characterized
by
reduced
genetic
diversity,
increased
inbreeding,
and
accumulation
of
harmful
mutations.
Yet,
genomic
erosion
estimates
modern-day
populations
often
lack
concordance
with
dwindling
sizes
conservation
status
threatened
species.
One
way
directly
quantify
consequences
is
compare
genome-wide
data
from
pre-decline
museum
samples
modern
samples.
However,
doing
so
requires
computational
processing
analysis
tools
specifically
adapted
comparative
analyses
degraded,
ancient
or
historical,
DNA
as
well
personnel
trained
perform
such
analyses.Here,
we
present
a
highly
flexible,
scalable,
modular
pipeline
patterns
using
disparate
time
periods.
The
GenErode
uses
state-of-the-art
bioinformatics
simultaneously
process
whole-genome
re-sequencing
ancient/historical
samples,
produce
comparable
several
indices.
No
programming
knowledge
required
run
all
bioinformatic
steps
are
well-documented,
making
accessible
users
different
backgrounds.
written
in
Snakemake
Python3
Conda
Singularity
containers
achieve
reproducibility
on
high-performance
compute
clusters.
source
code
freely
available
GitHub
(
https://github.com/NBISweden/GenErode
).GenErode
user-friendly
reproducible
that
enables
standardization
indices
temporally
sampled
whole
genome
data.
Communications Biology,
Journal Year:
2023,
Volume and Issue:
6(1)
Published: March 27, 2023
Bromus
tectorum
L.
is
arguably
the
most
successful
invasive
weed
in
world.
It
has
fundamentally
altered
arid
ecosystems
of
western
United
States,
where
it
now
found
on
an
excess
20
million
hectares.
Invasion
success
related
to
avoidance
abiotic
stress
and
human
management.
Early
flowering
a
heritable
trait
utilized
by
B.
tectorum,
enabling
species
temporally
monopolize
limited
resources
outcompete
native
plant
community.
Thus,
understanding
genetic
underpinning
time
critical
for
design
integrated
management
strategies.
To
study
traits
we
assembled
chromosome
scale
reference
genome
tectorum.
assess
utility
genome,
121
diverse
accessions
are
phenotyped
subjected
wide
association
(GWAS).
Candidate
genes,
representing
homologs
genes
that
have
been
previously
associated
with
height
or
phenology
located
near
QTLs
identified.
This
uses
high-resolution
GWAS
identify
reproductive
weedy
represents
considerable
step
forward
mechanisms
underlying
plasticity
one
species.
Research Square (Research Square),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Feb. 28, 2024
Abstract
Biological
invasions
are
a
major
threat
to
biodiversity.
Therefore,
monitoring
genomic
features
of
invasive
species
is
crucial
understand
their
population
structure
and
adaptive
processes.
However,
resources
scarce,
compromising
the
study
success.
Here,
we
present
reference
genome
Styela
plicata
,
one
most
widespread
marine
species,
combined
with
data
24
individuals
from
6
populations
distributed
worldwide.
We
characterized
large
inversions
in
four
chromosomes,
accounting
for
~
15%
size.
These
polymorphic
through
species’
distribution
area,
enriched
genes
enhancing
fitness
estuary
harbor
environments.
Nonetheless,
mask
detection
S.
structure.
When
these
structural
variants
removed,
successfully
identify
main
oceanographic
barriers
accurately
characterize
differentiation
between
within
ocean
basins.
Several
located
chromosome
3
showcased
as
drivers
biogeographic
regions.
Moreover,
recover
three
mitogenomic
clades,
involving
rearrangements
leading
cyto-nuclear
coevolution
likely
involved
mitochondrion
during
cell
division.
Our
results
suggest
that
contribute
structuring
adaptation
processes,
potentially
success
when
colonizing
new
habitats.
iScience,
Journal Year:
2022,
Volume and Issue:
25(7), P. 104474 - 104474
Published: May 26, 2022
Conservation
breeding
programs
aim
to
maintain
90%
wild
genetic
diversity,
but
rarely
assess
functional
diversity.
Here,
we
compare
both
genome-wide
and
diversity
(in
over
500
genes)
of
Tasmanian
devils
(Sarcophilus
harrisii)
within
the
insurance
metapopulation
across
species'
range
(64,519
km2).
Populations
have
declined
by
80%
since
1996
due
a
contagious
cancer,
devil
facial
tumor
disease
(DFTD).
However,
predicted
local
extinctions
not
occurred.
Recent
suggestions
selection
for
"resistance"
alleles
in
precipitated
concerns
that
population
may
be
unsuitable
translocations.
Using
830
samples
collected
at
31
locations
between
2012
2021,
553
devils,
show
is
representative
current
Allele
frequencies
DFTD-associated
loci
were
substantially
different
captive
devils.
Methods
presented
here
are
valuable
others
investigating
evolutionary
potential
threatened
species,
particularly
ones
under
significant
selective
pressures.
Molecular Ecology,
Journal Year:
2022,
Volume and Issue:
31(21), P. 5468 - 5486
Published: Sept. 3, 2022
Mammal
declines
across
northern
Australia
are
one
of
the
major
biodiversity
loss
events
occurring
globally.
There
has
been
no
regional
assessment
implications
these
species
for
genomic
diversity.
To
address
this,
we
conducted
a
species-wide
diversity
in
quoll
(Dasyurus
hallucatus),
an
Endangered
marsupial
carnivore.
We
used
next
generation
sequencing
methods
to
genotype
10,191
single
nucleotide
polymorphisms
(SNPs)
352
individuals
from
3220-km
length
continent,
investigating
patterns
population
structure
and
diversity,
identifying
loci
showing
signals
putative
selection.
found
strong
heterogeneity
distribution
characterized
by
(i)
biogeographical
barriers
driving
hierarchical
through
long-term
isolation,
(ii)
severe
reductions
resulting
declines,
exacerbated
spread
introduced
toxic
cane
toads
(Rhinella
marina).
These
results
warn
large
ongoing
associated
adaptive
capacity
as
mammals
decline
Australia.
Encouragingly,
populations
established
on
toad-free
islands
translocations
appear
have
maintained
most
initial
after
16
years.
By
mapping
within
among
populations,
context
can
provide
conservation
managers
with
data
critical
informed
decision-making.
This
includes
identification
that
candidates
genetic
management,
importance
remnant
island
insurance/translocated
characterization
evolutionarily
significant
units.
Gigabyte,
Journal Year:
2020,
Volume and Issue:
2020, P. 1 - 22
Published: Nov. 5, 2020
Antechinus
are
a
genus
of
mouse-like
marsupials
that
exhibit
rare
reproductive
strategy
known
as
semelparity
and
also
naturally
develop
age-related
neuropathologies
similar
to
those
in
humans.
We
provide
the
first
annotated
antechinus
reference
genome
for
brown
(Antechinus
stuartii).
The
is
3.3
Gb
size
with
scaffold
N50
73Mb
93.3%
complete
mammalian
BUSCOs.
Using
bioinformatic
methods
we
assign
scaffolds
chromosomes
identify
0.78
Mb
Y-chromosome
scaffolds.
Comparative
genomics
revealed
interesting
expansions
NMRK2
gene
protocadherin
gamma
family,
which
have
previously
been
associated
aging
dementias
respectively.
Transcriptome
data
displayed
expression
common
Alzheimer’s
related
genes
brain
highlight
potential
utilising
future
disease
model.
valuable
genomic
resources
provided
herein
will
enable
research
explore
genetic
basis
processes
antechinus.
Genome Biology and Evolution,
Journal Year:
2021,
Volume and Issue:
13(8)
Published: June 9, 2021
Conservation
genomics
has
made
dramatic
improvements
over
the
past
decade,
leveraging
power
of
genomes
to
infer
diverse
parameters
central
conservation
management
questions.
However,
much
this
effort
focused
upon
vertebrate
species,
despite
insects
providing
similar
flagship
status
with
added
benefit
smaller
genomes,
shorter
generation
times
and
extensive
historical
collections
in
museums.
Here
we
present
genome
Apollo
butterfly
(Parnassius
apollo,
Papilionidae),
an
iconic
endangered
butterfly,
which
like
many
species
genus,
needs
genomic
attention
yet
lacks
a
genome.
Using
68.7
Gb
long-read
data
(N50
=
15.2
kb)
assembled
1.4
for
making
largest
sequenced
Lepidopteran
date.
The
assembly
was
highly
contiguous
7.1
Mb)
complete
(97%
BUSCOs
were
single-copy
complete)
consisted
1,707
contigs.
RNAseq
Arthropoda
proteins,
annotated
28.3K
genes.
Alignment
closest-related
chromosome-level
assembly,
Papilio
bianor,
reveals
conserved
chromosomal
organization,
albeit
size
is
expanded
due
primarily
increase
repetitive
element
content.
alignment
superscaffolding
places
P.
apollo
31
scaffolds,
together
our
functional
annotation,
provides
essential
resource
advancing
insect
conservation.