Ecology and Evolution,
Год журнала:
2025,
Номер
15(4)
Опубликована: Апрель 1, 2025
ABSTRACT
With
the
increasing
interest
in
whole
genome
sequencing
of
eukaryotes,
it
is
becoming
evident
that
selecting
most
suitable
high
molecular
weight
DNA
extraction
method
crucial
for
maximizing
benefits
long‐read
technologies.
However,
many
species
cannot
be
processed
immediately
at
sampling
site
due
to
remoteness
location,
necessitating
tissue
preservation
may
affect
fragment
size.
This
study
aimed
identify
combination
four
approaches
and
six
methods
ensure
DNA.
A
single
Peltodoris
atromaculata
(Nudibranchia)
specimen
was
sliced
into
∼30
mg
sub‐samples,
ensuring
consistency
across
24
preservation‐extraction
combinations
triplicates.
Samples
were
either
stored
4°C,
dried
room
temperature,
flash‐frozen
liquid
nitrogen,
or
preserved
ethanol
−20°C.
Afterward,
they
using
five
commercially
available
kits
specific
extraction,
as
well
a
custom
protocol.
Three
aspects
quality
evaluated:
total
yield,
size
distribution,
availability
amplification.
Most
yielded
optimal
results
only
some
three
aspects.
We
identified
sequencing:
CTAB‐based
protocol
applied
frozen
samples,
Wizard
(Promega)
Nanobind
(PacBio)
both
ethanol‐preserved
paired
with
Monarch
(NEB)
kits.
The
suitability
selected
confirmed
by
PacBio
sequencing,
producing
yield
3.6
Gbp
(3.2x
estimated
coverage).
indicate
success
extractions
influenced
methods.
Although
tested
on
nudibranchs,
these
findings
are
highly
useful
genomic
studies
other
organisms,
which
need
remote
locations
before
being
transported
laboratory
processing.
PLoS neglected tropical diseases,
Год журнала:
2025,
Номер
19(4), С. e0013016 - e0013016
Опубликована: Апрель 11, 2025
Actinomadura
isolates
obtained
from
seven
human
mycetoma
cases
in
Mexico
were
characterized
using
nucleotide
sequence
analysis
of
a
portion
the
small
subunit
ribosomal
RNA
gene.
Most
identified
as
madurae.
However,
one
isolate,
LIID-AQ337,
showed
inconclusive
results.
To
determine
its
identity,
genomic
DNA
LIID-AQ337
was
subjected
to
whole-genome
sequencing
both
short-
and
long-read
sequencing,
resulting
genome
8,163,638-bp
spread
22
contigs.
Comparative
against
currently
available
genomes
other
species
suggested
that
belongs
new
species.
We
propose
name
it
welshii
sp.
nov
honor
Oliverio
Welsh,
Mexican
dermatologist
dedicated
studies
Mexico.
Frontiers in Zoology,
Год журнала:
2025,
Номер
22(1)
Опубликована: Апрель 17, 2025
Abstract
Reference
genome
assemblies
are
the
basis
for
comprehensive
genomic
analyses
and
comparisons.
Due
to
declining
sequencing
costs
growing
computational
power,
projects
now
feasible
in
smaller
labs.
De
novo
non-model
or
emerging
model
organisms
requires
knowledge
about
size
techniques
extracting
high
molecular
weight
DNA.
Next
quality,
amount
of
DNA
obtained
from
single
individuals
is
crucial,
especially,
when
dealing
with
small
organisms.
While
long-read
technologies
methods
choice
creating
quality
assemblies,
pure
short-read
might
bear
most
coding
parts
a
but
usually
much
more
fragmented
do
not
well
resolve
repeat
elements
structural
variants.
Several
initiatives
produce
organism
genomes
provide
rules
standards
assembly.
However,
sometimes
part
such
an
initiative
does
meet
its
standards.
Therefore,
if
scientific
question
can
be
answered
low
contiguity
intergenic
parts,
missing
chromosome
scale
assembly
should
prevent
publication.
This
review
describes
how
set
up
animal
project
lab,
estimate
resources,
deal
suboptimal
conditions.
Thus,
we
aim
suggest
optimal
strategies
that
fulfil
needs
according
specific
research
questions,
e.g.
“How
species
related
each
other
based
on
whole
genomes?”
(phylogenomics),
populations
within
differ?”
(population
genomics),
“Are
differences
between
relevant
conservation?”
(conservation
“Which
selection
pressure
acting
certain
genes?”
(identification
genes
under
selection),
“Did
repeats
expand
contract
recently?”
(repeat
dynamics).
Scientific Reports,
Год журнала:
2025,
Номер
15(1)
Опубликована: Апрель 18, 2025
DNA
extraction
is
a
fundamental
technique
in
molecular
biology.
For
Chimonanthus
praecox-a
winter-flowering
tree
species-extensive
and
rapid
necessary
to
support
genetic
analyses.
Currently,
C.
praecox
primarily
relies
on
the
traditional
cetyltrimethylammonium
bromide
(CTAB)
method,
which
time-consuming
labor-intensive,
hindering
large-scale
work.
In
this
study,
different
steps
CTAB
method
are
compared
evaluated
optimize
leaf
process.
The
water
bath
duration
significantly
impacts
efficiency;
longer
bath,
higher
concentration.
However,
10-min
sufficient
yield
of
ideal
concentration
purity.
Additionally,
single
step
appropriate,
with
precipitation
at
-
20
°C
yielding
high-quality
DNA.
pre-treatment
was
modified
by
using
frozen
pipette
tip
crush
samples
directly
centrifuge
tube,
reducing
operational
complexity
minimizing
liquid
nitrogen
sample
consumption.
Only
25
mg
required,
from
leaves
can
be
extracted
within
1
h.
amounts
required
were
reduced
75%
90%,
respectively.
Moreover,
time
for
simplified
77.14%.
applicability
scheme
tissues,
Calycanthaceae
family
members,
species
other
families.
tepals
protocol
biased
toward
family,
Nicotiana
tabacum,
Populus
tomentosa,
Lilium
brownii.
proposed
enables
efficient
plant
suitable
multiple
species.
This
reduces
consumption,
lowering
costs
while
shortening
procedure
enhancing
efficiency.
highly
applications
involving
large
low-concentration
across
various
Frontiers in Chemistry,
Год журнала:
2024,
Номер
12
Опубликована: Фев. 20, 2024
Introduction:
The
increasing
global
pressure
to
explore
alternative
protein
sources
derived
from
animal
by-products
has
opened-up
opportunities,
but
it
also
created
the
need
assess
their
compliance
with
labelling
statements,
ensure
consumer’s
trust
in
composition
of
both
feed
and
food
products.
Assessing
authenticity
highly
processed
by-products,
particularly
within
rapidly
expanding
Halal
market,
presents
a
significant
challenge
due
lack
robust
standardized
methodologies.
However,
success
DNA
based
system
is
dependent
on
extracted
quantity,
quality,
purity
ratios
heterogeneous
matrices.
Material
methods:
In
this
work,
nine
extraction
methods
were
tested
selected
high-value
interest
for
industry:
meals
poultry
meat,
blood
feather,
hydrolysates
swine
meat
bone,
fish,
black
soldier
fly.
proposed
are
developed
specifically
target
swine-specific
mitochondrial
region,
as
case
study.
Results
discussion:
Both
conventional
CTAB
method
commercial
kits,
Invisorb
®
Spin
Tissue
Mini
NucleoSpin™
Food,
demonstrated
superior
efficiency
quality
ratios.
Nevertheless,
kits
enabled
faster
detection
comparison
methods.
absence
was
successfully
validated
confirmed
all
that
did
not
contain
beforehand,
demonstrating
market
requirements.
