Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Feb. 5, 2024
Abstract
Using
long-read
sequencing,
we
assembled
and
unzipped
the
polyploid
genomes
of
Meloidogyne
incognita
,
M.
javanica
arenaria
three
most
devastating
plant-parasitic
nematodes.
We
found
canonical
nematode
telomeric
repeat
to
be
missing
in
these
other
genomes.
In
addition,
find
no
evidence
for
enzyme
telomerase
or
orthologs
C.
elegans
telomere-associated
proteins,
suggesting
alternative
lengthening
telomeres.
Instead,
analyzing
our
genomes,
identify
species-specific
composite
repeats
enriched
mostly
at
one
extremity
contigs.
These
are
G-rich,
oriented,
transcribed,
similarly
repeats.
confirm
them
as
using
fluorescent
situ
hybridization.
single
end
chromosomes
species.
The
discovery
unusual
specific
complex
opens
a
plethora
perspectives
highlights
evolutionary
diversity
telomeres
despite
their
central
roles
senescence,
aging,
chromosome
integrity.
Human Genomics,
Journal Year:
2023,
Volume and Issue:
17(1)
Published: Aug. 8, 2023
Long-read
DNA
sequencing
technologies
have
been
rapidly
evolving
in
recent
years,
and
their
ability
to
assess
large
complex
regions
of
the
genome
makes
them
ideal
for
clinical
applications
molecular
diagnosis
therapy
selection,
thereby
providing
a
valuable
tool
precision
medicine.
In
third-generation
duopoly,
Oxford
Nanopore
Technologies
Pacific
Biosciences
work
towards
increasing
accuracy,
throughput,
portability
long-read
methods
while
trying
keep
costs
low.
These
trades
made
an
attractive
use
research
settings.
This
article
provides
overview
current
limitations
explores
its
potential
point-of-care
testing
health
care
remote
Nature Methods,
Journal Year:
2024,
Volume and Issue:
21(5), P. 793 - 797
Published: March 20, 2024
SQANTI3
is
a
tool
designed
for
the
quality
control,
curation
and
annotation
of
long-read
transcript
models
obtained
with
third-generation
sequencing
technologies.
Leveraging
its
framework,
calculates
descriptors
models,
junctions
ends.
With
this
information,
potential
artifacts
can
be
identified
replaced
reliable
sequences.
Furthermore,
integrated
functional
feature
enables
subsequent
iso-transcriptomics
analyses.
BMC Genomics,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: May 28, 2024
Abstract
Background
Direct
RNA
sequencing
(dRNA-seq)
on
the
Oxford
Nanopore
Technologies
(ONT)
platforms
can
produce
reads
covering
up
to
full-length
gene
transcripts,
while
containing
decipherable
information
about
base
modifications
and
poly-A
tail
lengths.
Although
many
published
studies
have
been
expanding
potential
of
dRNA-seq,
its
accuracy
error
patterns
remain
understudied.
Results
We
present
first
comprehensive
evaluation
characterisation
systematic
errors
in
dRNA-seq
data
from
diverse
organisms
synthetic
vitro
transcribed
RNAs.
found
that
for
kits
SQK-RNA001
SQK-RNA002,
median
read
ranged
87%
92%
across
species,
deletions
significantly
outnumbered
mismatches
insertions.
Due
their
high
abundance
transcriptome,
heteropolymers
short
homopolymers
were
major
contributors
overall
errors.
also
observed
biases
all
species
at
levels
single
nucleotides
motifs.
In
general,
cytosine/uracil-rich
regions
more
likely
be
erroneous
than
guanines
adenines.
By
examining
raw
signal
data,
we
identified
underlying
signal-level
features
potentially
associated
with
dependency
sequence
contexts.
While
quality
scores
used
approximate
rates
levels,
failure
detect
DNA
adapters
may
a
source
loss.
comparing
distinct
basecallers,
reason
some
are
attributable
insufficiency
rather
algorithmic
(basecalling)
artefacts.
Lastly,
generated
using
latest
SQK-RNA004
kit
released
end
2023
although
increased,
largely
identical
compared
previous
kits.
Conclusions
As
investigation
errors,
this
study
offers
overview
reproducible
datasets,
identifies
insufficiency,
lays
foundation
correction
methods.
PLoS Biology,
Journal Year:
2024,
Volume and Issue:
22(5), P. e3002632 - e3002632
Published: May 20, 2024
Reconstructing
the
tree
of
life
remains
a
central
goal
in
biology.
Early
methods,
which
relied
on
small
numbers
morphological
or
genetic
characters,
often
yielded
conflicting
evolutionary
histories,
undermining
confidence
results.
Investigations
based
phylogenomics,
use
hundreds
to
thousands
loci
for
phylogenetic
inquiry,
have
provided
clearer
picture
life’s
history,
but
certain
branches
remain
problematic.
To
resolve
difficult
nodes
life,
2
recent
studies
tested
utility
synteny,
conserved
collinearity
orthologous
more
organisms,
phylogenetics.
Synteny
exhibits
compelling
phylogenomic
potential
while
also
raising
new
challenges.
This
Essay
identifies
and
discusses
specific
opportunities
challenges
that
bear
value
synteny
data
other
rare
genomic
changes
studies.
Synteny-based
analyses
highly
contiguous
genome
assemblies
mark
chapter
era
quest
reconstruct
life.
