Horticulture Advances,
Journal Year:
2024,
Volume and Issue:
2(1)
Published: Jan. 29, 2024
Abstract
Sequencing
strategies
have
continually
advanced,
with
high-throughput
sequencing
(HTS)
technologies
emerging
as
pivotal
tools
in
plant
phylogenomics.
As
a
standard
form
of
target
capture
sequencing,
hybridization
enrichment
(Hyb-seq)
is
innovative
and
flexible,
then
HTS
strategy
widely
adopted
The
universal
Angiosperms353
probe
sets
(Angiosperms353)
are
instrumental
Hyb-seq
been
witnessed
increased
application
recent
years.
This
review
integrates
numerous
publications
empirical
datasets
to
comprehensively
assess
the
potential
applications
Angiosperms353.
Through
evaluations
using
18-taxa
343-taxa
genomic
datasets,
this
explores
factors
influencing
gene
capture.
RNA-seq
yielded
highest
number
genes,
followed
by
whole-genome
genome
skimming.
Increased
depth
enhanced
yields,
no
evident
bias
was
observed
across
all
tested
angiosperm
groups.
In
genomics
era
extensive
data,
provides
comprehensive
guidelines
for
practical
Angiosperms353,
promoting
resource
recycling
maximizing
data
sharing
utilization.
Molecular Ecology Resources,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 26, 2024
The
dimensions
of
phylogenetic
research
have
expanded
to
encompass
the
study
large-scale
populations
at
microevolutionary
level
and
comparisons
between
different
species
or
taxonomic
units
macroevolutionary
level.
Traditional
tools
often
struggle
handle
diverse
complex
data
required
for
these
evolutionary
scales.
In
response
this
challenge,
we
introduce
PhyloForge,
a
robust
tool
designed
seamlessly
integrate
demands
both
micro-
macroevolution,
comprehensively
utilising
phylogenomic
signals,
such
as
genes,
SNPs,
structural
variations,
well
mitochondrial
chloroplast
genomes.
PhyloForge's
innovation
lies
in
its
capability
multiple
enabling
unified
analysis
multidimensional
genomic
data.
This
unique
feature
empowers
researchers
gain
more
comprehensive
understanding
aspects
biological
evolution.
PhyloForge
not
only
provides
highly
customisable
experienced
but
also
features
an
intuitively
interface,
facilitating
effortless
beginners.
Extensive
testing
across
various
domains,
including
animals,
plants
fungi,
attests
broad
applicability
field
phylogenetics.
summary,
has
significant
potential
era
genomics,
offering
new
perspective
toolset
deeper
evolution
life.
codes
could
be
found
GitHub
(https://github.com/wangyayaya/PhyloForge/),
program
installed
Conda
(https://anaconda.org/wangxiaobei/phyloforge).
Plant Diversity,
Journal Year:
2023,
Volume and Issue:
46(4), P. 435 - 447
Published: Aug. 14, 2023
is
an
orchid
genus
containing
73
species
of
mainly
epiphytic
on
trees
or
rocks
in
mountain
forests
tropical
and
subtropical
Asia.
Previous
phylogenetic
analyses
morphological
assessments
have
failed
to
produce
a
well-resolved
phylogeny
at
the
infrageneric
level.
In
present
study,
new
classification
Authorea (Authorea),
Journal Year:
2023,
Volume and Issue:
unknown
Published: April 17, 2023
The
advancement
of
Next-generation
Sequencing
(NGS)
technologies
has
led
to
a
revolution
in
the
field
evolutionary
biology.
With
increasing
number
available
genomes
and
transcriptomes,
researchers
can
mine
various
types
molecular
markers
that
are
vital
for
phylogenetic,
evolutionary,
ecological
studies.
Numerous
tools
have
been
developed
extract
these
from
NGS
data.
However,
due
limited
well-annotated
reference
non-model
organisms,
it
is
still
challenging
obtain
accurately
efficiently.
Here,
we
present
GeneMiner,
an
improved
expanded
version
our
previous
tool,
Easy353.
GeneMiner
involves
reference-guided
de
Bruijn
Graph
assembly
with
seed
self-discovery
greedy
extension.
Additionally,
includes
verification
step
using
parameter-bootstrap
method
reduce
negative
impact
on
caused
by
relatively
distant
reference.
Our
results
both
experimental
simulation
data
showed
acquire
phylogenetic
plants
transcriptomic,
genomic,
other
designed
be
user-friendly,
fast,
memory-efficient,
compatible
Linux,
Windows,
macOS.
All
source
codes
publicly
GitHub
easy
accessibility
transparency
(https://github.com/happywithxpl/GeneMiner).
Ecology and Evolution,
Journal Year:
2023,
Volume and Issue:
13(6)
Published: June 1, 2023
,
a
new
species
of
Gesneriaceae
in
sclerophyllous
oak
community
from
Yunnan,
Southwest
China,
is
described
and
illustrated.
Morphologically,
it
resembles
both
Horticulture Advances,
Journal Year:
2024,
Volume and Issue:
2(1)
Published: Jan. 29, 2024
Abstract
Sequencing
strategies
have
continually
advanced,
with
high-throughput
sequencing
(HTS)
technologies
emerging
as
pivotal
tools
in
plant
phylogenomics.
As
a
standard
form
of
target
capture
sequencing,
hybridization
enrichment
(Hyb-seq)
is
innovative
and
flexible,
then
HTS
strategy
widely
adopted
The
universal
Angiosperms353
probe
sets
(Angiosperms353)
are
instrumental
Hyb-seq
been
witnessed
increased
application
recent
years.
This
review
integrates
numerous
publications
empirical
datasets
to
comprehensively
assess
the
potential
applications
Angiosperms353.
Through
evaluations
using
18-taxa
343-taxa
genomic
datasets,
this
explores
factors
influencing
gene
capture.
RNA-seq
yielded
highest
number
genes,
followed
by
whole-genome
genome
skimming.
Increased
depth
enhanced
yields,
no
evident
bias
was
observed
across
all
tested
angiosperm
groups.
In
genomics
era
extensive
data,
provides
comprehensive
guidelines
for
practical
Angiosperms353,
promoting
resource
recycling
maximizing
data
sharing
utilization.
