Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes
Biomolecules,
Год журнала:
2023,
Номер
13(9), С. 1403 - 1403
Опубликована: Сен. 17, 2023
The
availability
of
multiple
sequenced
genomes
from
a
single
species
made
it
possible
to
explore
intra-
and
inter-specific
genomic
comparisons
at
higher
resolution
build
clade-specific
pan-genomes
several
crops.
crops
constructed
various
cultivars,
accessions,
landraces,
wild
ancestral
represent
compendium
genes
structural
variations
allow
researchers
search
for
the
novel
alleles
that
were
inadvertently
lost
in
domesticated
during
historical
process
crop
domestication
or
extensive
plant
breeding.
Fortunately,
many
valuable
associated
with
desirable
traits
like
disease
resistance,
abiotic
stress
tolerance,
architecture,
nutrition
qualities
exist
species,
relatives.
ancestors
landraces
can
be
introduced
back
high-yielding
varieties
modern
by
implementing
classical
breeding,
selection,
transgenic/gene
editing
approaches.
Thus,
pan-genomic
represents
great
leap
research
offers
new
avenues
targeted
breeding
mitigate
impact
global
climate
change.
Here,
we
summarize
tools
used
pan-genome
assembly
annotations,
web-portals
hosting
pan-genomes,
etc.
Furthermore,
highlight
few
discoveries
using
approach
future
potential
this
emerging
field
study.
Язык: Английский
The Arabidopsis Information Resource in 2024
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Ноя. 7, 2023
Abstract
Since
1999,
The
Arabidopsis
Information
Resource
(
www.arabidopsis.org
)
has
been
curating
data
about
the
thaliana
genome.
Its
primary
focus
is
integrating
experimental
gene
function
information
from
peer-reviewed
literature
and
codifying
it
as
controlled
vocabulary
annotations.
Our
goal
to
produce
a
‘gold
standard’
functional
annotation
set
that
reflects
current
state
of
knowledge
At
same
time,
resource
serves
nexus
for
community-based
collaborations
aimed
at
improving
quality,
access
reuse.
For
past
decade,
our
work
made
possible
by
subscriptions
global
user
base.
This
update
covers
ongoing
biocuration
work,
some
modernization
efforts
contribute
first
major
infrastructure
overhaul
since
2011,
introduction
JBrowse2,
resource’s
role
in
community
activities
such
organizing
structural
reannotation
assessment,
we
used
Gene
Ontology
annotations
metric
evaluate:
(1)
what
currently
known
function,
(2)
‘unknown’
genes.
Currently,
74%
proteome
annotated
least
one
term.
Of
those
loci,
half
have
support
following
aspects:
molecular
biological
process,
or
cellular
component.
sheds
light
on
genes
which
not
yet
identified
any
published
no
annotation.
Drawing
attention
these
unknown
highlights
gaps
potential
sources
novel
discoveries.
Article
Summary
(TAIR,
comprehensive
website
,
small
plant
that’s
very
easy
grow
analyze
laboratory
understand
how
many
other
plants
function.
We
share
progress
collection
organization,
tool
improvement,
involvement
projects.
Язык: Английский
Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation
Опубликована: Авг. 23, 2023
The
availability
of
multiple
sequenced
genomes
from
a
single
species
made
it
possible
to
explore
intra-
and
inter-specific
genomic
comparisons
at
higher
resolution
build
clade-specific
pangenomes
several
crops.
pan-genomes
crops
constructed
various
cultivars/accessions,
landraces,
wild
ancestral
represent
compendium
genes
structural
variations
allow
researchers
search
for
the
novel
alleles
that
were
inadvertently
lost
in
domesticated
during
historical
process
crop
domestication
or
extensive
plant
breeding.
Fortunately,
many
valuable
associated
with
desirable
traits
like
disease
resistance,
abiotic
stress
tolerance,
architecture,
nutrition
qualities
exist
species,
relatives.
novels
ancestors
landraces
can
be
introduced
back
high-yielding
varieties
modern
by
implementing
classical
breeding,
selection,
transgenic/gene
editing
approaches.
Thus,
pan-genomic
represents
great
leap
research
offers
new
avenues
targeted
breeding
mitigating
impact
global
climate
change.
Here
we
summarize
tools
used
pangenome
assembly
annotations,
web-portals
hosting
pangenomes.
Furthermore,
highlight
few
discoveries
using
approach
its
future
potential.
Язык: Английский
Agricultural Sciences in the Big Data Era: Genotype and Phenotype Data Standardization, Utilization and Integration
Опубликована: Июнь 14, 2023
The
Genotype-Phenotype
Working
Group
was
established
in
November
2021
as
part
of
the
AgBioData
Consortium
(https://www.agbiodata.org)
with
goal
identifying
current
challenges
annotating
and
integrating
large-scale
genotype
phenotype
data.
Over
course
year,
members
this
working
group
identified
different
types
data
sets,
explored
experimental
platforms
methods
for
generation,
examined
how
these
are
annotated
including
metadata
requirements.
We
conducted
a
thorough
review
publicly
funded
repositories
raw
processed
each
type.
also
several
secondary
databases
knowledgebases
that
enable
integration
heterogeneous
context
Genome
Browser,
Pathway
Networks
tissue-specific
gene
expression.
revealed
need
additional
infrastructural
support,
standards,
tools
to
connect
Genotype
Phenotype
enhance
interoperability
knowledge
synthesis
foster
translational
research.
Язык: Английский