Nucleic Acids Research,
Journal Year:
2021,
Volume and Issue:
50(D1), P. D1442 - D1447
Published: Oct. 13, 2021
Abstract
The
Green
Non-Coding
Database
(GreeNC)
is
one
of
the
reference
databases
for
study
plant
long
non-coding
RNAs
(lncRNAs).
Here
we
present
our
most
recent
update
where
16
species
have
been
updated,
while
78
added,
resulting
in
annotation
more
than
495
000
lncRNAs.
Moreover,
sequence
clustering
was
applied
providing
information
about
conservation
and
gene
families.
current
version
database
available
at:
http://greenc.sequentiabiotech.com/wiki2/Main_Page.
Annual Review of Plant Biology,
Journal Year:
2021,
Volume and Issue:
72(1), P. 437 - 462
Published: Jan. 11, 2021
Cotton
is
not
only
the
world's
most
important
natural
fiber
crop,
but
it
also
an
ideal
system
in
which
to
study
genome
evolution,
polyploidization,
and
cell
elongation.
With
assembly
of
five
different
cotton
genomes,
a
cotton-specific
whole-genome
duplication
with
allopolyploidization
process
that
combined
A-
D-genomes
became
evident.
All
existing
A-genomes
seemed
originate
from
A
0
-genome
as
common
ancestor,
several
transposable
element
bursts
contributed
A-genome
size
expansion
speciation.
The
ethylene
production
pathway
shown
regulate
tip-biased
diffuse
growth
mode
regulatory
mechanisms,
including
plant
hormones,
transcription
factors,
epigenetic
modifications,
are
involved
development.
Finally,
we
describe
involvement
gossypol
biosynthetic
manipulation
herbivorous
insects,
role
GoPGF
gland
formation,
host-induced
gene
silencing
for
pest
disease
control.
These
new
genes,
modules,
pathways
will
accelerate
genetic
improvement
cotton.
Nature,
Journal Year:
2021,
Volume and Issue:
590(7846), P. 438 - 444
Published: Jan. 27, 2021
Long-term
climate
change
and
periodic
environmental
extremes
threaten
food
fuel
security1
global
crop
productivity2-4.
Although
molecular
adaptive
breeding
strategies
can
buffer
the
effects
of
climatic
stress
improve
resilience5,
these
approaches
require
sufficient
knowledge
genes
that
underlie
productivity
adaptation6-knowledge
has
been
limited
to
a
small
number
well-studied
model
systems.
Here
we
present
assembly
annotation
large
complex
genome
polyploid
bioenergy
switchgrass
(Panicum
virgatum).
Analysis
biomass
survival
among
732
resequenced
genotypes,
which
were
grown
across
10
common
gardens
span
1,800
km
latitude,
jointly
revealed
extensive
genomic
evidence
adaptation.
Climate-gene-biomass
associations
abundant
but
varied
considerably
deeply
diverged
gene
pools.
Furthermore,
found
flow
accelerated
adaptation
during
postglacial
colonization
northern
habitats
through
introgression
alleles
from
pre-adapted
pool.
The
nature
also
enhanced
potential
fractionation
function,
as
there
was
an
increased
level
heritable
genetic
diversity
on
nondominant
subgenome.
In
addition
investigating
patterns
adaptation,
resources
gene-trait
developed
here
provide
breeders
with
necessary
tools
increase
yield
for
sustainable
production
bioenergy.
The
development
of
multiple
chromosome-scale
reference
genome
sequences
in
many
taxonomic
groups
has
yielded
a
high-resolution
view
the
patterns
and
processes
molecular
evolution.
Nonetheless,
leveraging
information
across
genomes
remains
significant
challenge
nearly
all
eukaryotic
systems.
These
challenges
range
from
studying
evolution
chromosome
structure,
to
finding
candidate
genes
for
quantitative
trait
loci,
testing
hypotheses
about
speciation
adaptation.
Here,
we
present
GENESPACE,
which
addresses
these
by
integrating
conserved
gene
order
orthology
define
expected
physical
position
genomes.
We
demonstrate
this
utility
dissecting
presence-absence,
copy-number,
structural
variation
at
three
levels
biological
organization:
spanning
300
million
years
vertebrate
sex
evolution,
diversity
Poaceae
(grass)
plant
family,
among
26
maize
cultivars.
methods
build
visualize
syntenic
GENESPACE
R
package
offer
addition
existing
family
synteny
programs,
especially
polyploid,
outbred,
other
complex
genomes.The
is
complete
DNA
sequence
an
individual.
It
crucial
foundation
studies
medicine,
agriculture,
conservation
biology.
Advances
genetics
have
made
it
possible
rapidly
sequence,
or
read
out,
organisms.
For
closely
related
species,
scientists
can
then
do
detailed
comparisons,
revealing
similar
with
shared
past
common
role,
but
comparing
more
distantly
organisms
difficult.
One
major
that
are
often
lost
duplicated
over
evolutionary
time.
way
be
confident
look
‘synteny’,
how
organized
ordered
within
genome.
In
some
persists
millions
Combining
similarity
could
make
comparisons
between
species
robust.
To
this,
Lovell
et
al.
developed
software
links
similarities
This
allows
researchers
explore
determine
whether
been
duplicated.
value
explored
vertebrates
flowering
plants.
was
able
highlight
unique
chromosomes
birds
mammals,
track
positions
important
grass
crops
including
maize,
wheat,
rice.
Exploring
genetic
code
lead
better
understanding
sections
might
also
allow
find
target
applications
like
crop
improvement.
designed
easy
use,
allowing
them
graphics
perform
analyses
few
programming
skills.
Nature Genetics,
Journal Year:
2021,
Volume and Issue:
53(9), P. 1385 - 1391
Published: Aug. 9, 2021
Abstract
Cotton
produces
natural
fiber
for
the
textile
industry.
The
genetic
effects
of
genomic
structural
variations
underlying
agronomic
traits
remain
unclear.
Here,
we
generate
two
high-quality
genomes
Gossypium
hirsutum
cv.
NDM8
and
barbadense
acc.
Pima90,
identify
large-scale
in
species
1,081
G
.
accessions.
density
is
higher
D-subgenome
than
A-subgenome,
indicating
that
undergoes
stronger
selection
during
formation
variety
development.
Many
genes
and/or
regulatory
regions
potentially
influencing
were
discovered.
Of
446
significantly
associated
variations,
those
quality
Verticillium
wilt
resistance
are
located
mainly
yield
A-subgenome.
Our
research
provides
insight
into
role
genotype-to-phenotype
relationships
their
potential
utility
crop
improvement.
Proceedings of the National Academy of Sciences,
Journal Year:
2022,
Volume and Issue:
119(4)
Published: Jan. 18, 2022
Green
plants
play
a
fundamental
role
in
ecosystems,
human
health,
and
agriculture.
As
de
novo
genomes
are
being
generated
for
all
known
eukaryotic
species
as
advocated
by
the
Earth
BioGenome
Project,
increasing
genomic
information
on
green
land
is
essential.
However,
setting
standards
generation
storage
of
complex
set
that
characterize
lineage
life
major
challenge
plant
scientists.
Such
will
need
to
accommodate
immense
variation
genome
size,
transposable
element
content,
structural
complexity
while
enabling
research
into
molecular
evolutionary
processes
have
resulted
this
enormous
variation.
Here
we
provide
an
overview
assessment
current
state
knowledge
genomes.
To
date
fewer
than
300
complete
chromosome-scale
assemblies
representing
900
been
across
estimated
450,000
500,000
clade.
These
range
size
from
12
Mb
27.6
Gb
biased
toward
agricultural
crops
with
large
branches
tree
untouched
genomic-scale
sequencing.
Locating
suitable
tissue
samples
most
plants,
especially
those
taxa
extreme
environments,
remains
one
biggest
hurdles
our
inventory.
Furthermore,
annotation
at
present
undergoing
intensive
improvement.
It
hope
fresh
help
development
quality
cohesive
meaningful
synthesis
scale
up
future.
