Plant Communications,
Journal Year:
2024,
Volume and Issue:
5(9), P. 100944 - 100944
Published: May 10, 2024
The
Caesalpinioideae
subfamily
contains
many
well-known
trees
that
are
important
for
economic
sustainability
and
human
health,
but
a
lack
of
genomic
resources
has
hindered
their
breeding
utilization.
Here,
we
present
chromosome-level
reference
genomes
the
two
food
industrial
Gleditsia
sinensis
(921
Mb)
Biancaea
sappan
(872
Mb),
three
shade
ornamental
Albizia
julibrissin
(705
Delonix
regia
(580
Acacia
confusa
(566
pioneer
hedgerow
Leucaena
leucocephala
(1338
Mimosa
bimucronata
(641
Mb).
Phylogenetic
inference
shows
mimosoid
clade
much
higher
evolutionary
rate
than
other
clades
Caesalpinioideae.
Macrosynteny
comparison
suggests
fusion
breakage
an
unstable
chromosome
responsible
difference
in
basic
number
(13
or
14)
After
ancient
whole-genome
duplication
(WGD)
shared
by
all
species
(CWGD,
∼72.0
million
years
ago
[MYA]),
there
were
recent
successive
WGD
events,
LWGD-1
(16.2-19.5
MYA)
LWGD-2
(7.1-9.5
MYA),
L.
leucocephala.
Thereafter,
∼40%
gene
loss
genome-size
contraction
have
occurred
during
diploidization
process
To
investigate
secondary
metabolites,
identified
copies
involved
mimosine
metabolism
these
found
abundance
biosynthesis
genes
largely
explains
its
high
production.
We
also
set
potential
triterpenoid
saponin
G.
sinensis,
which
is
more
complete
based
on
previous
transcriptome-derived
unigenes.
Our
results
will
facilitate
biological
studies
promote
utilization
valuable
metabolites.
Science Advances,
Journal Year:
2023,
Volume and Issue:
9(7)
Published: Feb. 17, 2023
Early
natural
historians—Comte
de
Buffon,
von
Humboldt,
and
De
Candolle—established
environment
geography
as
two
principal
axes
determining
the
distribution
of
groups
organisms,
laying
foundations
for
biogeography
over
subsequent
200
years,
yet
relative
importance
these
remains
unresolved.
Leveraging
phylogenomic
global
species
data
Mimosoid
legumes,
a
pantropical
plant
clade
c.
3500
species,
we
show
that
water
availability
gradient
from
deserts
to
rain
forests
dictates
turnover
lineages
within
continents
across
tropics.
We
demonstrate
95%
speciation
occurs
precipitation
niche,
showing
profound
phylogenetic
niche
conservatism,
lineage
boundaries
coincide
with
isohyets
precipitation.
reveal
similar
patterns
on
different
continents,
implying
evolution
dispersal
follow
universal
processes.
PhytoKeys,
Journal Year:
2024,
Volume and Issue:
240, P. 1 - 552
Published: April 3, 2024
Caesalpinioideae
is
the
second
largest
subfamily
of
legumes
(Leguminosae)
with
ca.
4680
species
and
163
genera.
It
an
ecologically
economically
important
group
formed
mostly
woody
perennials
that
range
from
large
canopy
emergent
trees
to
functionally
herbaceous
geoxyles,
lianas
shrubs,
which
has
a
global
distribution,
occurring
on
every
continent
except
Antarctica.
Following
recent
re-circumscription
15
genera
as
presented
in
Advances
Legume
Systematics
14,
Part
1,
using
basis
phylogenomic
analysis
997
nuclear
gene
sequences
for
420
all
but
five
currently
recognised
subfamily,
we
present
new
higher-level
classification
subfamily.
The
comprises
eleven
tribes,
are
either
new,
reinstated
or
re-circumscribed
at
this
rank:
Caesalpinieae
Rchb.
(27
/
223
species),
Campsiandreae
LPWG
(2
5–22),
Cassieae
Bronn
(7
695),
Ceratonieae
(4
6),
Dimorphandreae
Benth.
35),
Erythrophleeae
/13),
Gleditsieae
Nakai
(3
20),
Mimoseae
(100
3510),
Pterogyneae
(1
1),
Schizolobieae
(8
42–43),
Sclerolobieae
&
Hook.
f.
(5
113).
Although
many
these
lineages
have
been
named
past,
tribes
informal
generic
groups,
their
circumscriptions
varied
widely
changed
over
past
decades,
such
described
here
differ
membership
those
previously
recognised.
Importantly,
approximately
3500
100
former
Mimosoideae
now
placed
reinstated,
newly
circumscribed,
tribe
Mimoseae.
Because
size
ecological
importance
tribe,
also
provide
clade-based
system
includes
17
lower-level
clades.
Fourteen
remain
unplaced
clades:
eight
resolved
two
grades
six
phylogenetically
isolated
monogeneric
lineages.
In
addition
classification,
key
genera,
morphological
descriptions
notes
diversity
growth
forms,
foliage,
flowers
fruits
illustrated
each
genus
distribution
map,
based
quality-controlled
herbarium
specimen
localities.
A
glossary
specialised
terms
used
legume
morphology
provided.
This
provides
solid
communication
framework
downstream
analyses
biogeography,
trait
evolution
diversification,
well
taxonomic
revision
still
understudied
Frontiers in Plant Science,
Journal Year:
2022,
Volume and Issue:
13
Published: Feb. 23, 2022
Comprising
501
genera
and
around
14,000
species,
Papilionoideae
is
not
only
the
largest
subfamily
of
Fabaceae
(Leguminosae;
legumes),
but
also
one
most
extraordinarily
diverse
clades
among
angiosperms.
Papilionoids
are
a
major
source
food
forage,
ecologically
successful
in
all
biomes,
display
dramatic
variation
both
floral
architecture
plastid
genome
(plastome)
structure.
Plastid
DNA-based
phylogenetic
analyses
have
greatly
improved
our
understanding
relationships
groups
Papilionoideae,
yet
backbone
phylogeny
remains
unresolved.
In
this
study,
we
sequenced
assembled
39
new
plastomes
that
covering
key
representing
morphological
diversity
subfamily.
From
244
total
taxa,
produced
eight
datasets
for
maximum
likelihood
(ML)
based
on
entire
and/or
concatenated
sequences
77
protein-coding
(CDS)
two
multispecies
coalescent
(MSC)
individual
gene
trees.
We
additionally
combined
nucleotide
dataset
comprising
CDS
plus
matK
only,
which
papilionoid
were
sampled.
A
ML
tree
plastome
maximally
supported
deep
recent
divergences
papilionoids
(223
out
236
nodes).
The
Swartzieae,
ADA
(Angylocalyceae,
Dipterygeae,
Amburaneae),
Cladrastis,
Andira,
Exostyleae
formed
grade
to
remainder
concordant
with
nine
MSC
Phylogenetic
remaining
five
lineages
(Vataireoid,
Dermatophyllum,
Genistoid
s.l.,
Dalbergioid
Baphieae
+
Non-Protein
Amino
Acid
Accumulating
or
NPAAA
clade)
remained
uncertain,
because
insufficient
support
conflicting
Our
study
fully
resolved
nodes
however,
some
require
further
exploration.
More
genome-scale
data
rigorous
needed
disentangle
lineages.
PhytoKeys,
Journal Year:
2022,
Volume and Issue:
205, P. 3 - 58
Published: Aug. 22, 2022
Subfamily
Caesalpinioideae
with
ca.
4,600
species
in
152
genera
is
the
second-largest
subfamily
of
legumes
(Leguminosae)
and
forms
an
ecologically
economically
important
group
trees,
shrubs
lianas
a
pantropical
distribution.
Despite
major
advances
last
few
decades
towards
aligning
clades
across
Caesalpinioideae,
generic
delimitation
remains
state
considerable
flux,
especially
mimosoid
clade.
We
test
monophyly
via
phylogenomic
analysis
997
nuclear
genes
sequenced
targeted
enrichment
(Hybseq)
for
420
147
currently
recognised
subfamily.
show
that
22
are
non-monophyletic
or
nested
other
non-monophyly
concentrated
clade
where
25%
90
found
to
be
non-monophyletic.
suggest
two
main
reasons
this
pervasive
non-monophyly:
(i)
extensive
morphological
homoplasy
we
document
here
handful
traits
and,
particularly,
repeated
evolution
distinctive
fruit
types
were
historically
emphasised
delimiting
(ii)
artefact
lack
taxonomic
syntheses
sampling
previous
phylogenies
consequent
failure
identify
span
Old
World
New
conversely
amphi-Atlantic
non-monophyletic,
both
which
critical
large
Finally,
discuss
taxon
era
how
assessing
patterns
gene
tree
conflict
can
provide
additional
insights
into
delimitation.
This
new
framework
provides
foundations
series
papers
reclassifying
presented
New Phytologist,
Journal Year:
2022,
Volume and Issue:
235(6), P. 2365 - 2377
Published: July 28, 2022
Nitrogen-fixing
symbiosis
is
globally
important
in
ecosystem
functioning
and
agriculture,
yet
the
evolutionary
history
of
nodulation
remains
focus
considerable
debate.
Recent
evidence
suggesting
a
single
origin
followed
by
massive
parallel
losses
raises
questions
about
why
few
lineages
N
Taxon,
Journal Year:
2023,
Volume and Issue:
72(4), P. 811 - 847
Published: July 4, 2023
Abstract
Solanum
is
one
of
the
world's
largest
and
economically
most
important
plant
genera,
including
1245
currently
accepted
species
several
major
minor
crops
(e.g.,
tomato,
potato,
brinjal
eggplant,
scarlet
Gboma
lulo,
pepino).
Here
we
provide
an
overview
evolution
25
key
morphological
traits
for
clades
this
giant
genus
based
on
stochastic
mapping
using
a
well‐sampled
recently
published
phylogeny
.
The
evolutionarily
labile
(showing
>100
transitions
across
genus)
relate
to
structure
(growth
form
sympodial
unit
structure),
herbivore
defence
(glandular
trichomes),
pollination
(corolla
shape
colour),
dispersal
(fruit
colour).
Ten
further
show
evolutionary
lability
with
50–100
specialised
underground
organs,
trichome
structure,
leaf
type,
inflorescence
position
branching,
stamen
heteromorphism).
Our
results
reveal
number
highly
convergent
in
,
tubers,
rhizomes,
simple
leaves,
yellow
corollas,
heteromorphic
anthers,
dioecy,
dry
fruits,
some
unexpected
pathways
trait
that
could
be
explored
future
studies.
We
informally
named
can
morphologically
defined
by
combinations
providing
tool
identification
enabling
predictive
phylogenetic
placement
unsampled
species.
Journal of Integrative Plant Biology,
Journal Year:
2024,
Volume and Issue:
66(3), P. 546 - 578
Published: Jan. 30, 2024
Angiosperms
(flowering
plants)
are
by
far
the
most
diverse
land
plant
group
with
over
300,000
species.
The
sudden
appearance
of
angiosperms
in
fossil
record
was
referred
to
Darwin
as
"abominable
mystery,"
hence
contributing
heightened
interest
angiosperm
evolution.
display
wide
ranges
morphological,
physiological,
and
ecological
characters,
some
which
have
probably
influenced
their
species
richness.
evolutionary
analyses
these
characteristics
help
address
questions
diversification
require
well
resolved
phylogeny.
Following
great
successes
phylogenetic
using
plastid
sequences,
dozens
thousands
nuclear
genes
from
next-generation
sequencing
been
used
phylogenomic
analyses,
providing
phylogenies
new
insights
into
evolution
angiosperms.
In
this
review
we
focus
on
recent
large
clades,
orders,
families,
subdivisions
families
provide
a
summarized
Nuclear
Phylogenetic
Tree
Angiosperm
Families.
newly
established
relationships
highlighted
compared
previous
results.
sequenced
genomes
Amborella,
Nymphaea,
Chloranthus,
Ceratophyllum,
monocots,
Magnoliids,
basal
eudicots,
facilitated
phylogenomics
among
five
major
clades.
All
but
one
64
orders
were
included
except
placements
several
orders.
Most
robust
highly
supported
placements,
especially
for
within
important
families.
Additionally,
examine
divergence
time
estimation
biogeographic
basis
frameworks
discuss
differences
analyses.
Furthermore,
implications
ancestral
reconstruction
characters
groups,
limitations
current
studies,
taxa
that
future
attention.