Yeast,
Journal Year:
2023,
Volume and Issue:
40(7), P. 237 - 253
Published: May 27, 2023
Abstract
Two
strains
of
fission
yeast
were
isolated
from
honey.
They
differ
the
type
strain
Schizosaccharomyces
octosporus
by
three
substitutions
in
D1/D2
domain
nuclear
26S
large
subunit
ribosomal
RNA
(rRNA)
gene
sequence,
resulting
a
99.5%
identity.
In
internal
transcribed
spacer
(ITS)
region
(consisting
ITS1,
5.8S
rDNA,
and
ITS2),
S.
16
gaps
91
substitutions,
which
is
equivalent
to
an
identity
88.1%.
Genome
sequencing
on
one
new
revealed
that
average
nucleotide
(ANI)
between
its
genome
reference
90.43%
there
exist
major
rearrangements
two
genomes.
Mating
analysis
are
completely
reproductively
separated.
A
strong
prezygotic
barrier
exists
few
mating
products
consist
diploid
hybrids
do
not
form
recombinant
ascospores.
strains,
asci
either
zygotic,
arising
conjugation,
or
they
develop
without
conjugation
asexual
cells
(azygotic).
Compared
currently
recognized
species,
spectrum
nutrients
assimilated
restricted.
Of
43
carbohydrates
included
physiological
standard
tests,
only
7
assimilated.
According
results
sequence
analysis,
trials,
phenotypic
characterization,
species
lindneri
described
accommodate
(holotype:
CBS
18203
T
ex‐type:
MUCL
58363;
MycoBank
no.:
MB
847838).
PLoS Biology,
Journal Year:
2020,
Volume and Issue:
18(12), P. e3001007 - e3001007
Published: Dec. 2, 2020
Highly
divergent
sites
in
multiple
sequence
alignments
(MSAs),
which
can
stem
from
erroneous
inference
of
homology
and
saturation
substitutions,
are
thought
to
negatively
impact
phylogenetic
inference.
Thus,
several
different
trimming
strategies
have
been
developed
for
identifying
removing
these
prior
However,
a
recent
study
reported
that
doing
so
worsen
inference,
underscoring
the
need
alternative
alignment
strategies.
Here,
we
introduce
ClipKIT,
an
software
that,
rather
than
putatively
phylogenetically
uninformative
sites,
instead
aims
identify
retain
parsimony-informative
known
be
informative.
To
test
efficacy
examined
accuracy
support
phylogenies
inferred
14
strategies,
including
those
implemented
across
nearly
140,000
broad
sampling
evolutionary
histories.
Phylogenies
ClipKIT-trimmed
accurate,
robust,
time
saving.
Furthermore,
ClipKIT
consistently
outperformed
other
methods
diverse
datasets,
suggesting
based
on
retaining
provide
robust
framework
trimming.
Nature Microbiology,
Journal Year:
2022,
Volume and Issue:
7(5), P. 607 - 619
Published: May 4, 2022
Fungal
pathogens
cause
more
than
a
billion
human
infections
every
year,
resulting
in
1.6
million
deaths
annually.
Understanding
the
natural
history
and
evolutionary
ecology
of
fungi
is
helping
us
understand
how
disease-relevant
traits
have
repeatedly
evolved.
Different
types
mechanisms
genetic
variation
contributed
to
evolution
fungal
pathogenicity
specific
differences
distinguish
from
non-pathogens.
Insights
into
traits,
elements,
ecological
that
contribute
are
crucial
for
developing
strategies
both
predict
emergence
develop
drugs
combat
them.
Bioinformatics,
Journal Year:
2021,
Volume and Issue:
37(16), P. 2325 - 2331
Published: Feb. 5, 2021
Diverse
disciplines
in
biology
process
and
analyze
multiple
sequence
alignments
(MSAs)
phylogenetic
trees
to
evaluate
their
information
content,
infer
evolutionary
events
processes
predict
gene
function.
However,
automated
processing
of
MSAs
remains
a
challenge
due
the
lack
unified
toolkit.
To
fill
this
gap,
we
introduce
PhyKIT,
toolkit
for
UNIX
shell
environment
with
30
functions
that
trees,
including
but
not
limited
estimation
mutation
rate,
evaluation
composition
biases,
calculation
degree
violation
molecular
clock
collapsing
bipartitions
(internal
branches)
low
support.To
demonstrate
utility
detail
three
use
cases:
(1)
summarizing
content
diagnosing
potential
biases
or
tree
data;
(2)
evaluating
gene-gene
covariation
rates
identify
functional
relationships,
novel
ones,
among
genes
(3)
resolution
polytomies
which
are
suggestive
rapid
radiation
data.
We
anticipate
PhyKIT
will
be
useful
processing,
examining
deriving
biological
meaning
from
increasingly
large
phylogenomic
datasets.PhyKIT
is
freely
available
on
GitHub
(https://github.com/JLSteenwyk/PhyKIT),
PyPi
(https://pypi.org/project/phykit/)
Anaconda
Cloud
(https://anaconda.org/JLSteenwyk/phykit)
under
MIT
license
extensive
documentation
user
tutorials
(https://jlsteenwyk.com/PhyKIT).Supplementary
data
at
Bioinformatics
online.
Science,
Journal Year:
2024,
Volume and Issue:
384(6694)
Published: April 25, 2024
Organisms
exhibit
extensive
variation
in
ecological
niche
breadth,
from
very
narrow
(specialists)
to
broad
(generalists).
Two
general
paradigms
have
been
proposed
explain
this
variation:
(i)
trade-offs
between
performance
efficiency
and
breadth
(ii)
the
joint
influence
of
extrinsic
(environmental)
intrinsic
(genomic)
factors.
We
assembled
genomic,
metabolic,
data
nearly
all
known
species
ancient
fungal
subphylum
Saccharomycotina
(1154
yeast
strains
1051
species),
grown
24
different
environmental
conditions,
examine
evolution.
found
that
large
differences
carbon
utilization
traits
yeasts
stem
genes
encoding
specific
metabolic
pathways,
but
we
limited
evidence
for
trade-offs.
These
comprehensive
argue
factors
shape
microbes.
Molecular Biology and Evolution,
Journal Year:
2022,
Volume and Issue:
39(5)
Published: May 1, 2022
Accessory
genes
are
variably
present
among
members
of
a
species
and
reservoir
adaptive
functions.
In
bacteria,
differences
in
gene
distributions
individuals
largely
result
from
mobile
elements
that
acquire
disperse
accessory
as
cargo.
contrast,
the
impact
cargo-carrying
on
eukaryotic
evolution
remains
unknown.
Here,
we
show
variation
genome
content
within
multiple
fungal
is
facilitated
by
Starships,
newly
discovered
group
massive
110
kb
long
average,
share
conserved
components,
carry
diverse
arrays
genes.
We
identified
hundreds
Starship-like
regions
across
every
major
class
filamentous
Ascomycetes,
including
28
distinct
Starships
range
27
to
393
last
shared
common
ancestor
ca.
400
Ma.
Using
new
long-read
assemblies
plant
pathogen
Macrophomina
phaseolina,
characterize
four
additional
whose
activities
contribute
standing
structure
content.
One
these
elements,
Voyager,
inserts
into
5S
rDNA
contains
candidate
virulence
factor
increasing
copy
number
has
contrasting
associations
with
pathogenic
saprophytic
growth,
suggesting
Voyager's
activity
underlies
an
ecological
trade-off.
propose
analogs
bacterial
integrative
conjugative
based
parallels
between
their
components
may
therefore
represent
first
dedicated
agents
active
transfer
eukaryotes.
Our
results
suggest
have
shaped
genomes
for
millions
years
reveal
concerted
route
throughout
entire
phylum.
Fungal Diversity,
Journal Year:
2024,
Volume and Issue:
128(1), P. 1 - 165
Published: Oct. 15, 2024
Abstract
Fungi
are
one
of
the
most
diverse
groups
organisms
with
an
estimated
number
species
in
range
2–3
million.
The
higher-level
ranking
fungi
has
been
discussed
framework
molecular
phylogenetics
since
Hibbett
et
al.,
and
definition
higher
ranks
(e.g.,
phyla)
‘true
fungi’
have
revised
several
subsequent
publications.
Rapid
accumulation
novel
genomic
data
advancements
now
facilitate
a
robust
precise
foundation
for
classification
within
kingdom.
This
study
provides
updated
kingdom
,
drawing
upon
comprehensive
phylogenomic
analysis
Holomycota
which
we
outline
well-supported
nodes
fungal
tree
explore
more
contentious
groupings.
We
accept
19
phyla
Fungi,
viz
.
Aphelidiomycota
Ascomycota
Basidiobolomycota
Basidiomycota
Blastocladiomycota
Calcarisporiellomycota
Chytridiomycota
Entomophthoromycota
Entorrhizomycota
Glomeromycota
Kickxellomycota
Monoblepharomycota
Mortierellomycota
Mucoromycota
Neocallimastigomycota
Olpidiomycota
Rozellomycota
Sanchytriomycota,
Zoopagomycota
In
phylogenies,
Caulochytriomycota
resides
;
thus,
former
is
regarded
as
synonym
latter,
while
Caulochytriomycetes
viewed
class
provide
description
each
phylum
followed
by
its
classes.
A
new
subphylum,
Sanchytriomycotina
Karpov
introduced
only
subphylum
Sanchytriomycota
subclass
Pneumocystomycetidae
Kirk
al.
Pneumocystomycetes
invalid
thus
validated.
Placements
fossil
classes
also
discussed,
providing
examples.