A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations

Trichoderma genus includes soil-inhabiting fungi that provide important ecosystem services in their interaction with plants and other
fungi, as well as biocontrol of fungal plant diseases. A collection of Trichoderma isolates from Sardinia has been previously characterized,

but here we selected 113 isolates, representatives of the collection, and characterized their viral components. We carried
out high-throughput sequencing of ribosome-depleted total RNA following a bioinformatics pipeline that detects virus-derived RNAdirected
RNA
polymerases
(RdRps)
and
other
conserved
viral
protein
sequences.
This
pipeline
detected
seventeen
viral
RdRps
with
two

of
them
corresponding
to
viruses
already
detected
in
other
regions
of
the
world
and
the
remaining
ifteen
representing
isolates
of
new

putative
virus
species.
Surprisingly,
eight
of
them
are
from
new
negative-sense
RNA
viruses,
a
irst
in
the
genus
Trichoderma.
Among

them
is
a
cogu-like
virus,
closely
related
to
plant-infecting
viruses.
Regarding
the
positive-sense
viruses,
we
report
the
presence
of

an
'ormycovirus'
belonging
to
a
recently
characterized
group
of
bisegmented
single-stranded
RNA
viruses
with
uncertain
phylogenetic

assignment.
Finally,
for
the
irst
time,
we
report
a
bisegmented
member
of
Mononegavirales
which
infects
fungi.
The
proteins
encoded
by

the
second
genomic
RNA
of
this
virus
were
used
to
re-evaluate
several
viruses
in
the
Penicillimonavirus
and
Plasmopamonavirus
genera,

here
shown
to
be
bisegmented
and
encoding
a
conserved
polypeptide
that
has
structural
conservation
with
the
nucleocapsid
domain

of
rhabdoviruses.