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Recombination as a motor of host switches and virus emergence: geminiviruses as case studies.

01 Feb 2015-Current Opinion in Virology (Curr Opin Virol)-Vol. 10, pp 14-19

Abstract: Genetic recombination facilitates the transfer of genetic information in a parasexual reproduction manner even between distantly related species. Within the Geminiviridae family, a group of plant-infecting viruses that severely constrain cropping systems worldwide, it is highly suspected that recombination was pivotal in the emergence as a devastating phytopathological problem. Whereas extensive evidence of recombination suggests that this mechanism might be adaptive in this family, direct demonstration remains scarce. Here we assemble lines of evidences indicating that recombination was crucial in driving host switches and further emergence of geminiviruses, making these viruses such successful plant pathogens.
Topics: Genetic recombination (53%), Geminiviridae (51%)

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Recombination
as
a
motor
of
host
switches
and
virus
emergence:
geminiviruses
as
case
studies
Pierre
Lefeuvre
1
and
Enrique
Moriones
2
Genetic
recombination
facilitates
the
transfer
of
genetic
information
in
a
parasexual
reproduction
manner
even
between
distantly
related
species.
Within
the
Geminiviridae
family,
a
group
of
plant-infecting
viruses
that
severely
constrain
cropping
systems
worldwide,
it
is
highly
suspected
that
recombination
was
pivotal
in
the
emergence
as
a
devastating
phytopathological
problem.
Whereas
extensive
evidence
of
recombination
suggests
that
this
mechanism
might
be
adaptive
in
this
family,
direct
demonstration
remains
scarce.
Here
we
assemble
lines
of
evidences
indicating
that
recombination
was
crucial
in
driving
host
switches
and
further
emergence
of
geminiviruses,
making
these
viruses
such
successful
plant
pathogens.
Addresses
1
CIRAD,
UMR
PVBMT,
Po
ˆ
le
de
Protection
des
Plantes,
7
chemin
de
l’IRAT,
Saint-Pierre,
Ile
de
la
Re
´
union
97410,
France
2
Instituto
de
Hortofruticultura
Subtropical
y
Mediterra
´
nea
‘‘La
Mayora’’
(IHSM-UMA-CSIC),
Consejo
Superior
de
Investigaciones
Cientı
´ficas,
Estacio
´
n
Experimental
‘‘La
Mayora’’,
29750
Algarrobo-Costa,
Ma
´
laga,
Spain
Corresponding
author:
Moriones,
Enrique
(moriones@eelm.csic.es)
Current
Opinion
in
Virology
2015,
10:1419
This
review
comes
from
a
themed
issue
on
Emerging
viruses:
interspecies
transmission
Edited
by
Antoine
Gessain
and
Fernando
Garcia-Arenal
For
a
complete
overview
see
the
Issue
and
the
Editorial
Available
online
2nd
Janurary
2015
http://dx.doi.org/10.1016/j.coviro.2014.12.005
1879-6257/#
2014
Elsevier
B.V.
All
rights
reserved.
Introduction
Genetic
recombination
allows
parental
viruses
to
derive
genetic
information
to
their
progeny
in
a
parasexual
reproduction
manner.
This
mechanism
is
a
key
process
in
the
evolution
of
many
virus
families
and
has
been
extensively
recorded
for
members
of
the
family
Gemini-
viridae
[14].
Geminiviruses
are
plant-infecting
circular
single
stranded
(ss)
DNA
viruses
that
severely
constrain
production
in
a
variety
of
cropping
systems
throughout
the
world
[57].
They
comprise
seven
genera
that
differ
in
terms
of
phylogenetic
relationships,
genome
structure,
host
range
and
insect
vector
[8].
Besides
evolving
at
substitutions
rates
equivalent
to
those
found
for
RNA
viruses
[9],
in
this
virus
family,
extensive
evidence
of
recombination
is
available
at
every
level
of
the
diversity
spectrum
[10].
As
recorded
also
for
other
virus
groups
[11],
this
mechanism
was
most
probably
essential
in
the
mac-
roevolution
and
the
emergence
process
(see
[1,12
,13]
for
a
review
of
recombination
for
the
ssDNA
viruses
in
general).
Recombination
in
geminiviruses
facilitates
the
transfer
of
genetic
information
even
between
distantly
related
spe-
cies
in
such
extent
that
their
genomic
organization
is
thought
to
have
evolved
to
maximize
its
adaptive
value
and
minimize
potentially
deleterious
effects
[1].
In
fact,
the
risk
to
produce
defective
progeny
is
high
for
gemi-
niviruses
because
of
their
highly
compacted
genome
(2.7
kb)
with
overlapping
genes,
multifunctional
pro-
teins
and
optimized
interactions
between
different
parts
and
proteins
it
encodes.
While
the
preservation
of
coe-
volved
interactions
is
supported
by
wide
experimental
and
analytical
information,
in
some
cases
recombinants
with
novel
abilities
to
interact
with
hosts
or
vector
might
arise.
Thus,
for
example,
the
ability
to
infect
a
particular
host
depends
in
part
on
the
balance
between
host
defenses
and
virus
counterdefense.
Among
host
defenses,
it
is
now
apparent
that
gene
silencing
is
an
essential
plant
antiviral
mechanism
[14].
However,
as
for
other
plant
viruses,
geminiviruses
encode
proteins
that
can
suppress
gene
silencing
[15]
in
a
host
dependent
manner
[16
].
Genetic
exchanges
involving
these
proteins
might
drive
host
shift
and
emergence
[16
,17].
The
abilities
of
geminiviruses
to
rapidly
generate
poly-
morphisms
through
mutations
[9]
and
combine
new
ge-
netic
forms
through
recombination
were
probably
essential
in
responding
to
the
numerous
niche
extensions
events
offered
within
the
context
of
modern
agriculture
[1,57,1821].
However,
despite
a
large
amount
of
indi-
rect
evidence
and
some
degree
of
speculation,
there
are
few
well
supported
examples
of
this
having
occurred
in
nature
(see
[4,22,23,24
]
for
good
examples).
Recombination
patterns
in
geminiviruses
Whereas
non-homologous
recombination
(during
which
genome
regions
get
rearranged,
duplicated,
deleted)
is
mostly
apparent
above
the
genus
level
in
the
Geminivir-
idae
family,
homologous
recombination
is
a
widespread
phenomenon
as
almost
every
geminivirus
is
the
descen-
dent
of
some
inter-species
or
inter-strain
recombinant
[10].
Importantly,
analyses
of
viral
sequences
obtained
from
both
the
environment
and
experimental
studies
revealed
that
recombination
breakpoints
are
generally
Available
online
at
www.sciencedirect.com
ScienceDirect
Current
Opinion
in
Virology
2015,
10:1419
www.sciencedirect.com

not
randomly
distributed
with
conserved
recombination
hot
spots
and
cold
spots
[10].
Studies
demonstrated
that
these
distribution
patterns
are
strongly
influenced
by
mechanistical
factors
preserving
interaction
networks
[1,25,26,27

].
Remarkably,
recombination
is
intimately
associated
with
the
replication
process
of
geminiviruses.
It
notably
involves
the
so-called
‘recombination
depen-
dent
replication’
mechanism
that
is
able
to
recover
frag-
ments
of
geminiviral
DNA
that
may
result
from
incomplete
synthesis
or
from
nucleolytic
attack
to
create
recombinant
viruses
[28,29].
Doing
so,
it
has
the
potential
to
create
large
number
of
recombinant
viruses
displaying
specific
recombination
patterns
(e.g.
the
notorious
recom-
bination
hot-spot
around
the
origin
of
replication
[10])
when
multiple
viruses
co-infect
the
same
cell
[1].
While
mechanistic
predisposition
profoundly
affects
the
recombination
patterns,
these
also
bear
severe
imprints
of
selection.
Recombination
breakpoint
distribution
pat-
terns
are
partially
attributable
to
natural
selection
dis-
favouring
survival
of
recombinants
in
which
co-evolved
intra-genome
interaction
networks
are
disrupted
[25,30].
Whereas
the
vast
majority
of
recombinant
forms,
as
most
mutants,
are
likely
of
poorer
fitness
than
the
parents
[26,31],
recombinants
bearing
favourable
combinations
[27]
might
outcompete
the
parental
viruses
and
become
prevalent
in
the
population.
It
is
clearly
apparent
from
the
literature
that
genetic
material
is
exchanged
between
viruses
participating
into
epidemics
on
distinct
hosts.
Although
it
does
not
prove
that
recombination
allowed
host
shift
or
range
extension,
it
clearly
demonstrated
exchanges
of
genetic
material
between
distinct
viral
diversity
pools.
Additionally
in
the
Begomovirus
genus
of
the
Gemini-
viridae
family,
where
bipartite
genomes
occur,
mixed
infections
provide
opportunities
for
heterologous
ge-
nome
component
reassortment,
also-called
pseudo-re-
combination.
Evidences
of
exchange,
loose
or
gain
of
components
during
the
evolution
of
begomoviruses
is
shown
in
natural
infections
[3234].
Importantly,
pseu-
dorecombination
involving
non-essential
components
such
as
betasatellites,
can
modulate
the
expression
of
the
disease
in
a
host-dependent
manner,
and
drive
host
shift
[3537 ]
providing
another
determinant
for
host
adaptation.
Recombination
as
a
driving
force
of
emergence
Besides
experimental
studies
demonstrating
alteration
of
ecolog y
and
fitness
following
recombination
between
geminiviruses
[22,3845],
evidences
accumulate
for
re-
combination
as
in
natura
mechanism
of
modification
of
host
ranges
[4,22 ,3 2, 40 , 46 48,49

].
These
notably
in-
clude
the
invasive
spread
of
tomato
yellow
leaf
curl
disease
(TYLCD)-associated
begomoviruses
across
the
Western
Mediterranean
during
the
past
three
decades
[22,50]
or
the
emergence
of
maize
streak
disease
as
a
major
agricultural
threat
throughout
the
African
conti-
nent
[4,51].
It
should
be
highlighted
that
these
diseases
were
absent
in
the
centre
of
origin
of
the
host
plants
(both
from
the
Americas)
and
have
emerged
in
the
areas
where
these
plants
where
later
introduced.
Recombina-
tion
might
have
contributed
to
the
likely
host
switches
events
and
adaptation
of
locally
circulating
gemini-
viruses.
Recombination
as
a
driving
force
in
dicot
geminiviruses:
begomoviruses
Begomovirus
is
one
of
the
largest
plant
virus
genus
com-
prising
almost
300
viral
species
[52].
Several
lines
of
evidence
indicate
that
the
emergence
of
a
highly
polyph-
agous
and
invasive
type
of
the
vector
of
begomoviruses,
the
whitefly
(Hemiptera:
Aleyrodidae)
Bemisia
tabaci,
is
contributing
to
transferring
begomoviruses
among
a
large
set
of
distinct
hosts
[7,53],
increasing
the
opportunities
of
mixed
infection
and
further
diversification
through
re-
combination
[21].
Some
instances
of
such
events
have
been
recorded
with,
for
example,
the
recent
pandemic
on
cassava
in
Africa
caused
by
a
recombinant
virus
with
an
extremely
increased
severity
[54,45],
or
the
emergence
of
the
resistance-breaking
recombinant
virus
named
cotton
leaf
curl
Burewala
virus
(CLCuBuV)
that
causes
devas-
tating
damage
to
cotton
production
in
India
and
Pakistan
[24].
One
of
the
best
studied
examples
is
the
one
that
refers
to
TYLCD-associated
begomoviruses.
The
TYLCD
has
emerged
during
the
last
decades
in
almost
every
region
of
the
world
where
tomato
is
commercially
grown
[50]
and
is
caused
by
a
complex
of
begomovirus
species
related
to
the
highly
invasive
tomato
yellow
leaf
curl
virus
(TYLCV)
[55].
Complex
recombination-
derived
progenies
were
shown
to
arise
at
high
frequencies
and
in
relatively
short
periods
during
mixed
infections
of
TYLCD-related
species
[3,56]
or
with
other
distantly
related
begomoviruses
[30,57].
Interestingly,
although
natural
selection
preserves
co-evolved
intra-genome
in-
teraction
networks
[30],
numerous
and
diverse
viable
recombinants
can
be
produced
during
mixed
infections
[30,57
]
or
artificially
[58],
highlighting
the
tolerance
to
disruption
of
begomoviruses
genomes.
Scarce
informa-
tion,
however,
is
available
on
the
fitness
of
recombinants
arising
in
natura.
Again,
studies
conducted
on
natural
populations
of
TYLCD-associated
viruses
inform
about
this
aspect.
In
Spain
and
Italy,
a
diversity
of
recombinant
viruses
between
TYLCD-associated
begomoviruses
was
described
[22,23,59].
Importantly,
both
field
and
experi-
mental
studies
demonstrated
that
successful
recombinant
viruses
exhibited
host
shift
in
respect
to
parental
viruses,
being
able
to
infect
a
larger
set
of
hosts
[22,23].
This
was
the
case,
for
example,
of
the
recombinant
virus
named
tomato
yellow
leaf
curl
Ma
´
laga
virus
(TYLCMalV)
that
has
an
enlarged
host
range
and
outcompeted
the
parental
viruses
in
Phaseolus
vulgaris
epidemics
[3,22].
Recombination
and
emergence
in
geminiviruses
Lefeuvre
and
Moriones
15
www.sciencedirect.com
Current
Opinion
in
Virology
2015,
10:1419

Recombination
as
a
driving
force
in
monocot
geminiviruses:
MSV
Maize
streak
virus
(MSV),
a
well
charact eriz ed
leafhop-
per-transmitted
geminivirus
from
the
Mastrevirus
genus
of
the
family
Geminiviridae,
is
the
causal
agent
of
maize
streak
disease.
It
ranks
amongst
the
most
serious
bio-
logical
threats
to
food
security
in
sub-Saharan
Africa
[5].
Clear
imprints
of
both
ancient
and
recent
recombina-
tion
events
can
be
detected
on
most
MSV
genomes.
The
ability
of
recombination
to
rapidly
produce
viruses
with
altered
characteristics
was
confirmed
in
a
study
that
us
sub-optimal
synthetic
recombinant
viruses
and
where
fitter
genome
were
quickly
restored
[27].
Anoth-
er
step
further,
it
was
also
suggested
that
recombination
was
cardinal
in
the
emergence
of
new
biological
features.
In
fact,
whereas
at
least
eleven
distinct
MSV
strains
have
been
reported
so
far
from
several
common
grasse s
in
Africa,
only
the
MSV-A
causes
severe
disease
in
maize
[4].
Interestingly,
it
was
sug-
gested
that
this
MSV-A
strain
is
in
fact
a
recombinant
between
two
Digitaria-adapted
MSV
strains
that
repli-
cate
to
low
level
in
maize
and
barely
cause
symptoms
[4].
From
a
phylogeographic
reconstruction,
it
was
inferred
that
this
recombinant
emerge d
in
the
1860s
in
southern
Africa
before
spreading
throughout
Africa
in
the
1950s
where
it
is
today
found
widespread
[51, 60 ].
While
this
recombination
event
might
have
produced
a
virus
with
increased
severity
in
maize,
the
studies
highligh t
the
possibility
that
it
may
also
have
enabled
MSV-A
to
spread
more
efficiently
by
allowing
it
to
16
Emerging
viruses:
interspecies
transmission
Figure
1
1
4
2
3
Current Opinion in Virology
Schematic
representation
of
geminivirus
communities
in
a
multi-host
plant
system,
with
a
virus
free
host
(here,
tomato
plants
in
the
middle
of
the
figure)
and
three
uncultivated
plant
species.
Each
of
the
uncultivated
plants
is
the
host
of
a
set
of
viruses
(1)
with
contrasting
degree
of
fitness.
Rate
of
virus
exchanges
between
the
hosts
(2)
is
determined
by
vector
populations
densities
and
preferences
and
by
virus
adaptation
to
each
host.
The
topology
of
the
network
and
the
available
sequence
space
determine
in
part
the
set
of
viruses
(several
of
which
being
recombinant)
that
can
appear.
Whereas
some
viruses
won’t
be
able
to
infect
the
yet
disease
free
plant
(3),
some
others
(4)
with
the
appropriate
combinations
of
genetic
determinants
will
eventually
be
successful
and
potentially
emerge
as
a
proper
circulating
viruses
on
this
new
host.
Although
the
figure
represents
the
first
steps
of
an
emergence
event
on
a
crop,
a
process
facilitated
by
its
high
density,
it
must
be
noticed
that
viral
emergence
function
as
a
natural
process
within
the
ecosystems
on
potentially
every
plant
species,
cultivated
or
not.
Current
Opinion
in
Virology
2015,
10:1419
www.sciencedirect.com

infect
a
wider
variety
of
hosts.
In
fact,
MSV-A
was
detected
on
members
of
eight
different
grass
genera,
thus
having
the
largest
host
range
of
all
MSV
strains
[4].
Although
it
remains
unknown
whether
this
recombina-
tion
event
was
pivotal
in
the
emergence
of
MSV-A
in
maize,
its
enlarged
host
range
might
explain
the
eco-
logical
success
of
this
recombinant
virus.
Conclusions
future
work
The
expansion
of
monocultures
and/or
spread
of
poly-
phageous
vectors
(such
as
specific
types
of
B.
tabaci
for
begomoviruses),
that
favour
movement
of
indigenous
viruses
between
plants,
are
major
ecological
drivers
of
recent
geminivirus
host
switches.
While
the
contribution
of
recombination
is
clearly
apparent
(Figure
1),
one
of
the
greate st
challenges
is
understanding
the
interplay
between
recombination
and
viral
ecology.
Whereas
the
vast
majority
of
geminivirus
sequences
obtained
in
the
last
years
are
from
viruses
infecting
cultivated
plants,
they
most
likely
emerge
from
non-cult ivated
plants
(stands
for
plant
pathogens
in
general
[61]).
In
this
context,
it
would
be
extremely
informative
to
first
isolate
large
sets
of
virus
sequences
at
the
ecosystem
scale
before
exhaustively
inferring
their
host
ranges.
Several
ongoing
projects
using
metagenomics
approaches
will
certainly
pave
the
way
to
such
understanding
[62
,63,64].
The
analyses
of
the
recombination
patterns
within
these
viral
communities
could
inform
about
virus
ecology.
Since
recombining
viruses
obviously
have
somewhat
overlapping
geographical
distributions,
host
ranges
and
tissue
tropisms,
and
patterns
of
sequence
exchange
amongst
viruses
sampled
from
nature
could
also
be
used
to
retrace
the
ecological
interactions
be-
tween
populations
(see
[65,66]
for
a
good
examples
on
bacteria).
Whereas
the
networks
of
genetic
exchanges
amongst
viruses
could
inform
about
virus
populations
that
are
the
most
active
recombiners,
their
analyses
could
reveal
key
host
species,
environmental
or
cultural
conditions
favouring
specific
patterns
of
viral
encounter
and
from
where
host
switch
is
most
likely
to
originate.
The
topology
of
the
circuits
of
genetic
exchanges
within
and
between
virus
communities
would
determine
the
probability
of
viruses
to
form
new
genetic
combinations
and
to
emerge
in
a
specific
spot
of
the
fitness
landscape
[67].
Knowing
their
great
success
as
emerging
pathogens
and
their
presumed
high
prevalence
in
most
ecosystems
[63,64,6870],
geminiviruses
stand
as
an
excellent
model
to
further
study
emergence
at
the
global
ecosystem
scale
where
it
functions
as
a
natural
process
during
virus
evolution.
Acknowledgements
This
work
was
funded
by
grants
awarded
to
E.M.
(Grant
AGL2013-48913-
C2-1-R
from
the
Ministerio
de
Ciencia
e
Innovacio
´
n
with
assistance
from
the
European
Regional
Development
Fund,
and
Co
´
digo
P10-AGR-6516
from
Junta
de
Andalucı
´
a).
P.L.
is
funded
by
the
Re
´
gion
Re
´
union,
the
European
Union
(FEDER)
and
the
CIRAD.
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and
recommended
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have
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18
Emerging
viruses:
interspecies
transmission
Current
Opinion
in
Virology
2015,
10:1419
www.sciencedirect.com

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Book ChapterDOI
TL;DR: The explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade is surveyed, similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences are highlighted, and the ecology and evolution of eUKaryoticCRESS DNA viruses are discussed.
Abstract: While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.

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Journal ArticleDOI
21 Sep 2017-Viruses
TL;DR: ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus.
Abstract: The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade Special emphasis has been given to gene silencing suppression ability in order to counteract host plant defense responses The importance of the interaction with DNA alphasatellites and betasatellites in the biology of the virus has been demonstrated ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus Recombination and pseudorecombination have been shown as motors of diversification and adaptive evolution Important progress has also been made in control strategies to reduce disease damage This review highlights these various achievements in the context of the previous knowledge of begomoviruses and their interactions with plants

58 citations


Cites background from "Recombination as a motor of host sw..."

  • ...Genetic recombination allows parental viruses present in mixed infections to exchange genetic information and derive it to their progeny in a parasexual reproduction manner; this mechanism is a key process in the evolution of many virus families and has been extensively recorded for members of the family Geminiviridae [54]....

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  • ...The tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus species (genus Begomovirus, family Geminiviridae) whose isolates are transmitted in nature by the whitefly Bemisia tabaci (order Hemiptera, family Aleyrodidae) in a circulative and persistent manner [1]....

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Journal ArticleDOI
TL;DR: An understanding of the capacity of ToLCNDV to infect a variety of hosts and spread across a broad and ecologically variable geographical range could illuminate the potential economic threats associated with similar begomoviral invasions.
Abstract: ummary Tomato leaf curl New Delhi virus (ToLCNDV) is an exceptional Old World bipartite begomovirus. On the Indian subcontinent, a region in which monopartite DNA satellite-associated begomoviruses with mostly narrow geographical ranges predominate, it is widespread, with a geographical range also including the Far East, Middle East, North Africa and Europe. The success of ToLCNDV probably derives from its broad host range and highly flexible genomic configuration: its DNA-A component is capable of productively interacting with, and trans-replicating, diverse DNA-B components and betasatellites. An understanding of the capacity of ToLCNDV to infect a variety of hosts and spread across a broad and ecologically variable geographical range could illuminate the potential economic threats associated with similar begomoviral invasions. Towards this end, we used available ToLCNDV sequences to reconstruct the history of ToLCNDV spread. Taxonomy Family Geminiviridae, Genus Begomovirus. ToLCNDV is a bipartite begomovirus. Following the revised begomovirus taxonomic criteria of 91% and 94% nucleotide identity for species and strain demarcation, respectively, ToLCNDV is a distinct species with two strains: ToLCNDV and ToLCNDV-Spain. Host range The primary cultivated host of ToLCNDV is tomato (Solanum lycopersicum), but the virus is also known to infect 43 other plant species from a range of families, including Cucurbitaceae, Euphorbiaceae, Solanaceae, Malvaceae and Fabaceae. Disease symptoms Typical symptoms of ToLCNDV infection in its various hosts include leaf curling, vein thickening, puckering, purpling/darkening of leaf margins, leaf area reduction, internode shortening and severe stunting.

56 citations


Journal ArticleDOI
TL;DR: Analysis of samples collected in the survey indicates that ChiLCD-infected plants are associated with a complex of begomoviruses (including one previously unreported species) with a diverse group of betasatellites found in crops and weeds, and demonstrates the crucial role of betAsatellites in severe disease development in Capsicum spp.
Abstract: Chilli, which encompasses several species in the genus Capsicum, is widely consumed throughout the world. In the Indian subcontinent, production of chilli is constrained due to chilli leaf curl disease (ChiLCD) caused by begomoviruses. Despite the considerable economic consequences of ChiLCD on chilli cultivation in India, there have been scant studies of the genetic diversity and structure of the begomoviruses that cause this disease. Here we report on a comprehensive survey across major chilli-growing regions in India. Analysis of samples collected in the survey indicates that ChiLCD-infected plants are associated with a complex of begomoviruses (including one previously unreported species) with a diverse group of betasatellites found in crops and weeds. The associated betasatellites neither enhanced the accumulation of the begomovirus components nor reduced the incubation period in Nicotiana benthamiana. The ChiLCD-associated begomoviruses induced mild symptoms on Capsicum spp., but both the level of helper virus that accumulated and the severity of symptoms were increased in the presence of cognate betasatellites. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The betasatellites possess high nucleotide variability, and recombination among them was also evident. The nucleotide substitution rates were determined for the AV1 gene of begomoviruses (2.60 × 10- 3 substitutions site- 1 year- 1) and the βC1 gene of betasatellites [chilli leaf curl betasatellite (ChiLCB), 2.57 × 10- 4 substitution site- 1 year- 1; tomato leaf curl Bangladesh betasatellite (ToLCBDB), 5.22 × 10- 4 substitution site- 1 year- 1]. This study underscores the current understanding of Indian ChiLCD-associated begomoviruses and also demonstrates the crucial role of betasatellites in severe disease development in Capsicum spp.

52 citations


Cites background or result from "Recombination as a motor of host sw..."

  • ...Detection of recombination among ChiLCDassociated begomoviruses and betasatellites Recombination is known to play a major role in the emergence and evolution of geminiviruses (George et al., 2015; Lefeuvre & Moriones, 2015; Padidam et al., 1999)....

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  • ...These results are in line with previous observations of AV1 and AC1 regions as the recombination hotspots (George et al., 2015; Lefeuvre et al., 2007; Lefeuvre & Moriones, 2015)....

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Journal ArticleDOI
R. Vinoth Kumar1Institutions (1)
TL;DR: This review summarizes the current knowledge concerning virus movement within and between cells, as well as the recent advances in the understanding of the biological roles of virus-encoded proteins in manipulating host-mediated responses and insect transmission.
Abstract: The family Geminiviridae includes plant-infecting viruses whose genomes are composed of one or two circular non-enveloped ssDNAs(+) of about 2.5-5.2 kb each in size. These insect-transmissible geminiviruses cause significant crop losses across continents and pose a serious threat to food security. Under the control of promoters generally located within the intergenic region, their genomes encode five to eight ORFs from overlapping viral transcripts. Most proteins encoded by geminiviruses perform multiple functions, such as suppressing defense responses, hijacking ubiquitin-proteasomal pathways, altering hormonal responses, manipulating cell cycle regulation, and exploiting protein-signaling cascades. Geminiviruses establish complex but coordinated interactions with several host elements to spread and facilitate successful infection cycles. Consequently, plants have evolved several multilayered defense strategies against geminivirus infection and distribution. Recent studies on the evasion of host-mediated resistance factors by various geminivirus proteins through novel mechanisms have provided new insights into the development of antiviral strategies against geminiviruses. This review summarizes the current knowledge concerning virus movement within and between cells, as well as the recent advances in our understanding of the biological roles of virus-encoded proteins in manipulating host-mediated responses and insect transmission. This review also highlights unexplored areas that may increase our understanding of the biology of geminiviruses and how to combat these important plant pathogens.

43 citations


Cites background from "Recombination as a motor of host sw..."

  • ...Several factors such as recombination, pseudo-recombination, microsatellites, mutations, nucleotide substitutions, synergism, and vectormediated transmission drive the rapid emergence and evolution of geminiviruses (Rojas et al., 2005; Lefeuvre and Moriones, 2015; Czosnek et al., 2017; Kumar and Chakraborty, 2018)....

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  • ...…as recombination, pseudo-recombination, microsatellites, mutations, nucleotide substitutions, synergism, and vectormediated transmission drive the rapid emergence and evolution of geminiviruses (Rojas et al., 2005; Lefeuvre and Moriones, 2015; Czosnek et al., 2017; Kumar and Chakraborty, 2018)....

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References
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Journal ArticleDOI
20 Dec 1999-Virology
TL;DR: Geminiviruses are a group of plant viruses characterized by a genome of circular single-stranded DNA encapsidated in twinned quasi-isometric particles and recombination is very frequent and occurs between species and within and across genera.
Abstract: Although exchange of genetic information by recombination plays a role in the evolution of viruses, the extent to which it generates diversity is not clear. We analyzed genomes of geminiviruses for recombination using a new statistical procedure developed to detect gene conversions. Geminiviruses (family, Geminiviridae) are a group of plant viruses characterized by a genome of circular single-stranded DNA (∼2700 nucleotides in length) encapsidated in twinned quasi-isometric particles. Complete nucleotide sequences of geminiviruses were aligned, and recombination events were detected by searching pairs of viruses for sequences that are significantly more similar than expected based on random distribution of polymorphic sites. The analyses revealed that recombination is very frequent and occurs between species and within and across genera. Tests identified 420 statistically significant recombinant fragments distributed across the genome. The results suggest that recombination is a significant contributor to geminivirus evolution. The high rate of recombination may be contributing to the recent emergence of new geminivirus diseases.

1,316 citations


Journal ArticleDOI
TL;DR: It is shown that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.
Abstract: Understanding the factors that determine the rate at which genomes generate and fix mutations provides important insights into key evolutionary mechanisms. We review our current knowledge of the rates of mutation and substitution, as well as their determinants, in RNA viruses, DNA viruses and retroviruses. We show that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.

1,185 citations


"Recombination as a motor of host sw..." refers background in this paper

  • ...Besides evolving at substitutions rates equivalent to those found for RNA viruses [9], in this virus family, extensive evidence of...

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  • ...The abilities of geminiviruses to rapidly generate polymorphisms through mutations [9] and combine new genetic forms through recombination were probably essential in responding to the numerous niche extensions events offered within the context of modern agriculture [1,5–7,18–21]....

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Journal ArticleDOI
Shou-Wei Ding1Institutions (1)
TL;DR: Recent studies on the features of viral siRNAs and other virus-derived small RNAs from virus-infected fungi, plants, insects, nematodes and vertebrates are reviewed and the innate and adaptive properties of RNA-based antiviral immunity are discussed.
Abstract: In eukaryotic RNA-based antiviral immunity, viral double-stranded RNA is recognized as a pathogen-associated molecular pattern and processed into small interfering RNAs (siRNAs) by the host ribonuclease Dicer. After amplification by host RNA-dependent RNA polymerases in some cases, these virus-derived siRNAs guide specific antiviral immunity through RNA interference and related RNA silencing effector mechanisms. Here, I review recent studies on the features of viral siRNAs and other virus-derived small RNAs from virus-infected fungi, plants, insects, nematodes and vertebrates and discuss the innate and adaptive properties of RNA-based antiviral immunity.

682 citations


"Recombination as a motor of host sw..." refers background in this paper

  • ...Among host defenses, it is now apparent that gene silencing is an essential plant antiviral mechanism [14]....

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Journal ArticleDOI
TL;DR: Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes inThe vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants.
Abstract: Virus diseases that have emerged in the past two decades limit the production of important vegetable crops in tropical, subtropical, and temperate regions worldwide, and many of the causal viruses are transmitted by whiteflies (order Hemiptera, family Aleyrodidae). Most of these whitefly-transmitted viruses are begomoviruses (family Geminiviridae), although whiteflies are also vectors of criniviruses, ipomoviruses, torradoviruses, and some carlaviruses. Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes in the vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants. The role of humans in increasing the emergence of virus diseases is obvious, and the effect that climate change may have in the future is unclear.

612 citations


Journal ArticleDOI
TL;DR: What is known about host switching leading to viral emergence from known examples is reviewed, considering the evolutionary mechanisms, virus-host interactions, host range barriers to infection, and processes that allow efficient host-to-host transmission in the new host population.
Abstract: Host range is a viral property reflecting natural hosts that are infected either as part of a principal transmission cycle or, less commonly, as "spillover" infections into alternative hosts. Rarely, viruses gain the ability to spread efficiently within a new host that was not previously exposed or susceptible. These transfers involve either increased exposure or the acquisition of variations that allow them to overcome barriers to infection of the new hosts. In these cases, devastating outbreaks can result. Steps involved in transfers of viruses to new hosts include contact between the virus and the host, infection of an initial individual leading to amplification and an outbreak, and the generation within the original or new host of viral variants that have the ability to spread efficiently between individuals in populations of the new host. Here we review what is known about host switching leading to viral emergence from known examples, considering the evolutionary mechanisms, virus-host interactions, host range barriers to infection, and processes that allow efficient host-to-host transmission in the new host population.

606 citations


"Recombination as a motor of host sw..." refers background in this paper

  • ...As recorded also for other virus groups [11], this mechanism was most probably essential in the macroevolution and the emergence process (see [1,12 ,13] for a review of recombination for the ssDNA viruses in general)....

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