Bernardo et al-Poster-PVEN-2011

A new genus-level geminivirus lineage isolated from the
South African fynbos
Pauline Bernardo1, Emmanuel Fernandez1, Martine Granier1, Cica Urbino, Michel Perterschmitt1, Darren P. Martin2 and Philippe Roumagnac1
1) CIRAD/UMR BGPI, TA A-54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 5, France
2)Institute of Infectious Disease and Molecular Medecine, University of Cap Town, South Africa
Viruses are the major cause of
emerging diseases (47%) in plants
The state of the art on the diversity of plant viruses mainly concerns those causing symptoms
affecting plants of economic interest. However, wild plants have the potential to be
reservoirs of viral biodiversity which contribute to the emergence of virus without
necessarily showing symptoms. It is very important to study the viral diversity in natural
environments in order to predict future outbreaks and know how to manage them. Among the
virus-DNA plants, the family Geminiviridae is known for being responsible of many plant
diseases of economic interest, including tomato, cotton and cassava. Africa is a continent
particularly affected by the impact of geminiviruses that threaten its main crops.
Here, we describe a new genus-level geminivirus lineage isolated
from the fynbos wild ecosystem (South Africa) :
Euphorbia caput-medusae Virus (EucmV)
Methodological approach
Study area:
Total DNA extraction, RCA, Cloning and
Host plant:
sequencing:
Euphorbia caput-medusae EcoR1 restriction:
RCA
Sequencing
Clo
n in
g
DNA extraction
Re
str
An indigenous wild species…
ict
ion
•Confirmation of the genera made by the sequencing of ndhf
chloroplastic gene
•October 2010
•100 points
•510 samples
Operating sequence of EucmV
Genome map and ORFs:
Figure made with neb cutter. The
putatives ORFs were obtained with
blastp on NCBI GenBank.
vs=virion sense
• Organization similar
to mastrevirus:
-a spliced rep in the
complementary sense
(ORF a and c)
-a cp on the virion
sense (ORF b)
• But a lack of mp
• 3 unknown ORFs
Phylogenetic tree (Maximum likelihood):
rep
cp
AAO34410.1ACMV
80
Begomovirus
CAD58399.1TYLCSV
AAG27472.1TYLCCV
6
NP 991336.1HYVV
ABG26017.1 ClerodendrumGMV
CAJ57712.1 TYLCCV
24
NP 871717.1TLCJV
CAF04471.1 TLCNDV
40
ABO31248.1TLCNDV
14
CAD97701.1 TLCYV
CAM58876.1CLCRV
98
46
NP 871720.1TLCJV
86
AAF75534.1TLCYV
AAM00362.1 ACMV
22073996TLCSV
44
34
NP 443744.1 CLCRV
CAD62698.1HYVV
56
10
28
ABG26019.1 ClGMV
18
AAP23255.1MYMV
96
AAA47955.1 TYLCSV
18
74
AAU87293.1CpGMV
YP 006469.1TLCSV
34
94
CAI91270.1DolYMV
AAB87607.1 CpGMV
48
YP 001333684.1CorchorusGMV
30
AAL05272.1 MaMPRV
NP 671458.1 MaMPRV
100
BAG68473.1SPLCV
ABC74535.1TSLCV
10
54
48
YP 001333687.1 CoGMV
8
98
NP 041238.1TGMV
88
NP 958046.1 DoYMV
62
70
CAD67488.1BGYMV
Q88888.1 TPCTV
AAB87606.1CGMV
P14991.2 BCTV
ABY21699.1SPLCV
40
12
ACB97656.1 BMCTV
CAJ43623.1 NSPICMV
84
YP 006996.1SpCTV
100
NP 808805.1SqMLCV
98
YP 001274389.1PeCTV
84
94
YP 001974409.1TYVSV
100
NP 840048.1 BSCTV
100
ABQ12147.1PeGMV
38
ABN80221.1 TYVSV
ABQ08587.1SiGMV
54
P05175.1 BGYMV
78
98
• Weak signal of
recombination (15 aa)
• But the significance of this
signal remains unclear
because the sequence
alignment was not optimal
(because of the diversity of
sequences in the
Geminiviridae family)
• EucmV is probably not
recombinant
NP 040559.1BCTV
Curtovirus
ABQ12757.1 TGMV
84
NP 808753.1 SiMoV
34
66
NP 066185.1 HrCTV
70
56
NP 671475.1 PGMV
NP 840045.1BSCTV
NP 840037.1BMCTV
ABQ12761.1PepCTV
36
100
AAD33452.2 TSLCV
56
Prospects
Begomovirus
Topocuvirus
& Curtovirus
52
Recombinaison analysis:
Analysis made by RDP3 from an alignment of
63 whole genome sequences of representative
geminivirus(CLUSTALW/ MEGA)
AAU87296.1CGMV
34
44
Potential recombination area
NP 077091.1 MYMV
100
38
60
BCTIV
100
YP 006993.1SpCTV
ABB76203.1 SMLCV
62
NP 066183.1HrCTV
ECSV
Euphorbia caput-medusae Virus)
EucmV
Euphorbia caput-medusae Virus
66
Q88886.1 TPCTV
EucmV
Topocuvirus
BCTIVx
100
92
94
100
Mastrevirus
CAA71908.2 BYDV
NP 612220.1BeYDV
96
16
CAP69809.1 ChCDV
94
Mastrevirus
CAP69808.1ChCDSV
62
P31616.1 TYDV
P31618.2 TYDV
100
ABZ79689.1PanSV
70
Q80GM6.2 SSV-N
70
CAA12316.1MSV
54
P0C647.1 PanSV-K
32
100
90
62
ABZ03978.1SSV
P14988.2 MSV-K
P14985.1 CSMV
P18919.2 CSMV
BAA00833.1MiSV
30
Q67590.2 MiSV
62
ECSV
CAL30140.1 ODV
52
28
CAL30139.1ODV
100
CAL69917.1 BDV
100
100
CAA57624.1WDV
100
CAJ13700.1 WDV
90
CAL30135.1BDV
Candidatus Phytoplasma (OUTGROUP)
0.5
0.2
ML trees built from an alignment on MEGA whith STATALIGN/BALIPHY with 106 MCMC. They represents the consensus of 1000 trees
• EucmV is probably a new genus-level of geminivirus
• He is closest to the most recent common ancestor of mastrevirus than to
other geminivirus
• He is probably not recombinant, so he may give us information about
ancestral characters of mastreviruses
 Study the infectivity of EucmV
 Study the « genera concept » by finding EucmV vector
and host range investigation
 Study the function of each ORF
 Confirm the phylogenetic position of EucmV within the
Geminiviridae family