A new genus-level geminivirus lineage isolated from the South African fynbos

(1)

A new genus-level geminivirus lineage isolated from the

South African fynbos

Pauline Bernardo

1 _{, Emmanuel Fernandez}

1 _{, Martine Granier}

1 _{, Cica Urbino, Michel Perterschmitt}

1 _{, Darren P. Martin}

2 _{and Philippe Roumagnac}

1 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)

Viruses are the major cause of

emerging diseases (47%) in plants

Methodological approach

Study area:

_{Host plant:}

Euphorbia caput-medusae

Genome map and ORFs:

Total DNA extraction, RCA,

EcoR1 restriction:

Cloning and

sequencing:

Prospects

An indigenous wild species…

Phylogenetic tree (Maximum likelihood):

NP 077091.1 MYMV AAU87296.1CGMV NP 991336.1HYVV CAJ57712.1 TYLCCV CAF04471.1 TLCNDV CAD97701.1 TLCYV NP 871720.1TLCJV AAM00362.1 ACMV NP 443744.1 CLCRV ABG26019.1 ClGMV AAA47955.1 TYLCSV YP 006469.1TLCSV AAB87607.1 CpGMV AAL05272.1 MaMPRV BAG68473.1SPLCV YP 001333687.1 CoGMV NP 958046.1 DoYMV Q88888.1 TPCTV P14991.2 BCTV ACB97656.1 BMCTV YP 006996.1SpCTV YP 001274389.1PeCTV NP 840048.1 BSCTV ABN80221.1 TYVSV P05175.1 BGYMV ABQ12757.1 TGMV NP 808753.1 SiMoV NP 066185.1 HrCTV NP 671475.1 PGMV AAD33452.2 TSLCV ABB76203.1 SMLCV ECSV

Euphorbia caput-medusae Virus

BCTIVx CAP69809.1 ChCDV CAA71908.2 BYDV P31618.2 TYDV P0C647.1 PanSV-K Q80GM6.2 SSV-N P14988.2 MSV-K P18919.2 CSMV Q67590.2 MiSV CAL30140.1 ODV CAL69917.1 BDV CAJ13700.1 WDV Candidatus Phytoplasma (OUTGROUP) 100 32 100 100 100 94 70 62 28 62 94 92 62 56 100 100 70 84 100 98 100 84 44 34 94 40 12 54 62 10 8 86 94 28 60 38 10 34 34 24 46 18 18 0.2

rep

cp

AAO34410.1ACMV CAD58399.1TYLCSV AAG27472.1TYLCCV ABG26017.1 ClerodendrumGMV NP 871717.1TLCJV ABO31248.1TLCNDV CAM58876.1CLCRV AAF75534.1TLCYV 22073996TLCSV CAD62698.1HYVV AAP23255.1MYMV AAU87293.1CpGMV CAI91270.1DolYMV YP 001333684.1CorchorusGMV NP 671458.1 MaMPRV ABC74535.1TSLCV NP 041238.1TGMV CAD67488.1BGYMV AAB87606.1CGMV ABY21699.1SPLCV CAJ43623.1 NSPICMV NP 808805.1SqMLCV YP 001974409.1TYVSV ABQ12147.1PeGMV ABQ08587.1SiGMV NP 040559.1BCTV NP 840045.1BSCTV NP 840037.1BMCTV ABQ12761.1PepCTV BCTIV YP 006993.1SpCTV NP 066183.1HrCTV

Euphorbia caput-medusae Virus)

Q88886.1 TPCTV NP 612220.1BeYDV CAP69808.1ChCDSV P31616.1 TYDV CAA12316.1MSV ABZ79689.1PanSV ABZ03978.1SSV P14985.1 CSMV BAA00833.1MiSV ECSV CAL30139.1ODV CAA57624.1WDV CAL30135.1BDV 80 52 98 14 6 56 44 40 96 74 70 88 48 100 30 34 48 98 54 38 100 98 78 84 66 56 36 100 96 100 54 100 90 90 100 100 52 30 70 62 16 66 0.5

Begomovirus

Topocuvirus

& Curtovirus

Mastrevirus

EucmV

Mastrevirus

Begomovirus

Curtovirus

Topocuvirus

Recombinaison analysis:

Potential recombination area

Operating sequence of EucmV



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

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

•October 2010

•100 points

•510 samples

DNA extraction

RCA

S

eq

ue

nc

in

g

Cl

on

in

g

Res

trictio

n

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

Analysis made by RDP3 from an alignment of

63 whole genome sequences of representative

geminivirus(CLUSTALW/ MEGA)

• 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

• 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

ML trees built from an alignment on MEGA whith STATALIGN/BALIPHY with 10

6 _{MCMC. They represents the consensus of 1000 trees}

•Confirmation of the genera made by the sequencing of ndhf

chloroplastic gene

EucmV

A new genus-level geminivirus lineage isolated from the

South African fynbos

A new genus-level geminivirus lineage isolated from the

South African fynbos

Pauline Bernardo

1 _{, Emmanuel Fernandez}

1 _{, Martine Granier}

1 _{, Cica Urbino, Michel Perterschmitt}

1 _{, Darren P. Martin}

2 _{and Philippe Roumagnac}

1 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.

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)

Viruses are the major cause of

emerging diseases (47%) in plants

Viruses are the major cause of

emerging diseases (47%) in plants

Methodological approach

Study area:

_{Host plant:}

Euphorbia caput-medusae

Genome map and ORFs:

Total DNA extraction, RCA,

EcoR1 restriction:

Cloning and

sequencing:

Prospects

An indigenous wild species…

Phylogenetic tree (Maximum likelihood):

rep

cp

Begomovirus

Topocuvirus

& Curtovirus

Mastrevirus

EucmV

Mastrevirus

Begomovirus

Curtovirus

Topocuvirus

BCTIVx CAP69809.1 ChCDV CAA71908.2 BYDV P31618.2 TYDV P0C647.1 PanSV-K Q80GM6.2 SSV-N P14988.2 MSV-K P18919.2 CSMV Q67590.2 MiSV CAL30140.1 ODV CAL69917.1 BDV CAJ13700.1 WDV Candidatus Phytoplasma (OUTGROUP) 100 32 100 100 100 94 70 62 28 62 94 92 62 56 100 100 70 84 100 98 100 84 44 34 94 40 12 54 62 10 8 86 94 28 60 38 10 34 34 24 46 18 18 0.2 NP 077091.1 MYMV AAU87296.1CGMV NP 991336.1HYVV CAJ57712.1 TYLCCV CAF04471.1 TLCNDV CAD97701.1 TLCYV NP 871720.1TLCJV AAM00362.1 ACMV NP 443744.1 CLCRV ABG26019.1 ClGMV AAA47955.1 TYLCSV YP 006469.1TLCSV AAB87607.1 CpGMV AAL05272.1 MaMPRV BAG68473.1SPLCV YP 001333687.1 CoGMV NP 958046.1 DoYMV Q88888.1 TPCTV P14991.2 BCTV ACB97656.1 BMCTV YP 006996.1SpCTV YP 001274389.1PeCTV NP 840048.1 BSCTV ABN80221.1 TYVSV P05175.1 BGYMV ABQ12757.1 TGMV NP 808753.1 SiMoV NP 066185.1 HrCTV NP 671475.1 PGMV AAD33452.2 TSLCV ABB76203.1 SMLCV ECSV

rep

cp

Q88886.1 TPCTV NP 612220.1BeYDV CAP69808.1ChCDSV P31616.1 TYDV CAA12316.1MSV ABZ79689.1PanSV ABZ03978.1SSV P14985.1 CSMV BAA00833.1MiSV ECSV CAL30139.1ODV CAA57624.1WDV CAL30135.1BDV 80 52 98 14 6 56 44 40 96 74 70 88 48 100 30 34 48 98 54 38 100 98 78 84 66 56 36 100 96 100 54 100 90 90 100 100 52 30 70 62 16 66 0.5 AAO34410.1ACMV CAD58399.1TYLCSV AAG27472.1TYLCCV ABG26017.1 ClerodendrumGMV NP 871717.1TLCJV ABO31248.1TLCNDV CAM58876.1CLCRV AAF75534.1TLCYV 22073996TLCSV CAD62698.1HYVV AAP23255.1MYMV AAU87293.1CpGMV CAI91270.1DolYMV YP 001333684.1CorchorusGMV NP 671458.1 MaMPRV ABC74535.1TSLCV NP 041238.1TGMV CAD67488.1BGYMV AAB87606.1CGMV ABY21699.1SPLCV CAJ43623.1 NSPICMV NP 808805.1SqMLCV YP 001974409.1TYVSV ABQ12147.1PeGMV ABQ08587.1SiGMV NP 040559.1BCTV NP 840045.1BSCTV NP 840037.1BMCTV ABQ12761.1PepCTV BCTIV YP 006993.1SpCTV NP 066183.1HrCTV

Begomovirus

Topocuvirus

& Curtovirus

Mastrevirus

EucmV

Mastrevirus

Begomovirus

Curtovirus

Topocuvirus

Recombinaison analysis:

Potential recombination area

Operating sequence of EucmV



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

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