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Patterns and Distributions of Tallgrass Prairie Probable Viruses of Selected Virus Families. 11 July 2009 ASV Vancouver. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. ?. Issues in Plant Virus Biodiversity/Ecology.

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Patterns and Distributions of Tallgrass Prairie Probable Viruses of Selected Virus Families

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Patterns and Distributions of Tallgrass Prairie Probable Viruses of Selected Virus Families

11 July 2009 ASV Vancouver


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Issues in Plant Virus Biodiversity/Ecology

  • Virus = pathogen?

  • How much do we know?

  • Crop viruses = wild viruses?

  • Everywhere or local?

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?


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dsRNA Approach

Advantages

  • Encapsidation not required

  • Enrichment logical

Disadvantages

  • DNA viruses ignored

  • Technically difficult

    • dsRNA isolation

    • Conversion to DNA

Marilyn Roossinck & Co.


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Virus-like Particle Approach

Advantages

  • DNA viruses not ignored

  • Enrichment logical

Disadvantages

  • Encapsidation required

  • Low titer viruses?


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Patterns of Virus Distribution

Limited

Cosmopolitan

“Other”

Diverse

??


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Diverse Class

  • Multiple plant species

  • Multiple virus species

  • Approximate virus-plant species mapping

  • Exceptions to exclusive mapping

  • Taxa represented include viruses of fungi and plants

Diverse

Chrysoviruses

Endornaviruses

Totiviruses

Totivirids

Partitiviruses


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Limited Class--Characteristics

  • Single (or few) plant species

  • Single virus species

  • Titers vary

  • “Specialist” situation

Limited

  • Flexiviridae

    • Ambrosia associated virus 1

    • TGP Allexivirus 1

  • Closteroviridae

  • Luteoviridae

  • Rhabdoviridae

  • Potyviridae


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“Other” Class--Examples

TGP Oryzaviruses?

Pararetroviruses

Bacteriophages

“Other”

??


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Cosmopolitan Class

  • Multiple plant species

  • “Generalist” situation

  • Single virus species

  • High titer in one or a few plant species

  • Lower titer in others

Cosmopolitan

TGP Sobemovirus 1

Asclepias asymptomatic virus

TGP Comovirid 1

TGP Tobamovirus 1

TGP Panicovirus 1

TGP Carmovirus 1


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TGP Sobemovirus

% total reads

0.2

0.7

1.2

1.6

0.3

3.1

0.4

0.2

65.5

0.2

Host species

Physalis pumila

Medicago lupulina

Quercus marilandica

Quercus marilandica

Quercus stellata

Quercus macrocarpa

Bromus arvensis

Melilotus officinalis

Cirsium undulatum

Sorghastrum nutans


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Asclepias asymptomatic virus (AsAV)

Other Sampled AsAV Positive Species

Perideridia americana (1/1)

Asclepias sullivantii (1/5)

Asclepias tuberosa (1/6)

Asclepias verticillata (2/4)

Asplenium rhizophyllum (1/1)

Ambrosia bidentata (4/17)

Ambrosia trifida (1/3)

Euthamia gymnospermoides (1/1)

Evax prolifera (1/1)

Verbesina virginica (1/2)

Cyperus acuminatus (1/1)

Croton monanthogynus (1/1)

Euphorbia marginata (8/9)*

Acalypha gracilens (1/1)

Amorpha fruticosa (1/1)

Desmanthus illinoensis (1/1)

Lespedeza cuneata (1/3)

Mimosa quadrivalvis (1/1)

Quercus marilandica (1/9)

Lythrum alatum (1/2)

Callirhoe alcaeoides (1/2)

Calylophus serrulatus (1/2)

Ophioglossum engelmannii (1/3)

Dichanthelium oligosanthes (3/22)

Setaria parviflora (3/12)

Cephalanthus occidentalis (1/3)

Smilax bona-nox (1/1)

Solanum rostratum (1/1)

*most outside TPP

Repeated Sampling Targeted Species

Ruellia humilis (9/81)

Asclepias viridis (45/84)

Ambrosia psilostachya (18/79)

Vernonia baldwinii (8/75)

Panicum virgatum (10/81)

Sorghastrum nutans (10/79)

Plant Families (mulitple positives)

Asclepiadaceae (49/102)

Asteraceae (34/288)

Poaceae (26/330)

Acanthaceae (9/89)

Fabaceae (4/81)


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Distributions: spatial Tymovirus

= PCR-positive

= PCR-negative

8 9 10 11 12 13 23 24 25 27 29 32 31 33 35 36 39 40 49

15

10

5

Distance (m)

0

-15

-10

-5

0

5

10

15

20

-5

-10

-15

Rick Nelson

Distance (m)

Byoung Eun Min


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In planta Distribution of AsAV1

Percentage Tymovirus Content of E. marginata VLP-VNA

Plant

07JH012

07JH013

07JH014

07JH015

07JH016

07JH017

07JH020

07JH021

All plants

“Buds”

0.2

3.1

0.5

0.7

0

0

0.2

0.4

Flowers

15.3

0.3

0.8

1.0

0

0.5

0

3.5

Lower leaves

0.5

15.6

0.5

0

7.6

0

4.0

Upper leaves

1.0

2.2

0.3

0

0.4

0.5

Total

4.6

6.4

0.7

0.6

0

0.1

1.9

0.2

1.9

Numbers are the percentage of reads that were sequences of AsAV1. Reads per sample ranged from 382 to 2904. No entry was made for samples that were not analyzed

Jennifer Hackett


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Comoviridae

05TGP00448 Vernonia baldwinii TGP Nepovirus 1 2.3

05TGP00396 Vernonia baldwinii TGP Fabavirus 10.5

05TGP00183Desmodium paniculatumBean pod mottle virus 0.3

variousTGP Comovirid 1


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TGP Comovirid 1

RNA 1

PP1

RNA 2

PP2

C-Rich P

352

234

Kimberly Roewe


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TGP Comovirid 1: Plant Distribution

Asclepias viridis

Juncus torreyi

Panicum virgatum

Ruellia humilis

Vernonia baldwinii

Euphorbia marginata


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TGP Tobamovirus 1

% of reads

94.8

74.7

0.4

3.3

5.2

Passifloraceae

Asteraceae

Poaceae

Salicaceae

Passiflora incarnata (VNA)

Passiflora incarnata (dsRNA)

Vernonia baldwinii

Leersia virginica

Salix caroliniana

MP

CP

RdRP

MT-Hel

CR

Tobamovirus RNA

Nicole Cabalo


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Summary: Known Viruses

  • How much do we know?

06TGP01002 Poa compressa Oat necrotic mottle virus18.9

05TGP00030 Galium circaezansOat necrotic mottle virus 0.3

05TGP00183Desmodium paniculatumBean pod mottle virus 0.3

05TGP00421Rosa carolinaRose dwarf associated virus 1.8

X

?

?


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Summary: Uniqueness of Viruses

  • Crop viruses = wild viruses?

    • Extra RNA2 ORF in TGP Comovirid 1

    • Additional ORF in TGP Tobamovirus 1

    • Fused ORFs 1 and 2 in AAV2 Badnavirus 1

    • Novel 3’ ORF in AAV1Flexivirid 1

X

1Muthukumar et al (2008) Virus Res. 149:169-173


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Summary: Pathogens?

  • Virus = pathogen?

    • Few plants with noticeable symptoms (Palmer & Co.)

    • AsAV on milkweed vs. N. benthamiana (Min, Nelson & Co.)

    • Subtle effects on fitness and life history possible


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Summary: Distribution

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  • Everywhere or local?

    • Cosmopolitan type characteristics:

      • High accumulation in one plant species

      • Low accumulation in a diversity of other plant species

    • Obvious symptoms are rare

    • Previously known viruses rare on TPP


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Speculation

Preserve

Adjacent Ecosystem

“Tolerant”

Host


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PVBE Team

Marilyn Roossinck

Michael Palmer

Rick Nelson

Bruce Roe

Kay Scheets

Adam Zlotnick

Jonathan Wren

Jeanmarie Verchot-Lubicz

Kelly Craven

Andrew Doust

Akhtar Ali

Olga Blinkova

Tracy Feldman

Byoung Eun Min

Nikki Charlton

Vijay Muthukumar

Veenita Grover

Vaskar Thapa

Graham Wiley

Devinka Bamunusinghe

Guoan Shen

Judy Zhang

Yan Song

Shashank Bhide

And many others: Marlee Pierce, Dan McGlinn, Fumiko Shirakura, Peter Earls, Hua Weng,Tao Ding,Drew Porter, Will Heise, Minh Ngo, Jennifer Hackett, Alexandra Kondos, Tsuyoshi Asako, Will Lowry (Faculty, Postdoctorals, Graduate Students, Staff, Undergraduate Students)


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