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

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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  1. Patterns and Distributions of Tallgrass Prairie Probable Viruses of Selected Virus Families 11 July 2009 ASV Vancouver

  2. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Issues in Plant Virus Biodiversity/Ecology • Virus = pathogen? • How much do we know? • Crop viruses = wild viruses? • Everywhere or local? ? ?

  3. dsRNA Approach Advantages • Encapsidation not required • Enrichment logical Disadvantages • DNA viruses ignored • Technically difficult • dsRNA isolation • Conversion to DNA Marilyn Roossinck & Co.

  4. Virus-like Particle Approach Advantages • DNA viruses not ignored • Enrichment logical Disadvantages • Encapsidation required • Low titer viruses?

  5. Patterns of Virus Distribution Limited Cosmopolitan “Other” Diverse ??

  6. 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

  7. 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

  8. “Other” Class--Examples TGP Oryzaviruses? Pararetroviruses Bacteriophages “Other” ??

  9. 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

  10. 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

  11. 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)

  12. 20 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

  13. 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

  14. Comoviridae 05TGP00448 Vernonia baldwinii TGP Nepovirus 1 2.3 05TGP00396 Vernonia baldwinii TGP Fabavirus 10.5 05TGP00183 Desmodium paniculatum Bean pod mottle virus 0.3 variousTGP Comovirid 1

  15. TGP Comovirid 1 RNA 1 PP1 RNA 2 PP2 C-Rich P 352 234 Kimberly Roewe

  16. TGP Comovirid 1: Plant Distribution Asclepias viridis Juncus torreyi Panicum virgatum Ruellia humilis Vernonia baldwinii Euphorbia marginata

  17. 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

  18. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Summary: Known Viruses • How much do we know? 06TGP01002 Poa compressa Oat necrotic mottle virus 18.9 05TGP00030 Galium circaezans Oat necrotic mottle virus 0.3 05TGP00183 Desmodium paniculatum Bean pod mottle virus 0.3 05TGP00421 Rosa carolina Rose dwarf associated virus 1.8 X ? ?

  19. 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

  20. 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

  21. Summary: Distribution ? • 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

  22. Speculation Preserve Adjacent Ecosystem “Tolerant” Host

  23. 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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