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Wang X, Lai J, Hu H, Yang J, Zang K, Zhao F, Zeng G, Liao Q, Gu Z, Du Z. Infection of Nigrospora nonsegmented RNA Virus 1 Has Important Biological Impacts on a Fungal Host. Viruses 2022; 14:v14040795. [PMID: 35458525 PMCID: PMC9029208 DOI: 10.3390/v14040795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Nigrospora nonsegmented RNA virus 1 (NoNRV1) has been reported previously in the fungus Nigrospora oryzae, but its biological effects on its host are unknown. In this work, we isolated a strain 9-1 of N. oryzae from a chrysanthemum leaf and identified NoNRV1 infection in the isolated strain. The genome sequence of NoNRV1 identified here is highly homologous to that of the isolate HN-21 of NoNRV1 previously reported; thus, we tentatively designated the newly identified NoNRV1 as NoNRV1-ZJ. Drug treatment with Ribavirin successfully removed NoNRV1-ZJ from the strain 9-1, which provided us with an ideal control to determine the biological impacts of NoNRV1 infection on host fungi. By comparing the virus-carrying (9-1) and virus-cured (9-1C) strains, our results indicated that infection with NoNRV1 promoted the pigmentation of the host cells, while it had no discernable effects on host growth on potato dextrose agar plates when subjected to osmotic or oxidative stress. Interestingly, we observed inhibitory impacts of virus infection on the thermotolerance of N. oryzae and the pathogenicity of the host fungus in cotton leaves. Collectively, our work provides clear evidence of the biological relevance of NoNRV1 infection in N. oryzae, including pigmentation, hypovirulence, and thermotolerance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhouhang Gu
- Correspondence: (Z.G.); (Z.D.); Tel.: +86-571-8684-3195 (Z.D.)
| | - Zhiyou Du
- Correspondence: (Z.G.); (Z.D.); Tel.: +86-571-8684-3195 (Z.D.)
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Wu CF, Aoki N, Takeshita N, Fukuhara T, Chiura HX, Arie T, Kotta-Loizou I, Okada R, Komatsu K, Moriyama H. Unique Terminal Regions and Specific Deletions of the Segmented Double-Stranded RNA Genome of Alternaria Alternata Virus 1, in the Proposed Family Alternaviridae. Front Microbiol 2021; 12:773062. [PMID: 34745080 PMCID: PMC8570381 DOI: 10.3389/fmicb.2021.773062] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Alternaria alternata virus 1 (AaV1) has been identified in the saprophytic fungus Alternaria alternata strain EGS 35-193. AaV1 has four genomic double-stranded (ds)RNA segments (dsRNA1-4) packaged in isometric particles. The 3' end of each coding strand is polyadenylated (36-50nt), but the presence of a cap structure at each 5' end has not previously been investigated. Here, we have characterized the AaV1 genome and found that it has unique features among the mycoviruses. We confirmed the existence of cap structures on the 5' ends of the AaV1 genomic dsRNAs using RNA dot blots with anti-cap antibodies and the oligo-capping method. Polyclonal antibodies against purified AaV1 particles specifically bound to an 82kDa protein, suggesting that this protein is the major capsid component. Subsequent Edman degradation indicated that the AaV1 dsRNA3 segment encodes the major coat protein. Two kinds of defective AaV1 dsRNA2, which is 2,794bp (844 aa) in length when intact, appeared in EGS 35-193 during subculturing, as confirmed by RT-PCR and northern hybridization. Sequence analysis revealed that one of the two defective dsRNA2s contained a 231bp deletion, while the other carried both the 231bp deletion and an additional 465bp deletion in the open reading frame. Both deletions occurred in-frame, resulting in predicted proteins of 767 aa and 612 aa. The fungal isolates carrying virions with the defective dsRNA2s showed impaired growth and abnormal pigmentation. To our best knowledge, AaV1 is the first dsRNA virus to be identified with both 5' cap and 3'poly(A) structures on its genomic segments, as well as the specific deletions of dsRNA2.
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Affiliation(s)
- Chien-Fu Wu
- Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Nanako Aoki
- Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Naoki Takeshita
- Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Hiroshi X Chiura
- Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Ryo Okada
- Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Japan
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Roossinck MJ. Evolutionary and ecological links between plant and fungal viruses. THE NEW PHYTOLOGIST 2019; 221:86-92. [PMID: 30084143 DOI: 10.1111/nph.15364] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 86 I. Introduction 86 II. Lineages shared by plant and fungal viruses 87 III. Virus transmission between plants and fungi 90 IV. Additional plant virus families identified in fungi by metagenomics 91 Acknowledgements 91 References 91 SUMMARY: Plants and microorganisms have been interacting in both positive and negative ways for millions of years. They are also frequently infected with viruses that can have positive or negative impacts. A majority of virus families with members that infect fungi have counterparts that infect plants, and in some cases the phylogenetic analyses of these virus families indicate transmission between the plant and fungal kingdoms. These similarities reflect the host relationships; fungi are evolutionarily more closely related to animals than to plants but share very few viral signatures with animal viruses. The details of several of these interactions are described, and the evolutionary implications of viral cross-kingdom interactions and horizontal gene transfer are proposed.
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Affiliation(s)
- Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
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Pandey B, Naidu RA, Grove GG. Detection and analysis of mycovirus-related RNA viruses from grape powdery mildew fungus Erysiphe necator. Arch Virol 2018; 163:1019-1030. [PMID: 29356991 DOI: 10.1007/s00705-018-3714-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
Abstract
The fungus, Erysiphe necator Schw., is an important plant pathogen causing powdery mildew disease in grapevines worldwide. In this study, high-throughput sequencing of double-stranded RNA extracted from the fungal tissue combined with bioinformatics was used to examine mycovirus-related sequences associated with E. necator. The results showed the presence of eight mycovirus-related sequences. Five of these sequences representing three new mycoviruses showed alignment with sequences of viruses classified in the genus Alphapartitivirus in the family Partitiviridae. Another three sequences representing three new mycoviruses showed similarity to classifiable members of the genus Mitovirus in the family Narnaviridae. These mycovirus isolates were named Erysiphe necator partitivirus 1, 2, and 3 (EnPV 1-3) and Erysiphe necator mitovirus 1, 2, and 3 (EnMV 1-3) reflecting their E. necator origin and their phylogenetic affiliation with other mycoviruses.
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Affiliation(s)
- B Pandey
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, USA. .,Department of Plant Pathology, North Dakota State University, 306 Walster Hall, Fargo, ND, 58102, USA.
| | - R A Naidu
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, USA
| | - G G Grove
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, USA
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Chiba S, Lin YH, Kondo H, Kanematsu S, Suzuki N. A novel betapartitivirus RnPV6 from Rosellinia necatrix tolerates host RNA silencing but is interfered by its defective RNAs. Virus Res 2015; 219:62-72. [PMID: 26494168 DOI: 10.1016/j.virusres.2015.10.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/10/2015] [Accepted: 10/14/2015] [Indexed: 12/17/2022]
Abstract
The family Partitiviridae comprises of five genera with bi-segmented dsRNA genomes that accommodate members infecting plants, fungi or protists. All partitiviruses with only a few exceptions cause asymptomatic infections. We report the characterization of a novel betapartitivirus termed Rosellinia necatrix partitivirus 6 (RnPV6) from a field isolate of a plant pathogenic fungus, white root rot fungus. RnPV6 has typical partitivirus features: dsRNA1 and dsRNA2 are 2462 and 2499bps in length encoding RNA-dependent RNA polymerase and capsid protein. Purified particles are spherical with a diameter of 30nm. Taking advantage of infectivity as virions, RnPV6 was introduced into a model filamentous fungal host, chestnut blight fungus to investigate virus/host interactions. Unlike other partitiviruses tested previously, RnPV6 induced profound phenotypic alterations with symptoms characterized by a reduced growth rate and enhanced pigmentation and was tolerant to host RNA silencing. In addition, a variety of defective RNAs derived from dsRNA1 appear after virion transfection. These sub-viral RNAs were shown to interfere with RnPV6 replication, at least for that of cognate segment dsRNA1. Presence of these sub-viral elements resulted in reduced symptom expression by RnPV6, suggesting their nature as defective-interfering RNAs. The features of RnPV6 are similar to but distinct from those of a previously reported alphapartitivirus, Rosellinia necatrix partitivirus 2 that is susceptible to RNA silencing.
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Affiliation(s)
- Sotaro Chiba
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
| | - Yu-Hsin Lin
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
| | - Satoko Kanematsu
- Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Morioka, Iwate 020-0123, Japan.
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.
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Discovery and molecular characterization of a new cryptovirus dsRNA genome from Japanese persimmon through conventional cloning and high-throughput sequencing. Virus Genes 2014; 50:160-4. [PMID: 25315633 DOI: 10.1007/s11262-014-1127-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Abstract
Through the application of next generation sequencing, in synergy with conventional cloning of DOP-PCR fragments, two double-stranded RNA (dsRNA) molecules of about 1.5 kbp in size were isolated from leaf tissue of a Japanese persimmon (accession SSPI) from Apulia (southern Italy) showing veinlets necrosis. High-throughput sequencing allowed whole genome sequence assembly, yielding a 1,577 and a 1,491 bp contigs identified as dsRNA-1 and dsRNA-2 of a previously undescribed virus, provisionally named as Persimmon cryptic virus (PeCV). In silico analysis showed that both dsRNA fragments were monocistronic and comprised the RNA-dependent RNA polymerase (RdRp) and the capsid protein (CP) genes, respectively. Phylogenetic reconstruction revealed a close relationship of these dsRNAs with those of cryptoviruses described in woody and herbaceous hosts, recently gathered in genus Deltapartitivirus. Virus-specific primers for RT-PCR, designed in the CP cistron, detected viral RNAs also in symptomless persimmon trees sampled from the same geographical area of SSPI, thus proving that PeCV infection may be fairly common and presumably latent.
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Detection and characterization of a novel Gammapartitivirus in the phytopathogenic fungus Colletotrichum acutatum strain HNZJ001. Virus Res 2014; 190:104-9. [DOI: 10.1016/j.virusres.2014.05.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 10/25/2022]
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Peyambari M, Habibi MK, Fotouhifar KB, Dizadji A, Roossinck MJ. Molecular Characterization of a Novel Putative Partitivirus Infecting Cytospora sacchari, a Plant Pathogenic Fungus. THE PLANT PATHOLOGY JOURNAL 2014; 30:151-8. [PMID: 25288997 PMCID: PMC4174853 DOI: 10.5423/ppj.oa.01.2014.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/03/2014] [Accepted: 03/11/2014] [Indexed: 06/01/2023]
Abstract
Three double-stranded RNAs (dsRNAs), approximately 1.85, 1.65 and 1.27 kb in size, were detected in an isolate of Cytospora sacchari from Iran. Partial nucleotide sequence revealed a 1,284 bp segment containing one ORF that potentially encodes a 405 aa protein. This protein contains conserved motifs related to RNA dependent RNA polymerases (RdRp) that showed similarity to RdRps of partitiviruses. The results indicate that these dsRNAs represent a novel Partitivirus that we tentatively designate Cytospora sacchari partitivirus (CsPV). Treatment of the fungal strain by cyclohexamide and also hyphal tip culture had no effect on removing the putative virus. Phylogenetic analysis of putative RdRp of CsPV and other partitiviruses places CsPV as a member of the genus Partitivirus in the family Partitiviridae, and clustering with Aspergillus ochraceous virus 1.
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Affiliation(s)
- Mahtab Peyambari
- Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mina Koohi Habibi
- Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Khalil-Berdi Fotouhifar
- Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Akbar Dizadji
- Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Marilyn J. Roossinck
- The Huck Institutes of the Life Sciences, Center for Infectious Disease Dynamics, Millennium Science Complex, The Pennsylvania State University, University Park, PA 16802, USA
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Abstract
Partitiviruses constitute one of the nine currently recognized families of viruses with encapsidated, double-stranded (ds)RNA genomes. The partitivirus genome is bisegmented, and each genome segment is packaged inside a separate viral capsid. Different partitiviruses infect plants, fungi, or protozoa. Recent studies have shed light on the three-dimensional structures of the virions of three representative fungal partitiviruses. These structures include a number of distinctive features, allowing informative comparisons with the structures of dsRNA viruses from other families. The results and comparisons suggest several new conclusions about the functions, assembly, and evolution of these viruses.
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10
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Molecular characterization of five betacryptoviruses infecting four clover species and dill. Arch Virol 2013; 158:1943-52. [DOI: 10.1007/s00705-013-1691-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 03/02/2013] [Indexed: 11/26/2022]
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Liu H, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Peng Y, Yi X, Jiang D. Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages. BMC Evol Biol 2012; 12:91. [PMID: 22716092 PMCID: PMC3483285 DOI: 10.1186/1471-2148-12-91] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 06/06/2012] [Indexed: 12/12/2022] Open
Abstract
Background Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses. Results In this study, we report the molecular properties of two novel dsRNA mycoviruses that were isolated from a field strain of Sclerotinia sclerotiorum, Sunf-M: one is a large monopartite virus representing a distinct evolutionary lineage of dsRNA viruses; the other is a new member of the family Partitiviridae. Comprehensive phylogenetic analysis and genome comparison revealed that there are at least ten monopartite, three bipartite, one tripartite and three quadripartite lineages in the known dsRNA mycoviruses and that the multipartite lineages have possibly evolved from different monopartite dsRNA viruses. Moreover, we found that homologs of the S7 Domain, characteristic of members of the genus phytoreovirus in family Reoviridae are widely distributed in diverse dsRNA viral lineages, including chrysoviruses, endornaviruses and some unclassified dsRNA mycoviruses. We further provided evidence that multiple HGT events may have occurred among these dsRNA viruses from different families. Conclusions Our study provides an insight into the phylogeny and evolution of mycovirus-related dsRNA viruses and reveals that the occurrence of HGT between different virus species and the development of multipartite genomes during evolution are important macroevolutionary mechanisms in dsRNA viruses.
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Affiliation(s)
- Huiquan Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
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Vainio EJ, Hakanpää J, Dai YC, Hansen E, Korhonen K, Hantula J. Species of Heterobasidion host a diverse pool of partitiviruses with global distribution and interspecies transmission. Fungal Biol 2011; 115:1234-43. [DOI: 10.1016/j.funbio.2011.08.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/22/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
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Ziegler A, Matoušek J, Steger G, Schubert J. Complete sequence of a cryptic virus from hemp (Cannabis sativa). Arch Virol 2011; 157:383-5. [DOI: 10.1007/s00705-011-1168-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 10/29/2011] [Indexed: 11/29/2022]
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Abstract
The vast majority of well-characterized eukaryotic viruses are those that cause acute or chronic infections in humans and domestic plants and animals. However, asymptomatic persistent viruses have been described in animals, and are thought to be sources for emerging acute viruses. Although not previously described in these terms, there are also many viruses of plants that maintain a persistent lifestyle. They have been largely ignored because they do not generally cause disease. The persistent viruses in plants belong to the family Partitiviridae or the genus Endornavirus. These groups also have members that infect fungi. Phylogenetic analysis of the partitivirus RNA-dependent RNA polymerase genes suggests that these viruses have been transmitted between plants and fungi. Additional families of viruses traditionally thought to be fungal viruses are also found frequently in plants, and may represent a similar scenario of persistent lifestyles, and some acute or chronic viruses of crop plants may maintain a persistent lifestyle in wild plants. Persistent, chronic and acute lifestyles of plant viruses are contrasted from both a functional and evolutionary perspective, and the potential role of these lifestyles in host evolution is discussed.
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Affiliation(s)
- Marilyn J Roossinck
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA.
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