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Simmons HE, Prendeville HR, Dunham JP, Ferrari MJ, Earnest JD, Pilson D, Munkvold GP, Holmes EC, Stephenson AG. Transgenic Virus Resistance in Crop-Wild Cucurbita pepo Does Not Prevent Vertical Transmission of Zucchini yellow mosaic virus. Plant Dis 2015; 99:1616-1621. [PMID: 30695961 DOI: 10.1094/pdis-10-14-1062-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) is an economically important pathogen of cucurbits that is transmitted both horizontally and vertically. Although ZYMV is seed-transmitted in Cucurbita pepo, the potential for seed transmission in virus-resistant transgenic cultivars is not known. We crossed and backcrossed a transgenic squash cultivar with wild C. pepo, and determined whether seed-to-seedling transmission of ZYMV was possible in seeds harvested from transgenic backcrossed C. pepo. We then compared these transmission rates to those of non-transgenic (backcrossed and wild) C. pepo. The overall seed-to-seedling transmission rate in ZYMV was similar to those found in previous studies (1.37%), with no significant difference between transgenic backcrossed (2.48%) and non-transgenic (1.03%) backcrossed and wild squash. Fewer transgenic backcrossed plants had symptom development (7%) in comparison with all non-transgenic plants (26%) and may be instrumental in preventing yield reduction due to ZYMV. Our study shows that ZYMV is seed transmitted in transgenic backcrossed squash, which may affect the spread of ZYMV via the movement of ZYMV-infected seeds. Deep genome sequencing of the seed-transmitted viral populations revealed that 23% of the variants found in this study were present in other vertically transmitted ZYMV populations, suggesting that these variants may be necessary for seed transmission or are distributed geographically via seeds.
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Affiliation(s)
- H E Simmons
- Seed Science Center, Iowa State University, Ames, IA 50011; and Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - H R Prendeville
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588; and Department of Biology, University of Virginia, Charlottesville, VA 22904
| | - J P Dunham
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90033
| | - M J Ferrari
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - J D Earnest
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - D Pilson
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588
| | - G P Munkvold
- Seed Science Center, Iowa State University, Ames, IA 50011
| | - E C Holmes
- Department of Biology, The Pennsylvania State University, University Park, PA 16802; and Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Medical School, The University of Sydney, NSW 2006, Australia
| | - A G Stephenson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
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Dunham JP, Simmons HE, Holmes EC, Stephenson AG. Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine. Virus Res 2014; 191:172-179. [PMID: 25107623 PMCID: PMC4176823 DOI: 10.1016/j.virusres.2014.07.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/23/2014] [Accepted: 07/26/2014] [Indexed: 01/04/2023]
Abstract
Determining the extent and structure of intra-host genetic diversity and the magnitude and impact of population bottlenecks is central to understanding the mechanisms of viral evolution. To determine the nature of viral evolution following systemic movement through a plant, we performed deep sequencing of 23 leaves that grew sequentially along a single Cucurbita pepo vine that was infected with zucchini yellow mosaic virus (ZYMV), and on a leaf that grew in on a side branch. Strikingly, of 112 genetic (i.e. sub-consensus) variants observed in the data set as a whole, only 22 were found in multiple leaves. Similarly, only three of the 13 variants present in the inoculating population were found in the subsequent leaves on the vine. Hence, it appears that systemic movement is characterized by sequential population bottlenecks, although not sufficient to reduce the population to a single virion as multiple variants were consistently transmitted between leaves. In addition, the number of variants within a leaf increases as a function of distance from the inoculated (source) leaf, suggesting that the circulating sap may serve as a continual source of virus. Notably, multiple mutational variants were observed in the cylindrical inclusion (CI) protein (known to be involved in both cell-to-cell and systemic movement of the virus) that were present in multiple (19/24) leaf samples. These mutations resulted in a conformational change, suggesting that they might confer a selective advantage in systemic movement within the vine. Overall, these data reveal that bottlenecks occur during systemic movement, that variants circulate in the phloem sap throughout the infection process, and that important conformational changes in CI protein may arise during individual infections.
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Affiliation(s)
- J P Dunham
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - H E Simmons
- Seed Science Center, Iowa State University, Ames, IA 50011, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - E C Holmes
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Marie Bashir Institute for Emerging Diseases & Biosecurity, Charles Perkins Centre, School of Biological Sciences and Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - A G Stephenson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Simmons HE, Dunham JP, Zinn KE, Munkvold GP, Holmes EC, Stephenson AG. Zucchini yellow mosaic virus (ZYMV, Potyvirus): vertical transmission, seed infection and cryptic infections. Virus Res 2013; 176:259-64. [PMID: 23845301 PMCID: PMC3774540 DOI: 10.1016/j.virusres.2013.06.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 12/31/2022]
Abstract
The role played by seed transmission in the evolution and epidemiology of viral crop pathogens remains unclear. We determined the seed infection and vertical transmission rates of zucchini yellow mosaic virus (ZYMV), in addition to undertaking Illumina sequencing of nine vertically transmitted ZYMV populations. We previously determined the seed-to-seedling transmission rate of ZYMV in Cucurbita pepo ssp. texana (a wild gourd) to be 1.6%, and herein observed a similar rate (1.8%) in the subsequent generation. We also observed that the seed infection rate is substantially higher (21.9%) than the seed-to-seedling transmission rate, suggesting that a major population bottleneck occurs during seed germination and seedling growth. In contrast, that two thirds of the variants present in the horizontally transmitted inoculant population were also present in the vertically transmitted populations implies that the bottleneck at vertical transmission may not be particularly severe. Strikingly, all of the vertically infected plants were symptomless in contrast to those infected horizontally, suggesting that vertical infection may be cryptic. Although no known virulence determining mutations were observed in the vertically infected samples, the 5' untranslated region was highly variable, with at least 26 different major haplotypes in this region compared to the two major haplotypes observed in the horizontally transmitted population. That the regions necessary for vector transmission are retained in the vertically infected populations, combined with the cryptic nature of vertical infection, suggests that seed transmission may be a significant contributor to the spread of ZYMV.
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Affiliation(s)
- H E Simmons
- Seed Science Center, Iowa State University, Ames, IA 50011, USA.
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Simmons HE, Dunham JP, Stack JC, Dickins BJA, Pagán I, Holmes EC, Stephenson AG. Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus. J Gen Virol 2012; 93:1831-1840. [PMID: 22592263 DOI: 10.1099/vir.0.042622-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The genetic diversity present in populations of RNA viruses is likely to be strongly modulated by aspects of their life history, including mode of transmission. However, how transmission mode shapes patterns of intra- and inter-host genetic diversity, particularly when acting in combination with de novo mutation, population bottlenecks and the selection of advantageous mutations, is poorly understood. To address these issues, this study performed ultradeep sequencing of zucchini yellow mosaic virus in a wild gourd, Cucurbita pepo ssp. texana, under two infection conditions: aphid vectored and mechanically inoculated, achieving a mean coverage of approximately 10 ,000×. It was shown that mutations persisted during inter-host transmission events in both the aphid vectored and mechanically inoculated populations, suggesting that the vector-imposed transmission bottleneck is not as extreme as previously supposed. Similarly, mutations were found to persist within individual hosts, arguing against strong systemic bottlenecks. Strikingly, mutations were seen to go to fixation in the aphid-vectored plants, suggestive of a major fitness advantage, but remained at low frequency in the mechanically inoculated plants. Overall, this study highlights the utility of ultradeep sequencing in providing high-resolution data capable of revealing the nature of virus evolution, particularly as the full spectrum of genetic diversity within a population may not be uncovered without sequence coverage of at least 2500-fold.
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Affiliation(s)
- H E Simmons
- Seed Science Center, Iowa State University, Ames, IA 50011, USA.,Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - J P Dunham
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - J C Stack
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - B J A Dickins
- The Huck Institutes for the Life Sciences and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - I Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, 28223, Pozuelo de Alarcón (Madrid), Spain.,Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - E C Holmes
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - A G Stephenson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Kelly S, Dunham JP, Murray F, Read S, Donaldson LF, Lawson SN. Spontaneous firing in C-fibers and increased mechanical sensitivity in A-fibers of knee joint-associated mechanoreceptive primary afferent neurones during MIA-induced osteoarthritis in the rat. Osteoarthritis Cartilage 2012; 20:305-13. [PMID: 22285737 DOI: 10.1016/j.joca.2012.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 12/15/2011] [Accepted: 01/01/2012] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) pain mechanisms are poorly understood. We used the monosodium iodoacetate (MIA) model of knee OA to characterize changes in excitability during the course of OA in different classes of mechanosensitive afferents projecting to joint-associated tissues, and examine whether these afferent responses and pain behavior are correlated. METHODS Rats were injected intra-articularly with MIA (1mg in 50 μl). Hind-limb weight bearing was studied 3 (MIA3) and 14 (MIA14) days after MIA, followed by deep anesthesia and teased-nerve-fiber recordings. Spontaneous activity (SA) and mechanically evoked responses of A- and C-mechanosensitive fibers (AM and CM respectively, probably nociceptive) innervating tissues associated with the ipsilateral knee joint were examined. RESULTS MIA3 and MIA14 rats exhibited reduced ipsilateral weight bearing. SA (>0.02 impulses/s) occurred in ∼50% of CMs from MIA rats vs 0% in normals. SA firing rates in CMs were significantly higher than normal; decreased weight bearing was correlated with increased CM SA rates. Neither percentages of AMs with SA (20%) nor their firing rates (0-0.01 impulses/s) significantly increased after MIA. In contrast, in MIA rats AMs, but not CMs, exhibited decreased mechanical thresholds and increased firing rates in response to suprathreshold mechanical stimulation. CONCLUSIONS These findings of increased SA firing rate in CMs but not AMs and increased mechanical sensitivity of AMs, but not CMs, have not previously been reported. These are two distinct important physiological mechanisms that may underpin spontaneous pain (CMs) and stimulus-evoked pain (AMs) in OA. Our data contribute to a mechanism-based understanding of OA pain.
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Affiliation(s)
- S Kelly
- School of Physiology and Pharmacology, Medical Sciences Building, University of Bristol, BS8 1TD, UK
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Sze SH, Dunham JP, Carey B, Chang PL, Li F, Edman RM, Fjeldsted C, Scott MJ, Nuzhdin SV, Tarone AM. A de novo transcriptome assembly of Lucilia sericata (Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms and transcript expression estimates. Insect Mol Biol 2012; 21:205-221. [PMID: 22283785 DOI: 10.1111/j.1365-2583.2011.01127.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The blow fly Lucilia sericata (Diptera: Calliphoridae) (Meigen) is a nonmodel organism with no reference genome that is associated with numerous areas of research spanning the ecological, evolutionary, medical, veterinary and forensic sciences. To facilitate scientific discovery in this species, the transcriptome was assembled from more than six billion bases of Illumina and twenty-one million bases of 454 sequence derived from embryonic, larval, pupal, adult and larval salivary gland libraries. The assembly was carried out in a manner that enabled identification of putative single nucleotide polymorphisms (SNPs) and alternative splices, and that provided expression estimates for various life history stages and for salivary tissue. The assembled transcriptome was also used to identify transcribed transposable elements in L. sericata. The results of this study will enable blow fly biologists, dipterists and comparative genomicists to more rapidly develop and test molecular and genetic hypotheses, especially those regarding blow fly development and salivary gland biology.
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Affiliation(s)
- S-H Sze
- Department of Computer Science and Engineering, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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