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Lowder SR, Neill TM, Peetz AB, Miles TD, Moyer MM, Oliver C, Stergiopoulos I, Ding S, Mahaffee WF. A Rapid Glove-Based Inoculum Sampling Technique to Monitor Erysiphe necator in Commercial Vineyards. Plant Dis 2023; 107:3096-3105. [PMID: 37079020 DOI: 10.1094/pdis-02-23-0216-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Information on the presence and severity of grape powdery mildew (GPM), caused by Erysiphe necator, has long been used to guide management decisions. While recent advances in the available molecular diagnostic assays and particle samplers have made monitoring easier, there is still a need for more efficient field collection of E. necator. The use of vineyard worker gloves worn during canopy manipulation as a sampler (glove swab) of E. necator was compared with samples identified by visual assessment with subsequent molecular confirmation (leaf swabs) and airborne spore samples collected by rotating-arm impaction traps (impaction traps). Samples from United States commercial vineyards in Oregon, Washington, and California were analyzed using two TaqMan qPCR assays targeting the internal transcribed spacer regions or cytochrome b gene of E. necator. Based on qPCR assays, visual disease assessments misidentified GPM up to 59% of the time with a higher frequency of misidentification occurring earlier in the growing season. Comparison of the aggregated leaf swab results for a row (n = 915) to the row's corresponding glove swab had 60% agreement. The latent class analysis (LCA) indicated that glove swabs were more sensitive than leaf swabs in detecting E. necator presence. The impaction trap results had 77% agreement to glove swabs (n = 206) taken from the same blocks. The LCAs estimated that the glove swabs and impaction trap samplers varied each year in which was more sensitive for detection. This likely indicates that these methods have similar levels of uncertainty and provide equivalent information. Additionally, all samplers, once E. necator was detected, were similarly sensitive and specific for detection of the A-143 resistance allele. Together, these results suggest that glove swabs are an effective sampling method for monitoring the presence of E. necator and, subsequently, the G143A amino acid substitution associated with resistance to quinone outside inhibitor fungicides in vineyards. Glove swabs could reduce sampling costs due to the lack of need for specialized equipment and time required for swab collection and processing.
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Affiliation(s)
- Sarah R Lowder
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Tara M Neill
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| | - Amy B Peetz
- Revolution Crop Consultants, LLC, Albany, OR 97321
| | - Timothy D Miles
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48824
| | - Michelle M Moyer
- Department of Viticulture and Enology, Washington State University, Prosser, WA 99350
| | | | | | - Shunping Ding
- Department of Wine and Viticulture, California Polytechnic State University, San Luis Obispo, CA 93407
| | - Walter F Mahaffee
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
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Wram CL, Hesse CN, Wasala SK, Howe DK, Peetz AB, Denver DR, Humphreys-Pereira D, Zasada IA. Genome Announcement: The Draft Genomes of Two Radopholus similis populations from Costa Rica. J Nematol 2019; 51:e2019-52. [PMID: 34179798 PMCID: PMC6909021 DOI: 10.21307/jofnem-2019-052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Radopholus similis is an economically important pest of both banana and citrus in tropical regions. Here we present draft genomes from two populations of R. similis from Costa Rica that were created and assembled using short read libraries from Illumina HiSeq technology.
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Affiliation(s)
- Catherine L Wram
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Cedar N Hesse
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97331
| | - Sulochana K Wasala
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97331
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Danny Humphreys-Pereira
- Laboratorio de Nematología, Centro de Investigación en Protección de Cultivos, Escuela de Agronomía, Universidad de Costa Rica, San Jose, Costa Rica, 2060
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR 97331
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3
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Wasala SK, Brown AMV, Kang J, Howe DK, Peetz AB, Zasada IA, Denver DR. Variable Abundance and Distribution of Wolbachia and Cardinium Endosymbionts in Plant-Parasitic Nematode Field Populations. Front Microbiol 2019; 10:964. [PMID: 31134014 PMCID: PMC6513877 DOI: 10.3389/fmicb.2019.00964] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/16/2019] [Indexed: 01/10/2023] Open
Abstract
The bacterial endosymbiont Wolbachia interacts with different invertebrate hosts, engaging in diverse symbiotic relationships. Wolbachia is often a reproductive parasite in arthropods, but an obligate mutualist in filarial nematodes. Wolbachia was recently discovered in plant-parasitic nematodes, and, is thus far known in just two genera Pratylenchus and Radopholus, yet the symbiont's function remains unknown. The occurrence of Wolbachia in these economically important plant pests offers an unexplored biocontrol strategy. However, development of Wolbachia-based biocontrol requires an improved understanding of symbiont-host functional interactions and the symbiont's prevalence among nematode field populations. This study used a molecular-genetic approach to assess the prevalence of a Wolbachia lineage (wPpe) in 32 field populations of Pratylenchus penetrans. Populations were examined from eight different plant species in Washington, Oregon, and California. Nematodes were also screened for the endosymbiotic bacterium Cardinium (cPpe) that was recently shown to co-infect P. penetrans. Results identified wPpe in 9/32 and cPpe in 1/32 of P. penetrans field populations analyzed. No co-infection was observed in field populations. Wolbachia was detected in nematodes from 4/8 plant-hosts examined (raspberry, strawberry, clover, and lily), and in all three states surveyed. Cardinium was detected in nematodes from mint in Washington. In the wPpe-infected P. penetrans populations collected from raspberry, the prevalence of wPpe infection ranged from 11 to 58%. This pattern is unlike that in filarial nematodes where Wolbachia is an obligate mutualist and occurs in 100% of the host. Further analysis of wPpe-infected populations revealed female-skewed sex ratios (up to 96%), with the degree of skew positively correlating with wPpe prevalence. Uninfected nematode populations had approximately equal numbers of males and females. Comparisons of 54 wPpe 16S ribosomal RNA sequences revealed high similarity across the geographic isolates, with 45 of 54 isolates being identical at this locus. The complete absence of wPpe among some populations and low prevalence in others suggest that this endosymbiont is not an obligate mutualist of P. penetrans. The observed sex ratio bias in wPpe-infected nematode populations is similar to that observed in arthropods where Wolbachia acts as a reproductive manipulator, raising the question of a similar role in plant-parasitic nematodes.
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Affiliation(s)
- Sulochana K. Wasala
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Amanda M. V. Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Jiwon Kang
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Dana K. Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Amy B. Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, United States
| | - Inga A. Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, United States
| | - Dee R. Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
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Howe DK, Smith M, Tom DM, Brown AM, Peetz AB, Zasada IA, Denver DR. Analysis of nematode-endosymbiont coevolution in the Xiphinema americanum species complex using molecular markers of variable evolutionary rates. NEMATOLOGY 2019. [DOI: 10.1163/15685411-00003233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Bacterial symbioses play important roles in shaping diverse biological processes in nematodes, and serve as targets in nematode biocontrol strategies. Focusing on the Xiphinema americanum species complex, we expanded upon recent research investigating patterns of coevolution between Xiphinema spp. and Xiphinematobacter spp., utilising two symbiont genetic markers of varying evolutionary rates. Phylogenetic analysis of nematode mitochondrial DNA (mtDNA) revealed five strongly supported major clades. Analysis of slow-evolving 16S rDNA in bacterial symbionts resulted in a phylogenetic topology composed of four major clades that grouped taxa highly congruent with the nematode mtDNA topology. A faster evolving protein-coding symbiont gene (nad) provided more phylogenetic resolution with seven well-supported clades, also congruent with the nematode mtDNA tree topology. Our results reinforce recent studies suggesting extensive coevolution between Xiphinema spp. and their vertically transmitted endosymbionts Xiphinematobacter spp. and illustrate the advantages of including genetic markers of varying evolutionary rates in coevolutionary and phylogenetic studies.
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Affiliation(s)
- Dana K. Howe
- 1Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - McKinley Smith
- 1Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Danielle M. Tom
- 1Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Amanda M.V. Brown
- 2Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Amy B. Peetz
- 3USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Inga A. Zasada
- 3USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Dee R. Denver
- 1Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
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Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR. Comparative Genomics of Wolbachia- Cardinium Dual Endosymbiosis in a Plant-Parasitic Nematode. Front Microbiol 2018; 9:2482. [PMID: 30459726 PMCID: PMC6232779 DOI: 10.3389/fmicb.2018.02482] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022] Open
Abstract
Wolbachia and Cardinium are among the most important and widespread of all endosymbionts, occurring in nematodes and more than half of insect and arachnid species, sometimes as coinfections. These symbionts are of significant interest as potential biocontrol agents due to their abilities to cause major effects on host biology and reproduction through cytoplasmic incompatibility, sex ratio distortion, or obligate mutualism. The ecological and metabolic effects of coinfections are not well understood. This study examined a Wolbachia-Cardinium coinfection in the plant-parasitic nematode (PPN), Pratylenchus penetrans, producing the first detailed study of such a coinfection using fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and comparative genomic analysis. Results from FISH and single-nematode PCR showed 123/127 individuals in a focal population carried Cardinium (denoted strain cPpe), and 48% were coinfected with Wolbachia strain wPpe. Both endosymbionts showed dispersed tissue distribution with highest densities in the anterior intestinal walls and gonads. Phylogenomic analyses confirmed an early place of cPpe and long distance from a sister strain in another PPN, Heterodera glycines, supporting a long history of both Cardinium and Wolbachia in PPNs. The genome of cPpe was 1.36 Mbp with 35.8% GC content, 1,131 predicted genes, 41% having no known function, and missing biotin and lipoate synthetic capacity and a plasmid present in other strains, despite having a slightly larger genome compared to other sequenced Cardinium. The larger genome revealed expansions of gene families likely involved in host-cellular interactions. More than 2% of the genes of cPpe and wPpe were identified as candidate horizontally transferred genes, with some of these from eukaryotes, including nematodes. A model of the possible Wolbachia-Cardinium interaction is proposed with possible complementation in function for pathways such as methionine and fatty acid biosynthesis and biotin transport.
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Affiliation(s)
- Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Sulochana K Wasala
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, United States
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, United States
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
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6
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Phillips WS, Howe DK, Brown AMV, Eves-van den Akker S, Dettwyler L, Peetz AB, Denver DR, Zasada IA. The Draft Genome of Globodera ellingtonae. J Nematol 2017; 49:127-128. [PMID: 28706309 PMCID: PMC5507130 DOI: 10.21307/jofnem-2017-054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Indexed: 12/25/2023] Open
Abstract
Globodera ellingtonae is a newly described potato cyst nematode (PCN) found in Idaho, Oregon, and Argentina. Here, we present a genome assembly for G. ellingtonae, a relative of the quarantine nematodes G. pallida and G. rostochiensis, produced using data from Illumina and Pacific Biosciences DNA sequencing technologies.
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Affiliation(s)
- Wendy S Phillips
- USDA-ARS Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, OR 97331
| | - Amanda M V Brown
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, OR 97331
| | | | - Levi Dettwyler
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, OR 97331
| | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, OR 97331
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330
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7
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Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR. Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts. Sci Rep 2016; 6:34955. [PMID: 27734894 PMCID: PMC5062116 DOI: 10.1038/srep34955] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/21/2016] [Indexed: 12/31/2022] Open
Abstract
Wolbachia, one of the most widespread endosymbionts, is a target for biological control of mosquito-borne diseases (malaria and dengue virus), and antibiotic elimination of infectious filarial nematodes. We sequenced and analyzed the genome of a new Wolbachia strain (wPpe) in the plant-parasitic nematode Pratylenchus penetrans. Phylogenomic analyses placed wPpe as the earliest diverging Wolbachia, suggesting two evolutionary invasions into nematodes. The next branches comprised strains in sap-feeding insects, suggesting Wolbachia may have first evolved as a nutritional mutualist. Genome size, protein content, %GC, and repetitive DNA allied wPpe with mutualistic Wolbachia, whereas gene repertoire analyses placed it between parasite (A, B) and mutualist (C, D, F) groups. Conservation of iron metabolism genes across Wolbachia suggests iron homeostasis as a potential factor in its success. This study enhances our understanding of this globally pandemic endosymbiont, highlighting genetic patterns associated with host changes. Combined with future work on this strain, these genomic data could help provide potential new targets for plant-parasitic nematode control.
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Affiliation(s)
- Amanda M V Brown
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Sulochana K Wasala
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Dana K Howe
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330, USA
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330, USA
| | - Dee R Denver
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
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Phillips WS, Brown AMV, Howe DK, Peetz AB, Blok VC, Denver DR, Zasada IA. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. BMC Genomics 2016; 17:706. [PMID: 27595608 PMCID: PMC5011991 DOI: 10.1186/s12864-016-3047-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/27/2016] [Indexed: 01/21/2023] Open
Abstract
Background The evolution of animal mitochondrial (mt) genomes has resulted in a highly conserved structure: a single compact circular chromosome approximately 14 to 20 kb long. Within the last two decades exceptions to this conserved structure, such as the division of the genome into multiple chromosomes, have been reported in a diverse set of metazoans. We report on the two circle multipartite mt genome of a newly described cyst nematode, Globodera ellingtonae. Results The G. ellingtonae mt genome was found to be comprised of two circles, each larger than any other multipartite circular mt chromosome yet reported, and both were larger than the single mt circle of the model nematode Caenorhabditis elegans. The genetic content of the genome was disproportionately divided between the two circles, although they shared a ~6.5 kb non-coding region. The 17.8 kb circle (mtDNA-I) contained ten protein-coding genes and two tRNA genes, whereas the 14.4 kb circle (mtDNA-II) contained two protein-coding genes, 20 tRNA genes and both rRNA genes. Perhaps correlated with this division of genetic content, the copy number of mtDNA-II was more than four-fold that of mtDNA-I in individual nematodes. The difference in copy number increased between second-stage and fourth-stage juveniles. Conclusions The segregation of gene types to different mt circles in G. ellingtonae could provide benefit by localizing gene functional types to independent transcriptional units. This is the first report of both two-circle and several-circle mt genomes within a single genus. The differential copy number associated with this multipartite mt organization could provide a model system for deconstructing mechanisms regulating mtDNA copy number both in somatic cells and during germline development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3047-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wendy S Phillips
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA.
| | - Amanda M V Brown
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Amy B Peetz
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
| | - Vivian C Blok
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, UK
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Inga A Zasada
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
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9
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Affiliation(s)
- Dee R. Denver
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Amanda M. V. Brown
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Dana K. Howe
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Amy B. Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon, United States of America
| | - Inga A. Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon, United States of America
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10
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Peetz AB, Zasada IA. Species-specific diagnostics using a β-1,4-endoglucanase gene for Pratylenchus spp. occurring in the Pacific Northwest of North America. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00003026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A PCR assay was designed and optimised to differentiate fourPratylenchusspecies commonly encountered in soil and root samples from the Pacific Northwest of North America. Species-specific primers were designed to accessions fromPratylenchusspecies deposited in GenBank which encoded aβ-1,4-endoglucanase gene. The optimisedβ-1,4-endoglucanase gene primer sets produced amplicons that were 380, 293, 528 and 364 bp fromP. crenatus,P. neglectus,P. penetransandP. thornei, respectively. Primer sets were tested successfully for functionality and specificity within each of the four species as well as against other species not commonly found in the Pacific Northwest. This method allowed for the identification of juveniles to species, thereby precluding the necessity of the presence of females in a sample for accurate diagnostics. Ultimately, this diagnostic PCR assay could be used as an efficient tool for rapid diagnostics of thesePratylenchusspecies recovered from soil and root samples in any laboratory equipped for PCR.
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Affiliation(s)
- Amy B. Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Inga A. Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
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11
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Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis. Genome Biol Evol 2015; 7:2727-46. [PMID: 26362082 PMCID: PMC4607532 DOI: 10.1093/gbe/evv176] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bacterial mutualists can modulate the biochemical capacity of animals. Highly coevolved nutritional mutualists do this by synthesizing nutrients missing from the host’s diet. Genomics tools have advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (phylum Verrucomicrobia) from the dagger nematode Xiphinema americanum, a migratory ectoparasite of numerous crops that also vectors nepovirus. Previously, this endosymbiont was identified in the gut, ovaries, and eggs, but its role was unknown. We explored the potential role of this symbiont using fluorescence in situ hybridization, genome sequencing, and comparative functional genomics. We report the first genome of an intracellular Verrucomicrobium and the first exclusively intracellular non-Wolbachia nematode symbiont. Results revealed that Xiphinematobacter had a small 0.916-Mb genome with only 817 predicted proteins, resembling genomes of other mutualist endosymbionts. Compared with free-living relatives, conserved proteins were shorter on average, and there was large-scale loss of regulatory pathways. Despite massive gene loss, more genes were retained for biosynthesis of amino acids predicted to be essential to the host. Gene ontology enrichment tests showed enrichment for biosynthesis of arginine, histidine, and aromatic amino acids, as well as thiamine and coenzyme A, diverging from the profiles of relatives Akkermansia muciniphilia (in the human colon), Methylacidiphilum infernorum, and the mutualist Wolbachia from filarial nematodes. Together, these features and the location in the gut suggest that Xiphinematobacter functions as a nutritional mutualist, supplementing essential nutrients that are depleted in the nematode diet. This pattern points to evolutionary convergence with endosymbionts found in sap-feeding insects.
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Affiliation(s)
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | | | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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Peetz AB, Mahaffee WF, Gent DH. Effect of Temperature on Sporulation and Infectivity of Podosphaera macularis on Humulus lupulus. Plant Dis 2009; 93:281-286. [PMID: 30764182 DOI: 10.1094/pdis-93-3-0281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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
Hop powdery mildew, caused by Podosphaera macularis, can result in complete crop loss and requires numerous fungicide applications for effective management. To assess the impact of temperature on the production of infective conidia, 10-day-old sporulating colonies were exposed to 18, 30, 33, 36, 39, and 42°C for 6 h, and then incubated at 18°C for 18 h. Conidia were harvested, inoculated onto hop plants, incubated at 18°C for 10 days, and then lesions/cm2 of leaf area was determined. Disease was significantly reduced at temperatures ≥30°C with a nonlinear response in the production of infective conidia (P < 0.0001). Temperature effects on sporulation of P. macularis were examined using a custom impaction conidia sampler in growth chambers programmed at constant temperatures of 5, 10, 15, 20, 25, 30, and 35°C, or 18°C before and after ramping to 18, 22, 26, 30, 34, and 38°C for 6 h. The effect of constant temperature on sporulation was best described by a nonlinear thermodynamic model (P = 0.0001) with maximal production near 25°C. Exposure to fluctuating temperatures produced a curvilinear response in sporulation (P = 0.0122) with maximum production near 25°C. These data indicate that inoculum availability is reduced when ambient temperature exceeds 30°C and that modeling inoculum availability could help further refine current disease forecasting models.
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Affiliation(s)
- Amy B Peetz
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - Walter F Mahaffee
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Laboratory, and Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - David H Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
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