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Wu X, Simpson SA, Youngblood RC, Liu XF, Scheffler BE, Rinehart TA, Alexander LW, Hulse-Kemp AM. Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea ( Hydrangea macrophylla) and insights into Asterid evolution. Hortic Res 2023; 10:uhad217. [PMID: 38130599 PMCID: PMC10734616 DOI: 10.1093/hr/uhad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/07/2023] [Indexed: 12/23/2023]
Abstract
The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars 'Veitchii' and 'Endless Summer' [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.
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Affiliation(s)
- Xingbo Wu
- Department of Environmental Horticulture, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, United States
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, United States
| | - Xiaofen F Liu
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Timothy A Rinehart
- Crop Production and Protection, USDA-ARS, Beltsville, MD 20705, United States
| | - Lisa W Alexander
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, USDA-ARS, McMinnville, TN 37110, United States
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, United States
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Hatmaker EA, Wadl PA, Rinehart TA, Carroll J, Lane TS, Trigiano RN, Staton ME, Schilling EE. Complete chloroplast genome comparisons for Pityopsis (Asteraceae). PLoS One 2020; 15:e0241391. [PMID: 33370297 PMCID: PMC7769439 DOI: 10.1371/journal.pone.0241391] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/13/2020] [Indexed: 12/03/2022] Open
Abstract
Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.
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Affiliation(s)
- E. Anne Hatmaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Phillip A. Wadl
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, United States of America
| | - Timothy A. Rinehart
- U.S. Department of Agriculture, Agricultural Research Service, Crop Production and Protection, Beltsville, Maryland, United States of America
| | - Jennifer Carroll
- U.S. Department of Agriculture, Agricultural Research Service, Thad Cochran Southern Horticultural Laboratory, Poplarville, Mississippi, United States of America
| | - Thomas S. Lane
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Robert N. Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RNT); (MES); (EES)
| | - Margaret E. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RNT); (MES); (EES)
| | - Edward E. Schilling
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RNT); (MES); (EES)
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Wyman CR, Hadziabdic D, Boggess SL, Rinehart TA, Windham AS, Wadl PA, Trigiano RN. Low Genetic Diversity Suggests the Recent Introduction of Dogwood Powdery Mildew to North America. Plant Dis 2019; 103:2903-2912. [PMID: 31449437 DOI: 10.1094/pdis-01-19-0051-re] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cornus florida (flowering dogwood) is a popular understory tree endemic to the eastern hardwood forests of the United States. In 1996, dogwood powdery mildew caused by Erysiphe pulchra, an obligate biotrophic fungus of large bracted dogwoods, reached epidemic levels throughout the C. florida growing region. In the late 1990s, both sexual and asexual stages of E. pulchra were regularly observed; thereafter, the sexual stage was found less frequently. We examined the genetic diversity and population structure of 167 E. pulchra samples on C. florida leaves using 15 microsatellite loci. Samples were organized into two separate collection zone data sets, separated as eight zones and two zones, for the subsequent analysis of microsatellite allele length data. Clone correction analysis reduced the sample size to 90 multilocus haplotypes. Our study indicated low genetic diversity, a lack of definitive population structure, low genetic distance among multilocus haplotypes, and significant linkage disequilibrium among zones. Evidence of a population bottleneck was also detected. The results of our study indicated a high probability that E. pulchra reproduces predominately via asexual conidia and lend support to the hypothesis that E. pulchra is an exotic pathogen to North America.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Christopher R Wyman
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Timothy A Rinehart
- United States Department of Agriculture, Agriculture Research Service, Crop Production and Protection, Beltsville, MD 20705
| | - Alan S Windham
- Department of Entomology and Plant Pathology, University of Tennessee, Soil, Plant, and Pest Center, 5201 Marchant Drive, Nashville, TN 37211
| | - Phillip A Wadl
- United States Department of Agriculture, Agriculture Research Service, U.S. Vegetable Research, Charleston, SC 29414
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
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Wadl PA, Mack BM, Beltz SB, Moore GG, Baird RE, Rinehart TA, Molnar TJ, Staton ME, Hadziabdic D, Trigiano RN. Development of Genomic Resources for the Powdery Mildew, Erysiphe pulchra. Plant Dis 2019; 103:804-807. [PMID: 30864941 DOI: 10.1094/pdis-05-18-0719-a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 05/23/2023]
Abstract
Powdery mildews (PMs) are important plant pathogens causing widespread damage. Here, we report the first draft genome of Erysiphe pulchra, the causative agent of PM of flowering dogwood, Cornus florida. The assembled genome was 63.5 Mbp and resulted in formation of 19,442 contigs (N50 = 11,686 bp) that contained an estimated 6,860 genes with a genome coverage of 62×. We found 102 candidate secreted effector proteins (CSEPs) in E. pulchra similar to E. necator genes that are potentially involved in disease development. This draft genome is an initial step for understanding the evolutionary history of the PMs and will also provide insight into evolutionary strategies that led to the wide host expansion and environmental adaptations so effectively employed by the PM lineages.
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Affiliation(s)
- Phillip A Wadl
- 1 USDA-ARS, U.S. Vegetable Laboratory, Charleston, SC 29414
| | - Brian M Mack
- 2 USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124
| | - Shannon B Beltz
- 2 USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124
| | - Geromy G Moore
- 2 USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124
| | - Richard E Baird
- 3 Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | | | - Thomas J Molnar
- 5 Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; and
| | - Margaret E Staton
- 6 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Denita Hadziabdic
- 6 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Robert N Trigiano
- 6 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
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Payá-Milans M, Olmstead JW, Nunez G, Rinehart TA, Staton M. Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species. Gigascience 2018; 7:5168871. [PMID: 30418578 PMCID: PMC6275443 DOI: 10.1093/gigascience/giy132] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 04/19/2018] [Accepted: 10/21/2018] [Indexed: 11/12/2022] Open
Abstract
Background The usual analysis of RNA sequencing (RNA-seq) reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-seq data processing and limited information on how their decisions will impact the final outcome. Using both a diploid and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-seq analysis workflow on the recovery of useful processed data available for downstream analysis. Findings At the preprocessing step, we found error correction has a strong influence on de novo assembly but not on mapping results. After trimming, a greater percentage of reads could be used in downstream analysis by selecting gentle quality trimming performed with Skewer instead of strict quality trimming with Trimmomatic. This availability of reads correlated with size, quality, and completeness of de novo assemblies and with number of mapped reads. When selecting a reference genome from a related species to map reads, outcome was significantly improved when using mapping software tolerant of greater sequence divergence, such as Stampy or GSNAP. Conclusions The selection of bioinformatic software tools for RNA-seq data analysis can maximize quality parameters on de novo assemblies and availability of reads in downstream analysis.
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Affiliation(s)
- Miriam Payá-Milans
- Department of Entomology and Plant Pathology, University of Tennessee, 370 PBB, 2505 EJ Chapman Blvd, Knoxville, TN, 37996, United States
| | - James W Olmstead
- Horticultural Sciences Department, University of Florida, 2550 Hull Rd, PO Box 110690, Gainesville, FL, 32611, United States
| | - Gerardo Nunez
- Horticultural Sciences Department, University of Florida, 2550 Hull Rd, PO Box 110690, Gainesville, FL, 32611, United States
| | - Timothy A Rinehart
- Thad Cochran Southern Horticultural Laboratory, USDA-Agricultural Research Service, PO Box 287, Poplarville, MS, 39470, United States.,Crop Production and Protection, USDA-Agricultural Research Service, 5601 Sunnyside Ave, Beltsville, MD, 20705, United States
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 370 PBB, 2505 EJ Chapman Blvd, Knoxville, TN, 37996, United States
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Hatmaker EA, Staton ME, Dattilo AJ, Hadziabdic Ð, Rinehart TA, Schilling EE, Trigiano RN, Wadl PA. Population Structure and Genetic Diversity Within the Endangered Species Pityopsis ruthii (Asteraceae). Front Plant Sci 2018; 9:943. [PMID: 30050545 PMCID: PMC6050971 DOI: 10.3389/fpls.2018.00943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/12/2018] [Indexed: 06/02/2023]
Abstract
Pityopsis ruthii (Ruth's golden aster) is a federally endangered herbaceous perennial endemic to the Hiwassee and Ocoee Rivers in southeastern Tennessee, United States. Comprehensive genetic studies providing novel information to conservationists for preservation of the species are lacking. Genetic variation and gene flow were evaluated for 814 individuals from 33 discrete locations using polymorphic microsatellites: seven chloroplast and twelve nuclear. A total of 198 alleles were detected with the nuclear loci and 79 alleles with the chloroplast loci. Gene flow was estimated, with the Hiwassee River (Nm = 2.16; FST = 0.15) showing higher levels of gene flow and lower levels of population differentiation than the Ocoee River (Nm = 1.28; FST = 0.19). Population structure was examined using Bayesian cluster analyses. Nuclear and chloroplast analyses were incongruent. From the chloroplast microsatellites, three clusters were identified; all were present in sampling sites at both rivers, indicating a lack of allele fixation along rivers. Nuclear markers revealed two clusters and separated by river. When the Hiwassee River locations were analyzed, four clusters were identified for both the chloroplast and nuclear microsatellites, though the individuals clustered differently. Analysis of the Ocoee River revealed two clusters for the chloroplast microsatellites and three for the nuclear microsatellites. We recommend P. ruthii be managed as four populations for the Hiwassee River and three populations for the Ocoee River. Our results provide critical genetic information for P. ruthii that can be used for species management decisions to drive future population augmentation/reintroduction and ex situ conservation efforts.
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Affiliation(s)
- E. Anne Hatmaker
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Margaret E. Staton
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Adam J. Dattilo
- Biological Compliance, Tennessee Valley Authority, Knoxville, TN, United States
| | - Ðenita Hadziabdic
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Timothy A. Rinehart
- Thad Cochran Southern Horticultural Laboratory, United States Department of Agriculture-Agricultural Research Service, Poplarville, MS, United States
| | - Edward E. Schilling
- Department of Ecology & Evolutionary Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Robert N. Trigiano
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Phillip A. Wadl
- United States Vegetable Laboratory, United States Department of Agriculture-Agricultural Research Service, Charleston, SC, United States
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Payá-Milans M, Nunez GH, Olmstead JW, Rinehart TA, Staton M. Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq. BMC Genomics 2017; 18:580. [PMID: 28784085 PMCID: PMC5547544 DOI: 10.1186/s12864-017-3967-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 02/07/2017] [Accepted: 07/31/2017] [Indexed: 01/19/2023] Open
Abstract
Background Blueberries are one of the few horticultural crops adapted to grow in acidic soils. Neutral to basic soil pH is detrimental to all commonly cultivated blueberry species, including Vaccinium corymbosum (VC). In contrast, the wild species V. arboreum (VA) is able to tolerate a wider range of soil pH. To assess the molecular mechanisms involved in near neutral pH stress response, plants from pH-sensitive VC (tetraploid) and pH-tolerant VA (diploid) were grown at near neutral pH 6.5 and at the preferred pH of 4.5. Results Transcriptome sequencing of root RNA was performed for 4 biological replications per species x pH level interaction, for a total of 16 samples. Reads were mapped to the reference genome from diploid V. corymbosum, transforming ~55% of the reads to gene counts. A quasi-likelihood F test identified differential expression due to pH stress in 337 and 4867 genes in VA and VC, respectively. Both species shared regulation of genes involved in nutrient homeostasis and cell wall metabolism. VA and VC exhibited differential regulation of signaling pathways related to abiotic/biotic stress, cellulose and lignin biosynthesis, and nutrient uptake. Conclusions The specific responses in VA likely facilitate tolerance to higher soil pH. In contrast, response in VC, despite affecting a greater number of genes, is not effective overcoming the stress induced by pH. Further inspection of those genes with differential expression that are specific in VA may provide insight on the mechanisms towards tolerance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3967-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miriam Payá-Milans
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Gerardo H Nunez
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, USA
| | - James W Olmstead
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, USA
| | - Timothy A Rinehart
- Thad Cochran Southern Horticultural Laboratory, USDA-Agricultural Research Service, Poplarville, MS, USA.,Crop Production and Protection, USDA-Agricultural Research Service, Beltsville, MD, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.
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Sampson BJ, Rinehart TA, Kirker GT, Stringer SJ, Werle CT. Phenotypic Variation in Fitness Traits of a Managed Solitary Bee, Osmia ribifloris (Hymenoptera: Megachilidae). J Econ Entomol 2015; 108:2589-2598. [PMID: 26470379 DOI: 10.1093/jee/tov233] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/16/2015] [Indexed: 06/05/2023]
Abstract
We investigated fitness in natural populations of a managed solitary bee Osmia ribifloris Cockerell (Hymenoptera: Megachilidae) from sites separated from 400 to 2,700 km. Parental wild bees originated in central Texas (TX), central-northern Utah (UT), and central California (CA). They were then intercrossed and raised inside a mesh enclosure in southern Mississippi (MS). Females from all possible mated pairs of O. ribifloris produced F1 broods with 30-40% female cocoons and outcrossed progeny were 30% heavier. Mitochondrial (COI) genomes of the four populations revealed three distinct clades, a TX-CA clade, a UT clade, and an MS clade, the latter (MS) representing captive progeny of CA and UT bees. Although classified as separate subspecies, TX and CA populations from 30° N to 38° N latitude shared 98% similarity in COI genomes and the greatest brood biomass per nest straw (600- to 700-mg brood). Thus, TX and CA bees show greater adaptation for southern U.S. sites. In contrast, UT-sourced bees were more distantly related to TX and CA bees and also produced ∼50% fewer brood. These results, taken together, confirm that adult O. ribifloris from all trap-nest sites are genetically compatible, but some phenotypic variation exists that could affect this species performance as a commercial blueberry pollinator. Males, their sperm, or perhaps a substance in their sperm helped stabilize our captive bee population by promoting legitimate nesting over nest usurpation. Otherwise, without insemination, 50% fewer females nested (they nested 14 d late) and 20% usurped nests, killing 33-67% of brood in affected nests.
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Affiliation(s)
- B J Sampson
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, 810 Hwy 26 West, Poplarville, MS 39470.
| | - T A Rinehart
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, 810 Hwy 26 West, Poplarville, MS 39470
| | - G T Kirker
- USDA-FS Forest Products Laboratory, One Gifford Pinchot Dr., Madison, WI 53726
| | - S J Stringer
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, 810 Hwy 26 West, Poplarville, MS 39470
| | - C T Werle
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, 810 Hwy 26 West, Poplarville, MS 39470
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Trigiano RN, Rinehart TA, Dee MM, Wadl PA, Poplawski L, Ownley BH. First Report of Aerial Blight of Ruth's Golden Aster (Pityopsis ruthii) Caused by Rhizoctonia solani in the United States. Plant Dis 2014; 98:855. [PMID: 30708690 DOI: 10.1094/pdis-11-13-1181-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Ruth's golden aster (Pityopsis ruthii (Small) Small: Asteraceae) is an endangered, herbaceous perennial that occurs only at a few sites along the Hiwassee and Ocoee rivers in Polk County, Tennessee. This species is drought, heat, and submergence tolerant and has ornamental potential as a fall flowering landscape plant. In 2012, we vegetatively propagated various genotypes and established plantings in a landscape at Poplarville, Mississippi. In June and July of 2013, during periods of hot and humid weather, several well-established plants exhibited black or brown necrotic aerial blight symptoms including desiccation of stems and leaves. Blighted leaf samples were surface sterilized (10% commercial bleach, active ingredient 8.25% sodium hypochlorite, 1 min), rinsed in sterile water, air-dried, and plated on 2% water agar amended with 3.45 mg fenpropathrin/liter (Danitol 2.4 EC, Valent Chemical, Walnut Creek, CA) and 10 mg/liter rifampicin (Sigma-Aldrich, St. Louis, MO). Rhizoctonia sp. was identified based on hyphal morphology and cultures were maintained on potato dextrose agar. Colonies were fast growing, consisting of light tan to brown mycelia and tufts of crystalline aerial hyphae. Within 10 days, brown exudates were present in cultures and there was no pigmented reverse to the agar. Hyphae were a mean of 5.2 μm wide (4.6 to 6.1 μm; n = 10) and each compartment contained three or more nuclei. Hyphae were constricted at septa with right angle branching and no clamp connections, which is typical for Rhizoctonia solani (1). Light- to medium-brown, oblong to irregularly shaped sclerotia measuring 1.2 mm long (0.7 to 2.1 mm) × 0.9 mm wide (0.5 to 1.2 mm; n = 20) were formed in cultures after 3 weeks of growth. Total genomic DNA was extracted from two different colonies grown in potato dextrose broth for 7 days, amplified with PCR using ITS1 and ITS4 primers for amplification of the 18S rDNA subunit (2), the products purified, and sequenced. A consensus sequence of 657 bp was deposited in GenBank (Accession Nos. KF843729 and KF843730) and was 96% identical to two R. solani Kühn ITS sequences in GenBank (HF678125 and HF678122). R. solani was grown on twice autoclaved oats for 2 weeks at 21°C and incorporated into Pro-Mix BX, low fertility soilless medium (Premier Horticulture, Rivière-du-Loup, Quebec, Canada) at 4% (w/w) to inoculate seven P. ruthii plants grown in 10 cm-diameter pots; seven additional plants were grown in the same medium amended with 4% (w/w) sterile oats. Plants were grown in a greenhouse and covered with a plastic dome to maintain high humidity. After 2 weeks, six of the seven inoculated plants exhibited the same aerial blight symptoms as did the original infected plants from the field; none of the control plants developed disease symptoms. Colony morphology and hyphal characteristics as well as the sequence for the ITS region of rDNA from the re-isolated fungus were identical to the original isolate. To our knowledge, this is the first report of R. solani infecting Ruth's golden aster. We are not aware of the disease occurring in wild populations of the plant, but may impact plants grown in the landscape or greenhouse. References: (1) B. Sneh et al. Identification of Rhizoctonia Species. The American Phytopathological Society, St Paul, MN, 1991. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, CA, 1990.
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Affiliation(s)
- R N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - T A Rinehart
- USDA-ARS, Thad Chcoran Southern Horticultural Laboratory, Poplarville, MS 39470
| | - M M Dee
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - P A Wadl
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - L Poplawski
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - B H Ownley
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
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Abstract
Microsatellite loci were identified from Cornus kousa'National'. Primer pairs for 86 loci were developed and of these, eight were optimized and screened using genomic DNA from 22 kousa cultivars. All optimized loci were polymorphic and the number of alleles per locus ranged from three to 17. Observed heterozygosity ranged from 0 to 0.3 and expected heterozygosity ranged from 0.38 to 0.91. These microsatellites will be useful in population studies, and a breeding programme for cultivar development of Cornus species.
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Affiliation(s)
- Phillip A Wadl
- Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA, USDA-ARS-CGRU MSA Genomics Laboratory, 141 Experiment Station Road, Stoneville, MS 38776, USA, USDA-ARS Southern Horticultural Laboratory, 810 Highway 26 West, Poplarville, MS 39470, USA
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Hadziabdic D, Fitzpatrick BM, Wang X, Wadl PA, Rinehart TA, Ownley BH, Windham MT, Trigiano RN. Analysis of genetic diversity in flowering dogwood natural stands using microsatellites: the effects of dogwood anthracnose. Genetica 2010; 138:1047-57. [PMID: 20820882 DOI: 10.1007/s10709-010-9490-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 08/21/2010] [Indexed: 11/25/2022]
Abstract
Flowering dogwood (Cornus florida L.) populations recently have experienced severe declines caused by dogwood anthracnose. Mortality has ranged from 48 to 98%, raising the concern that genetic diversity has been reduced significantly. Microsatellite data were used to evaluate the level and distribution of genetic variation throughout much of the native range of the tree. Genetic variation in areas affected by anthracnose was as high as or higher than areas without die-offs. We found evidence of four widespread, spatially contiguous genetic clusters. However, there was little relationship between geographic distance and genetic difference. These observations suggest that high dispersal rates and large effective population sizes have so far prevented rapid loss of genetic diversity. The effects of anthracnose on demography and community structure are likely to be far more consequential than short-term genetic effects.
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Affiliation(s)
- D Hadziabdic
- Department of Entomology and Plant Pathology, The University of Tennessee, 2431 Joe Johnson Dr, Knoxville, TN, 37996-4560, USA
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Aurelle D, Baker AJ, Bottin L, Brouat C, Caccone A, Chaix A, Dhakal P, Ding Y, Duplantier JM, Fiedler W, Fietz J, Fong Y, Forcioli D, Freitas TRO, Gunnarsson GH, Haddrath O, Hadziabdic D, Hauksdottir S, Havill NP, Heinrich M, Heinz T, Hjorleifsdottir S, Hong Y, Hreggvidsson GO, Huchette S, Hurst J, Kane M, Kane NC, Kawakami T, Ke W, Keith RA, Klauke N, Klein JL, Kun JFJ, Li C, Li GQ, Li JJ, Loiseau A, Lu LZ, Lucas M, Martins-Ferreira C, Mokhtar-Jamaï K, Olafsson K, Pampoulie C, Pan L, Pooler MR, Ren JD, Rinehart TA, Roussel V, Santos MO, Schaefer HM, Scheffler BE, Schmidt A, Segelbacher G, Shen JD, Skirnisdottir S, Sommer S, Tao ZR, Taubert R, Tian Y, Tomiuk J, Trigiano RN, Ungerer MC, Van Wormhoudt A, Wadl PA, Wang DQ, Weis-Dootz T, Xia Q, Yuan QY. Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010-31 March 2010. Mol Ecol Resour 2010; 10:751-4. [PMID: 21565086 DOI: 10.1111/j.1755-0998.2010.02871.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This article documents the addition of 228 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described).
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Affiliation(s)
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- Aix-Marseille Université, Centre d'Océanologie de Marseille, CNRS-UMR 6540 DIMAR, rue de la Batterie des Lions, 13007 Marseille, France
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Baird RE, Wadl PA, Allen T, McNeill D, Wang X, Moulton JK, Rinehart TA, Abbas HK, Shier T, Trigiano RN. Variability of United States isolates of Macrophomina phaseolina based on simple sequence repeats and cross genus transferability to related genera within botryosphaeriaceae. Mycopathologia 2010; 170:169-80. [PMID: 20352493 DOI: 10.1007/s11046-010-9308-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 03/20/2010] [Indexed: 11/29/2022]
Abstract
Twelve simple sequence repeat (SSRs) loci were used to evaluate genetic diversity of 109 isolates of Macrophomina phaseolina collected from different geographical regions and host species throughout the United States (US). Genetic diversity was assessed using Nei's minimum genetic distance, and the usefulness of each locus was determined by calculating the polymorphism information content (PIC). A total of 98 alleles were detected and of these 31 were unique to individual genotypes. Eight of twelve loci were highly informative with PIC values greater than 0.50. The majority of pairwise comparisons of genetic distance were greater than 0.60 indicating moderate to high genetic diversity. Dendrograms based on the genetic dissimilarities were created for the 109 isolates of which 79 were from soybean. Some clustering by host and geography was noted, but, the dendrograms generally grouped isolates independent of host or geography. Additionally, sequencing of the internal transcribed spacer region (ITS) for 10 isolates revealed that all of these isolates were 99% similar. Three SSR loci from M. phaseolina were cross amplified in other genera in the Botryosphaeriaceae. This was the first study of genotyping and assessing genetic diversity of M. phaseolina isolates collected from a widespread host and geographic range across the US with SSRs. With an additional 34 loci publically available for M. phaseolina, the results indicate that previously developed SSRs from one species can be used in future population, ecological, and genetic studies of M. phaseolina and other genera within the Botryosphaeriaceae.
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Affiliation(s)
- Richard E Baird
- Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA.
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Baird RE, Wadl PA, Wang X, Johnson DH, Rinehart TA, Abbas HK, Shier T, Trigiano RN. Microsatellites from the charcoal rot fungus (Macrophomina phaseolina). Mol Ecol Resour 2009; 9:946-8. [PMID: 21564800 DOI: 10.1111/j.1755-0998.2008.02511.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Microsatellite loci were identified from the charcoal rot fungus (Macrophomina phaseolina). Primer pairs for 46 loci were developed, and of these, 13 were optimized and screened using genomic DNA from 55 fungal isolates collected predominantly from two soybean fields in Mississippi. Twelve of the optimized loci were polymorphic and the number of alleles per locus ranged from 6 to 22. These microsatellites will be useful in population and pathogenicity studies to correspond with development of potential disease-resistant soybean and other susceptible crops.
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Affiliation(s)
- Richard E Baird
- Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA, Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA, USDA-ARS Southern Horticultural Laboratory, Poplarville, MS 39470, USA, USDA-ARS-CGRU MSA, Stoneville, MS 38776, USA, University of Minnesota, Minneapolis, MN 54455 USA
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Li Y, Windham MT, Trigiano RN, Reed SM, Spiers JM, Rinehart TA. Bright-Field and Fluorescence Microscopic Study of Development of Erysiphe polygoni in Susceptible and Resistant Bigleaf Hydrangea. Plant Dis 2009; 93:130-134. [PMID: 30764105 DOI: 10.1094/pdis-93-2-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Temporal development of Erysiphe polygoni and responses of bigleaf hydrangeas (Hydrangea macrophylla) to the fungal attack were investigated using bright-field and fluorescence microscopy. Conidia germinated 2 h after inoculation (HAI) and formed primary appressoria at the tip of the primary germ tubes within 4 HAI. Secondary germ tubes were initiated from primary appressoria or other parts of conidia 12 HAI. Hyphae developed through elongation of secondary germ tubes, and paired lateral appressoria were formed along hyphae within 2 days after inoculation (DAI). Conidiophores and conidia were formed 5 DAI. In the susceptible cultivar Nikko Blue and the resistant cultivar Veitchii, the fungus established a parasitic relationship, which was indicated by the formation of haustoria under primary appressoria and development of secondary germ tubes at 1 DAI. A hypersensitive response (HR) and accumulation of callose were detected in both resistant and susceptible cultivars at 3 DAI. Resistance to powdery mildew in Veitchii was evident by manifestation of early accumulation of callose, relatively high percentage of necrotic infected cells, and restricted colony development compared to the susceptible cultivar Nikko Blue. Restricting hyphal growth and sporulation by early response of callose accumulation and HR are important resistance mechanisms that could be used in screening hydrangeas for resistance to powdery mildew.
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Affiliation(s)
- Yonghao Li
- Dept. of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560
| | - Mark T Windham
- Dept. of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560
| | - Robert N Trigiano
- Dept. of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560
| | - Sandra M Reed
- USDA/ARS Floral & Nursery Plants Research Unit, McMinnville, TN 37110
| | - James M Spiers
- USDA/ARS Thad Cochran Horticultural Research Laboratory, Poplarville, MS 39470
| | - Timothy A Rinehart
- USDA/ARS Thad Cochran Horticultural Research Laboratory, Poplarville, MS 39470
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DeVries RE, Trigiano RN, Windham MT, Windham AS, Sorochan JC, Rinehart TA, Vargas JM. Genetic Analysis of Fungicide-Resistant Sclerotinia homoeocarpa Isolates from Tennessee and Northern Mississippi. Plant Dis 2008; 92:83-90. [PMID: 30786356 DOI: 10.1094/pdis-92-1-0083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sclerotinia homoeocarpa is the causal agent of dollar spot disease that reduces the uniformity and aesthetic value of golf putting greens. Fungicide-resistant isolates of S. homoeocarpa were collected from putting greens at 10 locations across Tennessee and northern Mississippi. Genetic diversity among the 60 isolates was investigated using vegetative compatibility, conserved gene sequences, and amplified fragment length polymorphism (AFLP). Six tester strains were paired with Tennessee and northern Mississippi isolates on potato dextrose agar. Some of the 60 isolates were delineated into vegetative compatibility groups, but fungicide resistance could not be associated with a particular vegetative compatibility group. Genetic similarities of isolates at the vegetative compatibility level could be attributed to founder effects. Sequencing the regions of CAD, EF1-α, β-tubulin, and internal transcribed spacers revealed 100% homology among isolates. Capillary gel electrophoresis and analysis of AFLP fragments indicated 86 to 100% similarity between the isolates. Vegetative compatibility and molecular data indicate that the populations of the pathogen are clonal. Isolates did not cluster according to fungicide resistance during unweighted pair group with arithmetic means analysis, but did appear to cluster according to vegetative compatibility group and location. Although associations could not be made between molecular markers and fungicide resistance, links between vegetative compatibility and AFLP markers may provide a foundation from which other studies could be performed.
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Affiliation(s)
- R E DeVries
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - R N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - M T Windham
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - A S Windham
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560
| | - J C Sorochan
- Department of Plant Sciences, University of Tennessee, Knoxville 37996-4561
| | - T A Rinehart
- United States Department of Agriculture-Agricultural Research Service MSA, Southern Horticultural Laboratory, Poplarville, MS 39470
| | - J M Vargas
- Department of Botany and Plant Pathology, Michigan State University, East Lansing 48824
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Rinehart TA, Copes WE, Toda T, Cubeta MA. Genetic Characterization of Binucleate Rhizoctonia Species Causing Web Blight on Azalea in Mississippi and Alabama. Plant Dis 2007; 91:616-623. [PMID: 30780709 DOI: 10.1094/pdis-91-5-0616] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Web blight on containerized azalea is an annual problem for commercial nurseries during summer months in the southern United States. Losses to web blight are associated with the cost of fungicide applications, delayed marketing of diseased plants, and plant death. Two hundred and eleven isolates of binucleate Rhizoctonia were recovered from azalea leaves with web blight symptoms from two nurseries in Mississippi and Alabama over 3 years. The internal transcribed spacer region (ITS) of the ribosomal DNA (rDNA) was sequenced from all isolates to determine genetic identity. A single anastomosis group (AG) of binucleate Rhizoctonia represented 92% of the samples collected from infected leaves. Genetic data and hyphal fusion experiments confirmed that these isolates belong to AG-U, which was recently identified from root and stem infections on miniature rose in Japan. Isolates of binucleate Rhizoctonia belonging to anastomosis groups AG-R, CAG-7 (=AG-S), and AG-G were also identified in the sample in low frequency. This is the first report of the occurrence of binucleate Rhizoctonia AG-U in the United States.
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Affiliation(s)
- T A Rinehart
- United States Department of Agriculture, Agricultural Research Service, Thad Cochran Southern Horticultural Laboratory, 810 Highway 26 West, Poplarville, MS 39470
| | - W E Copes
- United States Department of Agriculture, Agricultural Research Service, Thad Cochran Southern Horticultural Laboratory, 810 Highway 26 West, Poplarville, MS 39470
| | - T Toda
- North Carolina State University, Department of Plant Pathology, Center for Integrated Fungal Research, 225 Partners III, Raleigh, NC 27695-7567
| | - M A Cubeta
- North Carolina State University, Department of Plant Pathology, Center for Integrated Fungal Research, 225 Partners III, Raleigh, NC 27695-7567
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Rinehart TA, Boyd DW. Rapid, high-throughput detection of azalea lace bug (Hemiptera: Tingidae) predation by Chrysoperla rufilabris (Neuroptera: Chrysopidae), using fluorescent-polymerase chain reaction primers. J Econ Entomol 2006; 99:2136-41. [PMID: 17195684 DOI: 10.1603/0022-0493-99.6.2136] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Azalea lace bugs, Stephanitis pyrioides (Scott) (Hemiptera: Tingidae), are the most common pest of azaleas (Rhododendron spp.) in nursery production and the landscape. Although pesticides are commonly used to control lace bugs, natural enemies can be a significant source of lace bug mortality. Lacewings (Neuroptera: Chrysopidae) are natural enemies of lace bugs and easily consume them in laboratory studies. Field studies on lacewing biocontrol of azalea lace bugs are underway; however, monitoring lacewing predation in a nursery environment by direct observation is impractical. Here, we describe a fluorescent-polymerase chain reaction method to estimate S. pyrioides consumption based on the gut contents of lacewing predators. Lace bug DNA was detected in fed lacewings up to 32 h after ingestion. More than 80% of the ingested lace bugs were detected using our method with only one false positive result. The assay is both high-throughput and relatively inexpensive, making it a practical approach to documenting lace bug predation in the field.
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Affiliation(s)
- Timothy A Rinehart
- USDA-ARS, Southern Horticultural Laboratory, 810 Highway 26 West, P.O. Box 287, Poplarville, MS 39470, USA.
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Rinehart TA, Grahn RA, Wichman HA. SINE extinction preceded LINE extinction in sigmodontine rodents: implications for retrotranspositional dynamics and mechanisms. Cytogenet Genome Res 2005; 110:416-25. [PMID: 16093694 DOI: 10.1159/000084974] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 03/07/2004] [Indexed: 11/19/2022] Open
Abstract
Short Interspersed Nuclear Elements, or SINEs, retrotranspose despite lacking protein-coding capability. It has been proposed that SINEs utilize enzymes produced in trans by Long Interspersed Nuclear Elements, or LINEs. Strong support for this hypothesis is found in LINE and SINE pairs that share sequence homology; however, LINEs and SINEs in primates and rodents are only linked by an insertion site motif. We have now profiled L1 LINE and B1 SINE activity in 24 rodent species including candidate taxa for the first documented L1 extinction. As expected, there was no evidence for recent activity of B1s in species that also lack L1 activity. However, B1 silencing appears to have preceded L1 extinction, since B1 activity is also lacking in the genus most closely related to those lacking active L1s despite the presence of active L1s in this genus. A second genus with active L1s but inactive B1s was also identified.
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Affiliation(s)
- T A Rinehart
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
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Grahn RA, Rinehart TA, Cantrell MA, Wichman HA. Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents. Cytogenet Genome Res 2005; 110:407-15. [PMID: 16093693 DOI: 10.1159/000084973] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 04/07/2004] [Indexed: 11/19/2022] Open
Abstract
LINE-1 transposable elements (L1s) are ubiquitous in mammals and are thought to have remained active since before the mammalian radiation. Only one L1 extinction event, in South American rodents in the genus Oryzomys, has been convincingly demonstrated. Here we examine the phylogenetic limits and evolutionary tempo of that extinction event by characterizing L1s in related rodents. Fourteen genera from five tribes within the Sigmodontinae subfamily were examined. Only the Sigmodontini, the most basal tribe in this group, demonstrate recent L1 activity. The Oryzomyini, Akodontini, Phyllotini, and Thomasomyini contain only L1s that appear to have inserted long ago; their L1s lack open reading frames, have mutations at conserved amino acid residues, and show numerous private mutations. They also lack restriction site-defined L1 subfamilies specific to any species, genus or tribe examined, and fail to form monophyletic species, genus or tribal L1 clusters. We determine here that this L1 extinction event occurred roughly 8.8 million years ago, near the divergence of Sigmodon from the remaining Sigmodontinae species. These species appear to be ideal model organisms for studying the impact of L1 inactivity on mammalian genomes.
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Affiliation(s)
- R A Grahn
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
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Affiliation(s)
- Timothy A Rinehart
- United States Department of Agriculture, Agricultural Research Services, Small Fruit Research Station, Poplarville, MS 39470, USA.
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Abstract
Ac/Ds transposable elements often leave short DNA rearrangements, or 'footprints,' at the sites where they excise. Previous studies at the maize waxy (wx) gene suggest that the DNA repair that forms transposon footprints is not random. Each excision site consistently displays a different, predominant repair product suggesting flanking DNA may influence footprint formation. We have expanded these studies to show that predominant end-joining products also form in association with Ac/Ds excision in Arabidopsis and that chromosomal location of the Ac-containing construct does not appear to influence this repair. The predominant repair product is identical in both maize and Arabidopsis for Ac elements with the same adjacent DNA sequences. However, a broader range of minor footprint types is observed in Arabidopsis, including footprints that are rare in maize, suggesting potential differences in the host proteins involved in either transposition, repair or both. The data also suggest that the sequences influencing footprint formation are within 39 bp 5' and 18 bp 3' of the transposon. These studies demonstrate that transgenic Ac/Ds-containing plants will be useful tools in dissecting plant DNA repair processes.
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Affiliation(s)
- T A Rinehart
- Department of Biological Sciences, University of Idaho, Moscow 83844-3051, USA
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Challener WA, Rinehart TA. Jones matrix analysis of magnetooptical media and read-back systems. Appl Opt 1987; 26:3974-3980. [PMID: 20490171 DOI: 10.1364/ao.26.003974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A Jones matrix approach is used to study a magnetooptic read-back system which uses a wave plate for maximizing the signal. The effects and interactions of Kerr rotation, Kerr ellipticity, birefringence in the substrate and in the optical system, and misalignment of the optical components are considered. Several criteria are developed for maximizing the signal and minimizing the noise.
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