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Vieira P, Subbotin SA, Alkharouf N, Eisenback J, Nemchinov LG. Expanding the RNA virome of nematodes and other soil-inhabiting organisms. Virus Evol 2022; 8:veac019. [PMID: 35371560 PMCID: PMC8967085 DOI: 10.1093/ve/veac019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 07/25/2023] Open
Abstract
In recent years, several newly discovered viruses infecting free-living nematodes, sedentary plant-parasitic nematodes, and migratory root lesion nematodes have been described. However, to the best of our knowledge, no comprehensive research focusing exclusively on metagenomic analysis of the soil nematode community virome has thus far been carried out. In this work, we have attempted to bridge this gap by investigating viral communities that are associated with soil-inhabiting organisms, particularly nematodes. This study demonstrates a remarkable diversity of RNA viruses in the natural soil environment. Over 150 viruses were identified in different soil-inhabiting hosts, of which more than 139 are potentially new virus species. Many of these viruses belong to the nematode virome, thereby enriching our understanding of the diversity and evolution of this complex part of the natural ecosystem.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD 20705, USA
| | - Sergei A Subbotin
- Plant Pest Diagnostics Branch, California Department of Food & Agriculture, Sacramento, CA 95832, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
| | - Nadim Alkharouf
- Department of Computer & Information Sciences Faculty, Towson University, Towson, MD 21204, USA
| | - Jonathan Eisenback
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Qi X, Ogden EL, Die JV, Ehlenfeldt MK, Polashock JJ, Darwish O, Alkharouf N, Rowland LJ. Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations. BMC Plant Biol 2019; 19:460. [PMID: 31711416 PMCID: PMC6844065 DOI: 10.1186/s12870-019-2073-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/14/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Blueberry is of high economic value. Most blueberry varieties selected for the fresh market have an appealing light blue coating or "bloom" on the fruit due to the presence of a visible heavy epicuticular wax layer. This waxy layer also serves as natural defense against fruit desiccation and deterioration. RESULTS In this study, we attempted to identify gene(s) whose expression is related to the protective waxy coating on blueberry fruit utilizing two unique germplasm populations that segregate for the waxy layer. We bulked RNA from waxy and non-waxy blueberry progenies from the two northern-adapted rabbiteye hybrid breeding populations ('Nocturne' x T 300 and 'Nocturne' x US 1212), and generated 316.85 million RNA-seq reads. We de novo assembled this data set integrated with other publicly available RNA-seq data and trimmed the assembly into a 91,861 blueberry unigene collection. All unigenes were functionally annotated, resulting in 79 genes potentially related to wax accumulation. We compared the expression pattern of waxy and non-waxy progenies using edgeR and identified overall 1125 genes in the T 300 population and 2864 genes in the US 1212 population with at least a two-fold expression difference. After validating differential expression of several genes by RT-qPCR experiments, a candidate gene, FatB, which encodes acyl-[acyl-carrier-protein] hydrolase, emerged whose expression was closely linked to the segregation of the waxy coating in our populations. This gene was expressed at more than a five-fold higher level in waxy than non-waxy plants of both populations. We amplified and sequenced the cDNA for this gene from three waxy plants of each population, but were unable to amplify the cDNA from three non-waxy plants that were tested from each population. We aligned the Vaccinium deduced FATB protein sequence to FATB protein sequences from other plant species. Within the PF01643 domain, which gives FATB its catalytic function, 80.08% of the amino acids were identical or had conservative replacements between the blueberry and the Cucumis melo sequence (XP_008467164). We then amplified and sequenced a large portion of the FatB gene itself from waxy and non-waxy individuals of both populations. Alignment of the cDNA and gDNA sequences revealed that the blueberry FatB gene consists of six exons and five introns. Although we did not sequence through two very large introns, a comparison of the exon sequences found no significant sequence differences between the waxy and non-waxy plants. This suggests that another gene, which regulates or somehow affects FatB expression, must be segregating in the populations. CONCLUSIONS This study is helping to achieve a greater understanding of epicuticular wax biosynthesis in blueberry. In addition, the blueberry unigene collection should facilitate functional annotation of the coming chromosomal level blueberry genome.
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Affiliation(s)
- Xinpeng Qi
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
| | - Elizabeth L. Ogden
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
| | - Jose V. Die
- Departmento de Genetica, University of Córdoba Campus Rabanales, Blg. C5, 14071 Córdoba, Spain
| | - Mark K. Ehlenfeldt
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, at Rutgers University P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019 USA
| | - James J. Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, at Rutgers University P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Chatsworth, NJ 08019 USA
| | - Omar Darwish
- Department of Mathematics and Computer Science, Texas Woman’s University, Denton, TX 76204 USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252 USA
| | - L. Jeannine Rowland
- USDA-ARS, BARC-West, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MD 20705 USA
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3
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Zhang C, Gao M, Seitz NC, Angel W, Hallworth A, Wiratan L, Darwish O, Alkharouf N, Dawit T, Lin D, Egoshi R, Wang X, McClung CR, Lu H. LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis. Nat Commun 2019. [PMID: 31186426 DOI: 10.1038/s41467-019-10485-10486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
The circadian clock is known to regulate plant innate immunity but the underlying mechanism of this regulation remains largely unclear. We show here that mutations in the core clock component LUX ARRHYTHMO (LUX) disrupt circadian regulation of stomata under free running and Pseudomonas syringae challenge conditions as well as defense signaling mediated by SA and JA, leading to compromised disease resistance. RNA-seq analysis reveals that both clock- and defense-related genes are regulated by LUX. LUX binds to clock gene promoters that have not been shown before, expanding the clock gene networks that require LUX function. LUX also binds to the promoters of EDS1 and JAZ5, likely acting through these genes to affect SA- and JA-signaling. We further show that JA signaling reciprocally affects clock activity. Thus, our data support crosstalk between the circadian clock and plant innate immunity and imply an important role of LUX in this process.
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Affiliation(s)
- Chong Zhang
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Min Gao
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Nicholas C Seitz
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - William Angel
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Amelia Hallworth
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Linda Wiratan
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Teklu Dawit
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Daniela Lin
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Riki Egoshi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Hua Lu
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
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4
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Zhang C, Gao M, Seitz NC, Angel W, Hallworth A, Wiratan L, Darwish O, Alkharouf N, Dawit T, Lin D, Egoshi R, Wang X, McClung CR, Lu H. LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis. Nat Commun 2019; 10:2543. [PMID: 31186426 PMCID: PMC6560066 DOI: 10.1038/s41467-019-10485-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 06/22/2017] [Accepted: 05/13/2019] [Indexed: 01/02/2023] Open
Abstract
The circadian clock is known to regulate plant innate immunity but the underlying mechanism of this regulation remains largely unclear. We show here that mutations in the core clock component LUX ARRHYTHMO (LUX) disrupt circadian regulation of stomata under free running and Pseudomonassyringae challenge conditions as well as defense signaling mediated by SA and JA, leading to compromised disease resistance. RNA-seq analysis reveals that both clock- and defense-related genes are regulated by LUX. LUX binds to clock gene promoters that have not been shown before, expanding the clock gene networks that require LUX function. LUX also binds to the promoters of EDS1 and JAZ5, likely acting through these genes to affect SA- and JA-signaling. We further show that JA signaling reciprocally affects clock activity. Thus, our data support crosstalk between the circadian clock and plant innate immunity and imply an important role of LUX in this process. Circadian control of plant defence likely reflects plants’ ability to coordinate development and defense. Here, Zhang et al. show that LUX regulates stomatal defense and SA/JA signaling, leading to broad-spectrum disease resistance, and that JA signaling can, in turn, regulate clock activity.
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Affiliation(s)
- Chong Zhang
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.,Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Min Gao
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Nicholas C Seitz
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - William Angel
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Amelia Hallworth
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Linda Wiratan
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Teklu Dawit
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Daniela Lin
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Riki Egoshi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, 712100, Yangling, Shaanxi, China
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Hua Lu
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
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5
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Hawkins C, Caruana J, Li J, Zawora C, Darwish O, Wu J, Alkharouf N, Liu Z. An eFP browser for visualizing strawberry fruit and flower transcriptomes. Hortic Res 2017; 4:17029. [PMID: 28674614 PMCID: PMC5478792 DOI: 10.1038/hortres.2017.29] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/05/2023]
Abstract
Wild strawberry Fragaria vesca is emerging as an important model system for the cultivated strawberry due to its diploid genome and availability of extensive transcriptome data and a range of molecular genetic tools. Being able to better utilize these tools, especially the transcriptome data, will greatly facilitate research progress in strawberry and other Rosaceae fruit crops. The electronic fluorescent pictograph (eFP) software is a useful and popular tool to display transcriptome data visually, and is widely used in other model organisms including Arabidopsis and mouse. Here we applied eFP to display wild strawberry RNA sequencing (RNA-seq) data from 42 different tissues and stages, including various flower and fruit developmental stages. In addition, we generated eight additional RNA-seq data sets to represent tissues from ripening-stage receptacle fruit from yellow-colored and red-colored wild strawberry varieties. Differential gene expression analysis between these eight data sets provides additional information for understanding fruit-quality traits. Together, this work greatly facilitates the utility of the extensive transcriptome data for investigating strawberry flower and fruit development as well as fruit-quality traits.
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Affiliation(s)
- Charles Hawkins
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Julie Caruana
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Jiaming Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
- Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Chris Zawora
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA
| | - Jun Wu
- Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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6
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Darwish O, Li S, Matthews B, Alkharouf N. Genome-wide functional annotation of Phomopsis longicolla isolate MSPL 10-6. Genom Data 2016; 8:67-9. [PMID: 27222801 PMCID: PMC4856852 DOI: 10.1016/j.gdata.2016.03.006] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 12/03/2022]
Abstract
Phomopsis seed decay of soybean is caused primarily by the seed-borne fungal pathogen Phomopsis longicolla (syn. Diaporthe longicolla). This disease severely decreases soybean seed quality, reduces seedling vigor and stand establishment, and suppresses yield. It is one of the most economically important soybean diseases. In this study we annotated the entire genome of P. longicolla isolate MSPL 10-6, which was isolated from field-grown soybean seed in Mississippi, USA. This study represents the first reported genome-wide functional annotation of a seed borne fungal pathogen in the Diaporthe-Phomopsis complex. The P. longicolla genome annotation will enable research into the genetic basis of fungal infection of soybean seed and provide information for the study of soybean-fungal interactions. The genome annotation will also be a valuable resource for the research and agricultural communities. It will aid in the development of new control strategies for this pathogen. The annotations can be found from: http://bioinformatics.towson.edu/phomopsis_longicolla/download.html. NCBI accession number is: AYRD00000000.
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Affiliation(s)
- Omar Darwish
- Department of Computer and Information Sciences, Towson University, MD 21252, USA
| | - Shuxian Li
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Crop Genetics Research Unit, Stoneville, MS 38776, USA
| | - Benjamin Matthews
- USDA-ARS, Beltsville Agriculture Research Center, Beltsville, MD 21075, USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, MD 21252, USA
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7
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Snyder M, Weichseldorfer M, Parker D, Qureshi M, Phan P, White T, Leicht B, Alkharouf N, Rasko D, Hemm M. Development of Dictyostelium discoideum as a model to identify evolutionarily-conserved virulence factors in Escherichia coli. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.66.26] [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: 01/02/2023]
Abstract
Abstract
Escherichia coli are a typical component of mammalian gut microbiota; however, a number of pathogenic strains remain a health concern for developing countries. Identification and disruption of virulence factors that promote infection could lead to reduction in infection. To identify novel bacterial virulence factors, we are using the soil amoeba, Dictyostelium discoideum, which preys upon bacteria, including E. coli, in the soil, as a model for mammalian phagocytic cells. Using random mutagenesis, we have created mutant stocks of MG1655 E. coli. These stocks were fed to D. discoideum, enriching the culture and selecting for mutants that were resistant to killing upon phagocytosis. After several rounds of selection, resistant mutant strains were isolated, and we found that some strains showed up to 100-fold increase in survival over a 2 h period. Once isolated, the genomes of the resistant mutant strains were sequenced and the sequences compared to that of the initial WT strain using Illumina’s MiSeq technology. While analyzing the sequences from these mutant strains, we found mutations in several potential genes of interest and are working to characterize their roles in the cell. We are testing E. coli strains reconstituted with specific mutations to identify particular mutations that are associated with phagocytosis-resistant phenotypes. These studies are aimed at identifying particular bacterial genes that may be involved in regulation of virulence. In addition, given that the development of mechanisms to resist D. discoideum predation may have contributed to the selection and maintenance of bacterial virulence factors against mammalian hosts, these studies may provide insight on the evolution of host-pathogen interactions.
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8
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Lakshman DK, Roberts DP, Garrett WM, Natarajan SS, Darwish O, Alkharouf N, Pain A, Khan F, Jambhulkar PP, Mitra A. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with Roles in Plant Cell Wall Degradation and Virulence. J Agric Food Chem 2016; 64:3101-3110. [PMID: 27019116 DOI: 10.1021/acs.jafc.5b05735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rhizoctonia solani AG 4 is a soilborne necrotrophic fungal plant pathogen that causes economically important diseases on agronomic crops worldwide. This study used a proteomics approach to characterize both intracellular proteins and the secretome of R. solani AG 4 isolate Rs23A under several growth conditions, the secretome being highly important in pathogenesis. From over 500 total secretome and soluble intracellular protein spots from 2-D gels, 457 protein spots were analyzed and 318 proteins positively matched with fungal proteins of known function by comparison with available R. solani genome databases specific for anastomosis groups 1-IA, 1-IB, and 3. These proteins were categorized to possible cellular locations and functional groups and for some proteins their putative roles in plant cell wall degradation and virulence. The majority of the secreted proteins were grouped to extracellular regions and contain hydrolase activity.
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Affiliation(s)
- Dilip K Lakshman
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Daniel P Roberts
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Wesley M Garrett
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Savithiry S Natarajan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Omar Darwish
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Nadim Alkharouf
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Arnab Pain
- Pathogen Genomics, KAUST , Thuwal, Saudi Arabia 23955
| | - Farooq Khan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | | | - Amitava Mitra
- Department of Plant Pathology, University of Nebraska , Lincoln, Nebraska 68583, United States
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9
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Li S, Darwish O, Alkharouf N, Matthews B, Ji P, Domier LL, Zhang N, Bluhm BH. Draft genome sequence of Phomopsis longicolla isolate MSPL 10-6. Genom Data 2015; 3:55-6. [PMID: 26484148 PMCID: PMC4535830 DOI: 10.1016/j.gdata.2014.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 11/10/2014] [Indexed: 11/26/2022]
Abstract
Phomopsis longicolla is the primary cause of Phomopsis seed decay in soybean. This disease severely affects soybean seed quality by reducing seed viability and oil content, altering seed composition, and increasing frequencies of moldy and/or split beans. It is one of the most economically important soybean diseases. Here, we report the de novo assembled draft genome sequence of the P. longicolla isolate MSPL10-6, which was isolated from field-grown soybean seed in Mississippi, USA. This study represents the first reported genome sequence of a seedborne fungal pathogen in the Diaporthe-Phomopsis complex. The P. longicolla genome sequence will enable research into the genetic basis of fungal infection of soybean seed and provide information for the study of soybean-fungal interactions. The genome sequence will also be valuable for molecular genetic marker development, manipulation of pathogenicity-related genes and development of new control strategies for this pathogen.
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Affiliation(s)
- Shuxian Li
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Crop Genetics Research Unit, Stoneville, MS 38776, USA
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University, MD 21252, USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, MD 21252, USA
| | - Benjamin Matthews
- USDA-ARS, Beltsville Agriculture Research Center, Beltsville, MD 21075, USA
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA 31794, USA
| | - Leslie L. Domier
- USDA-ARS, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Ning Zhang
- Department of Plant Biology Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Burton H. Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
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10
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Hollender CA, Kang C, Darwish O, Geretz A, Matthews BF, Slovin J, Alkharouf N, Liu Z. Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks. Plant Physiol 2014; 165:1062-1075. [PMID: 24828307 PMCID: PMC4081322 DOI: 10.1104/pp.114.237529] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 05/10/2014] [Indexed: 05/18/2023]
Abstract
Flowers are reproductive organs and precursors to fruits and seeds. While the basic tenets of the ABCE model of flower development are conserved in angiosperms, different flowering plants exhibit different and sometimes unique characteristics. A distinct feature of strawberry (Fragaria spp.) flowers is the development of several hundreds of individual apocarpous (unfused) carpels. These individual carpels are arranged in a spiral pattern on the subtending stem tip, the receptacle. Therefore, the receptacle is an integral part of the strawberry flower and is of significant agronomic importance, being the precursor to strawberry fruit. Taking advantage of next-generation sequencing and laser capture microdissection, we generated different tissue- and stage-transcriptomic profiling of woodland strawberry (Fragaria vesca) flower development. Using pairwise comparisons and weighted gene coexpression network analysis, we identified modules of coexpressed genes and hub genes of tissue-specific networks. Of particular importance is the discovery of a developing receptacle-specific module exhibiting similar molecular features to those of young floral meristems. The strawberry homologs of a number of meristem regulators, including LOST MERISTEM and WUSCHEL, are identified as hub genes operating in the developing receptacle network. Furthermore, almost 25% of the F-box genes in the genome are transiently induced in developing anthers at the meiosis stage, indicating active protein degradation. Together, this work provides important insights into the molecular networks underlying strawberry's unique reproductive developmental processes. This extensive floral transcriptome data set is publicly available and can be readily queried at the project Web site, serving as an important genomic resource for the plant biology research community.
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Affiliation(s)
- Courtney A Hollender
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
| | - Chunying Kang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
| | - Omar Darwish
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
| | - Aviva Geretz
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
| | - Benjamin F Matthews
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
| | - Janet Slovin
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
| | - Nadim Alkharouf
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20817 (C.A.H., C.K., A.G., Z.L.);Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252 (O.D., N.A.); andSoybean Genomics and Improvement (B.F.M.), and Genetic Improvement of Fruits and Vegetables (J.S.), United States Department of Agriculture-Agricultural Research Service, Beltsville, Maryland 20705
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11
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Kang C, Darwish O, Geretz A, Shahan R, Alkharouf N, Liu Z. Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. Plant Cell 2013; 25:1960-78. [PMID: 23898027 PMCID: PMC3723606 DOI: 10.1105/tpc.113.111732] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/19/2013] [Accepted: 06/07/2013] [Indexed: 05/18/2023]
Abstract
Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacle's surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution. The data suggest that the endosperm and seed coat may play a more prominent role than the embryo in auxin and gibberellin biosynthesis for fruit set. A model is proposed to illustrate how hormonal signals produced in the endosperm and seed coat coordinate seed, ovary wall, and receptacle fruit development. The comprehensive fruit transcriptome data set provides a wealth of genomic resources for the strawberry and Rosaceae communities as well as unprecedented molecular insight into fruit set and early stage fruit development.
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Affiliation(s)
- Chunying Kang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252
| | - Aviva Geretz
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Rachel Shahan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, Maryland 21252
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
- Address correspondence to
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12
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Lakshman DK, Alkharouf N, Roberts DP, Natarajan SS, Mitra A. Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors. Mycologia 2012; 104:1020-35. [DOI: 10.3852/11-226] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Rowland LJ, Alkharouf N, Darwish O, Ogden EL, Polashock JJ, Bassil NV, Main D. Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biol 2012; 12:46. [PMID: 22471859 PMCID: PMC3378433 DOI: 10.1186/1471-2229-12-46] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/02/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND There has been increased consumption of blueberries in recent years fueled in part because of their many recognized health benefits. Blueberry fruit is very high in anthocyanins, which have been linked to improved night vision, prevention of macular degeneration, anti-cancer activity, and reduced risk of heart disease. Very few genomic resources have been available for blueberry, however. Further development of genomic resources like expressed sequence tags (ESTs), molecular markers, and genetic linkage maps could lead to more rapid genetic improvement. Marker-assisted selection could be used to combine traits for climatic adaptation with fruit and nutritional quality traits. RESULTS Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum) cultivar Bluecrop and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. Over 600,000 reads were assembled into approximately 15,000 contigs and 124,000 singletons. The assembled sequences were annotated and functionally mapped to Gene Ontology (GO) terms. Frequency of the most abundant sequences in each of the libraries was compared across all libraries to identify genes that are potentially differentially expressed during cold acclimation and fruit development. Real-time PCR was performed to confirm their differential expression patterns. Overall, 14 out of 17 of the genes examined had differential expression patterns similar to what was predicted from their reads alone. The assembled sequences were also mined for SSRs. From these sequences, 15,886 blueberry EST-SSR loci were identified. Primers were designed from 7,705 of the SSR-containing sequences with adequate flanking sequence. One hundred primer pairs were tested for amplification and polymorphism among parents of two blueberry populations currently being used for genetic linkage map construction. The tetraploid mapping population was based on a cross between the highbush cultivars Draper and Jewel (V. darrowii is also in the background of 'Jewel'). The diploid mapping population was based on a cross between an F1 hybrid of V. darrowii and diploid V. corymbosum and another diploid V. corymbosum. The overall amplification rate of the SSR primers was 68% and the polymorphism rate was 43%. CONCLUSIONS These results indicate that this large collection of 454 ESTs will be a valuable resource for identifying genes that are potentially differentially expressed and play important roles in flower bud development, cold acclimation, chilling unit accumulation, and fruit development in blueberry and related species. In addition, the ESTs have already proved useful for the development of SSR and EST-PCR markers, and are currently being used for construction of genetic linkage maps in blueberry.
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Affiliation(s)
- Lisa J Rowland
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705, USA
| | - Nadim Alkharouf
- Department of Computer and Information Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
| | - Elizabeth L Ogden
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705, USA
| | - James J Polashock
- Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, Blueberry and Cranberry Research Center, 125A Lake Oswego Road, Chatsworth, NJ 08019, USA
| | - Nahla V Bassil
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333-2521, USA
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA
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14
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Brennan SE, Kuwano Y, Alkharouf N, Blackshear PJ, Gorospe M, Wilson GM. The mRNA-destabilizing protein tristetraprolin is suppressed in many cancers, altering tumorigenic phenotypes and patient prognosis. Cancer Res 2009; 69:5168-76. [PMID: 19491267 DOI: 10.1158/0008-5472.can-08-4238] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
AU-rich element-binding proteins (ARE-BP) regulate the stability and/or translational efficiency of mRNAs containing cognate binding sites. Many targeted transcripts encode factors that control processes such as cell division, apoptosis, and angiogenesis, suggesting that dysregulated ARE-BP expression could dramatically influence oncogenic phenotypes. Using several approaches, we evaluated the expression of four well-characterized ARE-BPs across a variety of human neoplastic syndromes. AUF1, TIA-1, and HuR mRNAs were not systematically dysregulated in cancers; however, tristetraprolin mRNA levels were significantly decreased across many tumor types, including advanced cancers of the breast and prostate. Restoring tristetraprolin expression in an aggressive tumor cell line suppressed three key tumorgenic phenotypes: cell proliferation, resistance to proapoptotic stimuli, and expression of vascular endothelial growth factor mRNA. However, the cellular consequences of tristetraprolin expression varied across different cell models. Analyses of gene array data sets revealed that suppression of tristetraprolin expression is a negative prognostic indicator in breast cancer, because patients with low tumor tristetraprolin mRNA levels were more likely to present increased pathologic tumor grade, vascular endothelial growth factor expression, and mortality from recurrent disease. Collectively, these data establish that tristetraprolin expression is frequently suppressed in human cancers, which in turn can alter tumorigenic phenotypes that influence patient outcomes.
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Affiliation(s)
- Sarah E Brennan
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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15
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Klink VP, Alkharouf N, MacDonald M, Matthews B. Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogen Heterodera glycines (soybean cyst nematode). Plant Mol Biol 2005; 59:965-79. [PMID: 16307369 DOI: 10.1007/s11103-005-2416-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2005] [Accepted: 08/22/2005] [Indexed: 05/05/2023]
Abstract
Roots of soybean, Glycine max cv. Kent L. Merr., plants susceptible to the soybean cyst nematode (SCN), Heterodera glycines Ichinohe, were inoculated and allowed to develop feeding sites (syncytia) for 8 days. Root samples enriched in syncytial cells were collected using laser capture microdissection (LCM). RNA was extracted and used to make a cDNA library and expressed sequence tags (ESTs) were produced and used for a Gene Ontology (GO) analysis. RT-PCR results indicated enhanced expression of an aquaporin (GmPIP2,2), alpha-tubulin (GmTubA1), beta-tubulin (GmTubB4) and several other genes in syncytium-enriched samples as compared to samples extracted from whole roots. While RT-PCR data showed increased transcript levels of GmPIP2,2 from LCM tissue enriched in syncytial cells, in situ hybridization showed prominent GmPIP2,2 hybridization to RNA in the parenchymal cells tightly juxtaposed to the syncytium. Immunolocalization indicated stronger alpha-tubulin signal within the syncytium as compared to surrounding tissue. However, alpha-tubulin labeling appeared diffuse or clumped. Thus, LCM allowed for the isolation of tissue enriched for syncytial cells, providing material suitable for a variety of molecular analyses.
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Affiliation(s)
- Vincent P Klink
- United States Department of Agriculture, 10300, Baltimore Ave., Bldg. 006, Rm. 118, Beltsville, MD, 20705-2350, USA.
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Khan R, Alkharouf N, Beard H, Macdonald M, Chouikha I, Meyer S, Grefenstette J, Knap H, Matthews B. Microarray analysis of gene expression in soybean roots susceptible to the soybean cyst nematode two days post invasion. J Nematol 2004; 36:241-248. [PMID: 19262812 PMCID: PMC2620781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Soybean root cells undergo dramatic morphological and biochemical changes during the establishment of a feeding site in a compatible interaction with the soybean cyst nematode (SCN). We constructed a cDNA microarray with approximately 1,300 cDNA inserts targeted to identify differentially expressed genes during the compatible interaction of SCN with soybean roots 2 days after infection. Three independent biological replicates were grown and inoculated with SCN, and 2 days later RNA was extracted for hybridization to microarrays and compared to noninoculated controls. Statistical analysis indicated that approximately 8% of the genes monitored were induced and more than 50% of these were genes of unknown function. Notable genes that were more highly expressed 2 days after inoculation with SCN as compared to noninoculated roots included the repetitive proline-rich glycoprotein, the stress-induced gene SAM22, ss-1,3-endoglucanase, peroxidase, and those involved in carbohydrate metabolism, plant defense, and signaling.
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Abstract
The soybean cyst nematode (SCN) Heterodera glycines is the most devastating pest of soybean in the U.S.A. The resistance response elicited by SCN in soybean is complex, and genes involved in the response to a large extent are unknown and not well characterized. We constructed cDNA libraries made from mRNA extracted from roots of the resistant soybean Glycine max L. Merr. 'Peking' at 12 h, 2 to 4 days, and 6 to 8 days post inoculation with the soybean cyst nematode, population NL1-RHp, similar to race 3. Expressed sequence tag analysis of the libraries provides rapid discovery of genes involved in the response of soybean to the nematode. A total of 3454 cDNA clones were examined from the three libraries, of which 25 cDNAs were derived from nematode RNA. The levels of certain stress-induced genes such as SAM22 and glutathione S-transferase (GST8) were elevated in the SCN-infected roots relative to uninoculated roots. Early defense response genes, particularly ascorbate peroxidase and lipoxygenase, were abundant in the 12-h library. By 6-8 days, the expression of most of those genes was not as abundant, whereas genes coding for unknown proteins and stress-induced proteins continued to be highly expressed. These ESTs and associated information will be useful to scientists examining gene and protein interactions between nematodes and plants.
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Affiliation(s)
- Nadim Alkharouf
- USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
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Min W, Lillehoj HS, Kim S, Zhu JJ, Beard H, Alkharouf N, Matthews BF. Profiling local gene expression changes associated with Eimeria maxima and Eimeria acervulina using cDNA microarray. Appl Microbiol Biotechnol 2003; 62:392-9. [PMID: 12712262 DOI: 10.1007/s00253-003-1303-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2002] [Revised: 02/22/2003] [Accepted: 03/06/2003] [Indexed: 10/26/2022]
Abstract
Eimeria parasites show preferential sites of invasion in the avian intestine and produce a species-specific host immune response. Two economically important species, Eimeria acervulina and Eimeria maxima, preferentially invade and develop in the avian duodenum and jejunum/ileum, respectively. To investigate local host immune responses induced by parasite infection, global transcriptional changes in intestinal intraepithelial lymphocytes (IELs) induced by oral inoculation of chickens with E. acervulina or E. maxima were monitored using cDNA microarrays containing 400 unique chicken genes. Multiple gene transcripts were significantly up- or down-regulated following primary or secondary infection with E. acervulina or E. maxima. In general, infection by either parasite resulted in the expression changes of more genes following primary infection than following secondary infection, and E. acervulina caused more changes than did E. maxima. Although different regions of the small intestine were infected, similar changes in the levels of several cytokine mRNAs were observed in both Eimeria species following primary infection. Also identified was a set of transcripts whose expression was commonly enhanced or repressed in intestinal IELs of chickens infected with either parasite. Microarray analysis of chicken genes induced or repressed following Eimeria infection offers a powerful tool to enhance our understanding of host-parasite interactions leading to protective immunity.
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Affiliation(s)
- W Min
- Parasite Biology, Epidemiology and Systematics Laboratory, Animal and Natural Resources Institute, Beltsville Agricultural Research Service, U.S. Department of Agriculture, Building 1040, BARC-East, Beltsville, MD 20705, USA
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Morimoto M, Zarlenga D, Beard H, Alkharouf N, Matthews BF, Urban JF. Ascaris suum: cDNA microarray analysis of 4th stage larvae (L4) during self-cure from the intestine. Exp Parasitol 2003; 104:113-21. [PMID: 14552858 DOI: 10.1016/s0014-4894(03)00139-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
There is spontaneous cure of a large portion of Ascaris suum 4th-stage larvae (L4) from the jejunum of infected pigs between 14 and 21 days after inoculation (DAI). Those L4 that remain in the jejunum continue to develop while those that have moved to the ileum are eventually expelled from the intestines. Although increases in intestinal mucosal mast cells and changes in local host immunity are coincidental with spontaneous cure, the population of L4 that continue to develop in the jejunum may counteract host protective mechanisms by the differential production of factors related to parasitism. To this end, a cDNA library was constructed from L4 isolated from pig jejunum at 21 DAI, and 93% of 1920 original clones containing a single amplicon in the range 400-1500 bp were verified by gel electrophoresis and printed onto glass slides for microarray analysis. Fluorescent probes were prepared from total RNA isolated from: (1) 3rd stage-larvae from lung at 7 DAI, (L3); (2) L4 from jejunum at 14 DAI (L4-14-J); (3) L4 from jejunum at 21 DAI (L4-21-J); (4) L4 from ileum at 21 DAI (L4-21-I, and; (5) adults (L5). Cy3-labeled L3, L4-14-J, L4-21-I and L5 cDNA, and Cy5-labeled L4-21-J cDNA were simultaneously used to screen the printed arrays containing the L4-21-J-derived cDNA library. Several clones showed consistent differential gene expression over two separate experiments and were grouped into 3 distinct transcription patterns. The data showed that sequences from muscle actin and myosin, ribosomal protein L11, glyceraldehyde-3-phosphate dehydrogenase and the flavoprotein subunit of succinate dehydrogenase were highly expressed in L4-21-J, but not in L4-21-I; as were a collection of un-annotated genes derived from a worm body wall-hypodermis library, and a testes germinal zone tissue library. These results suggest that only actively developing A. suum L4 are destined to parasitize the host and successfully neutralize host protective responses.
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Affiliation(s)
- Motoko Morimoto
- United States Department of Agriculture, Agricultural Research Service, Nutrient Requirements and Functions Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD 20705, USA
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