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Petrović K, Skaltsas D, Castlebury LA, Kontz B, Allen TW, Chilvers MI, Gregory N, Kelly HM, Koehler AM, Kleczewski NM, Mueller DS, Price PP, Smith DL, Mathew FM. Diaporthe Seed Decay of Soybean [ Glycine max (L.) Merr.] Is Endemic in the United States, But New Fungi Are Involved. Plant Dis 2021; 105:1621-1629. [PMID: 33231523 DOI: 10.1094/pdis-03-20-0604-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Diaporthe seed decay can compromise seed quality in soybean [Glycine max (L.) Merr.] in the warm and humid production areas of the United States during crop maturation. In the current study, 45 isolates of Diaporthe were recovered from seed sampled from soybean fields affected by Diaporthe-associated diseases in eight U.S. states in 2017. The isolates obtained belonged to 10 species of Diaporthe based on morphology and phylogenetic analyses of the internal transcribed spacer, partial translation elongation factor 1-α, and β-tubulin gene sequences. The associated species included D. aspalathi, D. caulivora, D. kongii, D. longicolla, D. sojae, D. ueckerae, D. unshiuensis, and three novel fungi, D. bacilloides, D. flavescens, and D. insulistroma. One isolate each of the 10 species was examined for pathogenicity on seed of cultivar Sava under controlled conditions. Seven days postinoculation, significant differences in the percentages of decayed seeds and seedling necrosis were observed among the isolates and the noninoculated control (P < 0.0001). While the isolates of D. bacilloides, D. longicolla, and D. ueckerae caused a significantly greater percentage of decayed seeds (P < 0.0001), the isolate of D. aspalathi caused the greatest seedling necrosis (P < 0.0001). The observation of new fungi causing Diaporthe seed decay suggests the need for a more comprehensive survey in U.S. soybean producing areas since members of the genus Diaporthe appear to form a complex that causes seed decay.
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Affiliation(s)
- Kristina Petrović
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
- Department of Soybean, Institute of Field and Vegetable Crops, Novi Sad 21000, Serbia
| | - Demetra Skaltsas
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Lisa A Castlebury
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Brian Kontz
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
| | - Tom W Allen
- Delta Research and Extension Center, Mississippi State University, Stoneville, MS 38776, U.S.A
| | - Martin I Chilvers
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Nancy Gregory
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, U.S.A
| | - Heather M Kelly
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - Alyssa M Koehler
- Department of Plant and Soil Sciences, University of Delaware, Georgetown, DE 19947, U.S.A
| | - Nathan M Kleczewski
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL 61820, U.S.A
| | - Daren S Mueller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Paul P Price
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Winnsboro, LA 71295, U.S.A
| | - Damon L Smith
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Febina M Mathew
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
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Li S. Development of a seedling inoculation technique for rapid evaluation of soybean for resistance to Phomopsis longicolla under controlled conditions. Plant Methods 2018; 14:81. [PMID: 30214468 PMCID: PMC6131871 DOI: 10.1186/s13007-018-0348-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/06/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Phomopsis seed decay (PSD) of soybean (Glycine max L. Merr.) is caused primarily by the seed-borne fungal pathogen Phomopsis longicolla T. W. Hobbs. The PSD disease reduces seed quality and yield worldwide. Development of effective techniques to evaluate soybean for resistance to PSD can facilitate identification of new sources of host resistance to manage the disease. This study was undertaken to develop and utilize a rapid cut-seedling inoculation technique to evaluate soybean genotypes for resistance to P. longicolla under controlled conditions. RESULTS There were no significant differences in stem lesion length determined as the area under disease progress curve at 24 °C and 30 °C. The 21 and 14-day-old seedlings were more susceptible than the older seedlings. Inoculation with 7 or 14-day-old pathogens caused higher values of AUDPC than older pathogen cultures. Isolates MS17-1 was the most aggressive isolate from the test of 25 isolates from seven states in the U.S. Eighteen previously reported field PSD-resistant accessions had significantly lower AUDPC than the susceptible checks and other entries (P ≤ 0.05). CONCLUSION This study provided rapid evaluation of soybeans for reaction to P. longicolla and identification of PSD-resistant genotypes. Although PSD is a soybean seed disease, results from the cut-seedling inoculation assays without waiting a whole growing season were comparable to those obtained from field tests. Additionally, concerns about the environmental effects and uneven distribution of the pathogen in the field were ameliorated. The cut-seedling inoculation technique can also be used to speed up evaluation of PSD populations for the discovery of PSD-resistance gene(s), and high throughput phenotyping of seed diseases at seedling stage for genetics and genomic studies.
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Affiliation(s)
- Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA, ARS), P. O. Box 345, Stoneville, MS 38776 USA
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Zaccaron M, Sharma S, Bluhm BH. MoNSTR-seq, a restriction site-associated DNA sequencing technique to characterize Agrobacterium-mediated transfer-DNA insertions in Phomopsis longicolla. Lett Appl Microbiol 2018; 66:19-24. [PMID: 29108115 DOI: 10.1111/lam.12817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 10/14/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Phomopsis longicolla (Hobbs) causes Phomopsis seed decay and stem lesions in soybean (Glycine max). In this study, a novel, high-throughput adaptation of RAD-seq termed MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions) was developed to determine the genomic location of T-DNA insertions in P. longicolla mutants. Insertional mutants were created via Agrobacterium tumefaciens-mediated transformation, and one mutant, strain PL343, was further investigated due to impaired stem lesion formation. Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions, in which DNA libraries are created with two distinct restriction enzymes and customized adapters to simultaneously enrich both T-DNA insertion borders, was developed to characterize the genomic lesion in strain PL343. MoNSTR-seq successfully identified a T-DNA insertion in the predicted promoter region of a gene encoding a cellobiose dehydrogenase (CDH1), and the position of the T-DNA insertion in strain PL343 was confirmed by Sanger sequencing. Thus, MoNSTR-seq represents an effective tool for molecular genetics in P. longicolla, and is readily adaptable for use in diverse fungal species. SIGNIFICANCE AND IMPACT OF THE STUDY This study describes MoNSTR-seq (Mutation analysis via Next-generation DNA Sequencing of T-DNA Regions), an adaptation of restriction site-associated DNA sequencing (RAD-seq) to identify the position of transfer-DNA (T-DNA) insertions in the genome of Phomopsis longicolla, an important pathogen of soybean. The technique enables high-throughput characterization of mutants generated via Agrobacterium tumefaciens-mediated transformation (ATMT), thus accelerating gene discovery via forward genetics. This technique represents a significant advancement over existing approaches to characterize T-DNA insertions in fungal genomes. With minor modifications, this technique could be easily adapted to taxonomically diverse fungal pathogens and additional mutagenesis cassettes.
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Affiliation(s)
- M Zaccaron
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - S Sharma
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - B H Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
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Li S, Darwish O, Alkharouf NW, Musungu B, Matthews BF. Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean. BMC Genomics 2017; 18:688. [PMID: 28870170 PMCID: PMC5584002 DOI: 10.1186/s12864-017-4075-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the mechanism of the disease development, the genome of an isolate, MSPL10-6, from Mississippi, USA was sequenced, de novo assembled, and analyzed. RESULTS The genome of MSPL 10-6 was estimated to be approximately 62 Mb in size with an overall G + C content of 48.6%. Of 16,597 predicted genes, 9866 genes (59.45%) had significant matches to genes in the NCBI nr database, while 18.01% of them did not link to any gene ontology classification, and 9.64% of genes did not significantly match any known genes. Analysis of the 1221 putative genes that encoded carbohydrate-activated enzymes (CAZys) indicated that 715 genes belong to three classes of CAZy that have a direct role in degrading plant cell walls. A novel fungal ulvan lyase (PL24; EC 4.2.2.-) was identified. Approximately 12.7% of the P. longicolla genome consists of repetitive elements. A total of 510 potentially horizontally transferred genes were identified. They appeared to originate from 22 other fungi, 26 eubacteria and 5 archaebacteria. CONCLUSIONS The genome of the P. longicolla isolate MSPL10-6 represented the first reported genome sequence in the fungal Diaporthe-Phomopsis complex causing soybean diseases. The genome contained a number of Pfams not described previously. Information obtained from this study enhances our knowledge about this seed-borne pathogen and will facilitate further research on the genomic basis and pathogenicity mechanism of P. longicolla and aids in development of improved strategies for efficient management of Phomopsis seed decay in soybean.
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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, Towson, MD, 21252, USA
| | - Nadim W Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Bryan Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901, USA
- Current address: USDA-ARS, Warm Water Aquaculture Unit, Stoneville, MS, 38776, USA
| | - Benjamin F Matthews
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville Agriculture Research Center, Beltsville, MD, 20705, USA
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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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Udayanga D, Castlebury LA, Rossman AY, Chukeatirote E, Hyde KD. The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops. Fungal Biol 2015; 119:383-407. [PMID: 25937066 DOI: 10.1016/j.funbio.2014.10.009] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 10/28/2014] [Indexed: 01/25/2023]
Abstract
Phytopathogenic species of Diaporthe are associated with a number of soybean diseases including seed decay, pod and stem blight and stem canker and lead to considerable crop production losses worldwide. Accurate morphological identification of the species that cause these diseases has been difficult. In this study, we determined the phylogenetic relationships and species boundaries of Diaporthe longicolla, Diaporthe phaseolorum, Diaporthe sojae and closely related taxa. Species boundaries for this complex were determined based on combined phylogenetic analysis of five gene regions: partial sequences of calmodulin (CAL), beta-tubulin (TUB), histone-3 (HIS), translation elongation factor 1-α (EF1-α), and the nuclear ribosomal internal transcribed spacers (ITS). Phylogenetic analyses revealed that this large complex of taxa is comprised of soybean pathogens as well as species associated with herbaceous field crops and weeds. Diaporthe arctii, Diaporthe batatas, D. phaseolorum and D. sojae are epitypified. The seed decay pathogen D. longicolla was determined to be distinct from D. sojae. D. phaseolorum, originally associated with stem and leaf blight of Lima bean, was not found to be associated with soybean. A new species, Diaporthe ueckerae on Cucumis melo, is introduced with description and illustrations.
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Affiliation(s)
- Dhanushka Udayanga
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture - Agricultural Research Service, Beltsville, MD 20705, USA; Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Lisa A Castlebury
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture - Agricultural Research Service, Beltsville, MD 20705, USA.
| | - Amy Y Rossman
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture - Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ekachai Chukeatirote
- Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kevin D Hyde
- Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China; World Agroforestry Centre, East and Central Asia, Kunming 650201, People's Republic of China
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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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