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da Silva LL, Tian H, Schemerhorn B, Xu JR, Cai G. Genome-Wide Informative Microsatellite Markers and Population Structure of Fusarium virguliforme from Argentina and the USA. J Fungi (Basel) 2023; 9:1109. [PMID: 37998914 PMCID: PMC10672573 DOI: 10.3390/jof9111109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/11/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
Soybean sudden death syndrome (SDS) is a destructive disease that causes substantial yield losses in South and North America. Whereas four Fusarium species were identified as the causal agents, F. virguliforme is the primary SDS-causing pathogen in North America and it also contributes substantially to SDS in Argentina. In this study, we comparatively analyzed genome assemblies of four F. virguliforme strains and identified 29 informative microsatellite markers. Sixteen of the 29 markers were used to investigate the genetic diversity and population structure of this pathogen in a collection of 90 strains from Argentina and the USA. A total of 37 multilocus genotypes (MLGs) were identified, including 10 MLGs in Argentina and 26 in the USA. Only MLG2, the most dominant MLG, was found in both countries. Analyses with three different approaches showed that these MLGs could be grouped into three clusters. Cluster IA consisting of four MLGs exclusively from the USA has much higher genetic diversity than the other two clusters, suggesting that it may be the ancestral cluster although additional data are necessary to support this hypothesis. Clusters IB and II consisted of 13 and 21 MLGs, respectively. MLGs belonging to these two clusters were present in all four sampled states in Argentina and all five sampled states in the USA.
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Affiliation(s)
- Leandro Lopes da Silva
- Crop Production and Pest Control Research Unit, Agricultural Research Service, United States Department of Agriculture (USDA), West Lafayette, IN 47907, USA
| | - Huan Tian
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN 47907, USA
| | - Brandi Schemerhorn
- Crop Production and Pest Control Research Unit, Agricultural Research Service, United States Department of Agriculture (USDA), West Lafayette, IN 47907, USA
| | - Jin-Rong Xu
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN 47907, USA
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, Agricultural Research Service, United States Department of Agriculture (USDA), West Lafayette, IN 47907, USA
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN 47907, USA
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Mattupalli C, Cuenca FP, Shiller JB, Watkins T, Hansen K, Garzon CD, Marek SM, Young CA. Genetic Diversity of Phymatotrichopsis omnivora Based on Mating Type and Microsatellite Markers Reveals Heterothallic Mating System. PLANT DISEASE 2022; 106:2105-2116. [PMID: 35156845 DOI: 10.1094/pdis-01-22-0013-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phymatotrichopsis omnivora is a member of Pezizomycetes and causes root rot disease on a broad range of dicotyledonous plants. Using recently generated draft genome sequence data from four P. omnivora isolates, we developed simple sequence repeat (SSR) markers and identified both mating type genes (MAT1-1-1 and MAT1-2-1) in this fungus. To understand the genetic diversity of P. omnivora isolates (n = 43) and spore mats (n = 29) collected from four locations (Oklahoma, Texas, Arizona, and Mexico) and four host crops (cotton, alfalfa, peach, and soybean), we applied 24 SSR markers and showed that of the 72 P. omnivora isolates and spore mats tested, 41 were distinct genotypes. Furthermore, the developed SSR markers did not show cross-transferability to other close relatives of P. omnivora in the class Pezizomycetes. A multiplex PCR detecting both mating type idiomorphs and a reference gene (TUB2) was developed to screen P. omnivora isolates. Based on the dataset we tested, P. omnivora is a heterothallic fungus with both mating types present in the United States in a ratio close to 1:1. We tested P. omnivora spore mats obtained from spatially distinct disease rings that developed in a center-pivot alfalfa field and showed that both mating types can be present not only in the same field but also within a single spore mat. This study shows that P. omnivora has the genetic toolkit for generating sexually diverse progeny, providing impetus for future studies that focus on identifying sexual morphs in nature.
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Affiliation(s)
- Chakradhar Mattupalli
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Plant Pathology, Washington State University, Mount Vernon NWREC, Mount Vernon, WA 98273, U.S.A
| | - Fernanda Proaño Cuenca
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK 74078, U.S.A
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
| | - Jason B Shiller
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Scion, Rotorua 3046, New Zealand
| | - Tara Watkins
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Karen Hansen
- Department of Botany, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Carla D Garzon
- Department of Plant Science and Landscape Architecture, Delaware Valley University, Doylestown, PA 18901, U.S.A
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
| | - Carolyn A Young
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
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He Y, Chen J, Tang C, Deng Q, Guo L, Cheng Y, Li Z, Wang T, Xu J, Gao C. Genetic Diversity and Population Structure of Fusarium commune Causing Strawberry Root Rot in Southcentral China. Genes (Basel) 2022; 13:genes13050899. [PMID: 35627284 PMCID: PMC9140712 DOI: 10.3390/genes13050899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Strawberry plants and fruits are vulnerable to infections by a broad range of pathogens and pests. However, knowledge about the epidemiology of pathogens causing strawberry diseases is limited. In this study, we analyzed Fusarium commune, a major fungal pathogen causing strawberry root rot, from diseased strawberry root tissues in southcentral China. A total of 354 isolates were obtained from 11 locations that spanned about 700 km from both south to north and east to west. Multilocus genotypes of all isolates were obtained using seven polymorphic simple sequence repeat markers developed in this study. Our analyses revealed significant genetic diversity within each of the 11 local populations of F. commune. STRUCTURE analysis revealed that the optimal number of genetic populations for the 354 strains was two, with most local geographic populations containing isolates in both genetic clusters. Interestingly, many isolates showed allelic ancestry to both genetic clusters, consistent with recent hybridization between the two genetic clusters. In addition, though alleles and genotypes were frequently shared among local populations, statistically significant genetic differentiations were found among the local populations. However, the observed F. commune population genetic distances were not correlated with geographic distances. Together, our analyses suggest that populations of F. commune causing strawberry root rot are likely endemic to southcentral China, with each local population containing shared and unique genetic elements. Though the observed gene flow among geographic regions was relatively low, human activities will likely accelerate pathogen dispersals, resulting in the generation of new genotypes through mating and recombination.
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Affiliation(s)
- Yunlu He
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Chao Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Qiao Deng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
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Saleh AA, Sharafaddin AH, El Komy MH, Ibrahim YE, Hamad YK. Molecular and physiological characterization of Fusarium strains associated with different diseases in date palm. PLoS One 2021; 16:e0254170. [PMID: 34293008 PMCID: PMC8297770 DOI: 10.1371/journal.pone.0254170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Several species of Fusarium cause serious diseases in date palm worldwide. In the present work, 14 SSR markers were used to assess the genetic variation of Fusarium strains isolated from diseased trees in Saudi Arabia. We also studied the effect of different temperatures on mycelial growth of these strains. The pathogenicity of four strains of F. proliferatum was also evaluated on local date palm cultivars. Eleven SSR markers amplified a total of 57 scorable alleles from Fusarium strains. Phylogenetic analysis showed that F. proliferatum strains grouped in one clade with 95% bootstrap value. Within F. proliferatum clade, 14 SSR genotypes were identified, 9 of them were singleton. Four out of the five multi-individual SSR genotypes contained strains isolated from more than one location. Most F. solani strains grouped in one clade with 95% bootstrap value. Overall, the SSR markers previously developed for F. verticillioides and F. oxysporum were very useful in assessing the genetic diversity and confirming the identity of Saudi Fusarium strains. The results from the temperature study showed significant differences in mycelial growth of Fusarium strains at different temperatures tested. The highest average radial growth for Fusarium strains was observed at 25°C, irrespective of species. The four F. proliferatum strains showed significant differences in their pathogenicity on date palm cultivars. It is anticipated that the assessment of genetic diversity, effect of temperature on hyphal growth and pathogenicity of potent pathogenic Fusarium strains recovered from date palm-growing locations in Saudi Arabia can help in effectively controlling these pathogens.
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Affiliation(s)
- Amgad A Saleh
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.,Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Anwar H Sharafaddin
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mahmoud H El Komy
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.,Plant Pathology Institute, Agriculture Research Center, Giza, Egypt
| | - Yasser E Ibrahim
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.,Plant Pathology Institute, Agriculture Research Center, Giza, Egypt
| | - Younis K Hamad
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.,Plant Pathology Department, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
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Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici. J Microbiol Methods 2017; 139:113-122. [PMID: 28457942 DOI: 10.1016/j.mimet.2017.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 11/20/2022]
Abstract
Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species.
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