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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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Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses. PLANTS 2022; 11:plants11151962. [PMID: 35956440 PMCID: PMC9370660 DOI: 10.3390/plants11151962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes.
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Gill US, Nandety RS, Krom N, Dai X, Zhuang Z, Tang Y, Zhao PX, Mysore KS. Draft Genome Sequence Resource of Switchgrass Rust Pathogen, Puccinia novopanici Isolate Ard-01. PHYTOPATHOLOGY 2019; 109:1513-1515. [PMID: 31050598 DOI: 10.1094/phyto-04-19-0118-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Puccinia novopanici is an important biotrophic fungal pathogen that causes rust disease in switchgrass. Lack of genomic resources for P. novopanici has hampered the progress toward developing effective disease resistance against this pathogen. Therefore, we have sequenced the whole genome of P. novopanici and generated a framework to understand pathogenicity mechanisms and identify effectors, repeat element invasion, genome evolution, and comparative genomics among Puccinia spp. in the future. Long- and short-read sequences were generated from P. novopanici genomic DNA by PacBio and Illumina technologies, respectively, and assembled a 99.9-Mb genome. Transcripts of P. novopanici were predicted from assembled genome using MAKER and were further validated by RNAseq data. The genome sequence information of P. novopanici will be a valuable resource for researchers working on monocot rusts and plant disease resistance in general.
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Affiliation(s)
- Upinder S Gill
- Noble Research Institute, LLC., Ardmore, OK, 73401, U.S.A
| | | | - Nick Krom
- Noble Research Institute, LLC., Ardmore, OK, 73401, U.S.A
| | - Xinbin Dai
- Noble Research Institute, LLC., Ardmore, OK, 73401, U.S.A
| | | | - Yuhong Tang
- Noble Research Institute, LLC., Ardmore, OK, 73401, U.S.A
| | - Patrick X Zhao
- Noble Research Institute, LLC., Ardmore, OK, 73401, U.S.A
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Kenaley SC, Quan M, Aime MC, Bergstrom GC. New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1434-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Development and Characterization of Novel Genic-SSR Markers in Apple-Juniper Rust Pathogen Gymnosporangium yamadae (Pucciniales: Pucciniaceae) Using Next-Generation Sequencing. Int J Mol Sci 2018; 19:ijms19041178. [PMID: 29649169 PMCID: PMC5979324 DOI: 10.3390/ijms19041178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/03/2018] [Accepted: 04/08/2018] [Indexed: 11/21/2022] Open
Abstract
The Apple-Juniper rust, Gymnosporangium yamadae, is an economically important pathogen of apples and junipers in Asia. The absence of markers has hampered the study of the genetic diversity of this widespread pathogen. In our study, we developed twenty-two novel microsatellite markers for G. yamadae from randomly sequenced regions of the transcriptome, using next-generation sequencing methods. These polymorphic markers were also tested on 96 G. yamadae individuals from two geographical populations. The allele numbers ranged from 2 to 9 with an average value of 6 per locus. The polymorphism information content (PIC) values ranged from 0.099 to 0.782 with an average value of 0.48. Furthermore, the observed (HO) and expected (HE) heterozygosity ranged from 0.000 to 0.683 and 0.04 to 0.820, respectively. These novel developed microsatellites provide abundant molecular markers for investigating the genetic structure and genetic diversity of G. yamadae, which will help us to better understand disease epidemics and the origin and migration routes of the Apple-Juniper rust pathogen. Further studies will also be completed to dissect how human activities influence the formation of current population structures. Furthermore, these SSR (simple sequence repeat) markers can also be used as tools to identify virulence by mapping the whole genomes of different virulent populations. These markers will, thus, assist the development of effective risk-assessment models and management systems for the Apple-Juniper rust pathogen.
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