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Rodrigues Jardim B, Gambley C, Tran-Nguyen LTT, Webster C, Kehoe M, Kinoti WM, Bond S, Davis R, Jones L, Pathania N, Sharman M, Chapman T, Rodoni BC, Constable FE. A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions. Microb Genom 2024; 10:001213. [PMID: 38446015 PMCID: PMC10999746 DOI: 10.1099/mgen.0.001213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group ('Ca. Phytoplasma stylosanthis'; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and 'Ca. Phytoplasma stylosanthis'. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of 'Ca. Phytoplasma australasiaticum' and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.
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Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | | | - Craig Webster
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Monica Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Samantha Bond
- Biosecurity and Animal Welfare, Department of Industry, Tourism and Trade, Darwin, Northern Territory, Australia
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Nandita Pathania
- Department of Agriculture and Fisheries, Mareeba, Queensland, Australia
| | - Murray Sharman
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - Toni Chapman
- Biosecurity and Food Safety, New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, 2567, Australia
| | - Brendan C. Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E. Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
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De Silva PR, Perera CN, Bahder BW, Attanayake RN. Nested PCR-Based Rapid Detection of Phytoplasma Leaf Wilt Disease of Coconut in Sri Lanka and Systemic Movement of the Pathogen. Pathogens 2023; 12:pathogens12020294. [PMID: 36839566 PMCID: PMC9966644 DOI: 10.3390/pathogens12020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Phytoplasmas are associated with many plant diseases. In palms, lethal bronzing disease, Texas Phoenix palm decline, and coconut lethal yellowing decline are some of them. In Sri Lanka, coconut leaf wilt decline has been reported in the Weligama area of the Southern province, and the disease is called Weligama coconut leaf wilt disease (WCLWD). Unlike other phytoplasma diseases of palms, WCLWD shows slow disease progress. Pathogen detection entirely relies on nested polymerase chain reaction (PCR). However, inconsistencies in pathogen detection have been experienced, i.e., symptomatic plants often produce negative results. The objectives of this study were to reconsider the choice of primers and to determine the best sampling tissue types for consistent detection of the pathogen. Among the six universal primer combinations tested, P1/Tint nested with fU5/rU3 produced consistent results. BLASTn searches of the sequences showed 99-100% similarity to sugarcane white leaf disease (SWL) or grassy shoot (SGS) disease-causing phytoplasma. The optimized nested PCR protocol was successful, with the minimum success rating of 88% and 100% specificity. Midribs of milky white bud leaf samples were the best tissue type for rapid detection. Systemic movement of the pathogen and a tentative latent period were also reported. The findings are helpful in the early detection of the disease.
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Affiliation(s)
- Prasad R. De Silva
- Crop Protection Division, Coconut Research Institute, Lunuwila 61150, Sri Lanka
| | - Chandrika N. Perera
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Brian W. Bahder
- Department of Entomology and Nematology, FLREC-University of Florida, Davie, FL 33314-7719, USA
| | - Renuka N. Attanayake
- Department of Plant and Molecular Biology, University of Kelaniya, Kelaniya 11600, Sri Lanka
- Correspondence:
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Ong S, Jonson GB, Calassanzio M, Rin S, Chou C, Oi T, Sato I, Takemoto D, Tanaka T, Choi IR, Nign C, Chiba S. Geographic Distribution, Genetic Variability and Biological Properties of Rice Orange Leaf Phytoplasma in Southeast Asia. Pathogens 2021; 10:pathogens10020169. [PMID: 33557226 PMCID: PMC7913950 DOI: 10.3390/pathogens10020169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rice orange leaf phytoplasma (ROLP) causes clear orange to yellowish leaf discoloration and severe stunting in rice seedlings. The ecological and biological characteristics of ROLP are largely unknown because the disease has not widely caused serious problems in rice cultivated areas, thereby leading to the low accumulation of research data. However, in the past decade, the disease became a threat to rice production, particularly in South China and India; it has also been recognised in other Asian countries, such as Vietnam, Thailand and the Philippines. Here, we observed the occurrence of ROLP in paddies of the Southeast Asian counties (Cambodia, Vietnam and the Philippines) and found that the isolates in the Philippines and Vietnam were monophyletic, while those in India, Thailand and Cambodia were more diverse, suggesting their potential origins. In Cambodia, it was revealed that following polymerase chain reaction (PCR) detection, the known ROLP-insect vectors, N. virescens Distant and Recilia dorsalis Motchulsky, were ROLP-positive, indicating their roles in pathogen dispersal. Moreover, fluorescent and scanning electron microscopy revealed the intensive accumulation of the phytoplasma in phloem tissues and massive accumulation of storage starch in vascular bundle sheath and parenchyma. Altogether, this study illustrated the genetic variability of global ROLP isolates and the pathogen’s biological impact on rice tissue.
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Affiliation(s)
- Socheath Ong
- Department of Crop Protection, Faculty of Agronomy, Royal University of Agriculture, Ministry of Agriculture, Forestry and Fisheries, Dangkor District, Phnom Penh 370, Cambodia;
- Nagoya University Asian Satellite Campuses Institute—Cambodian Campus, Royal University of Agriculture, Dangkor District, Phnom Penh 370, Cambodia; (S.R.); (I.-R.C.)
| | - Gilda B. Jonson
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Laguna 4031, Philippines;
| | - Matteo Calassanzio
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin, 40127 Bologna, Italy;
- Renolab Good Laboratory Practice, A Tentamus Company, Via XXV Aprile, San Giorgio di Piano, 40016 Bologna, Italy
| | - Soriya Rin
- Nagoya University Asian Satellite Campuses Institute—Cambodian Campus, Royal University of Agriculture, Dangkor District, Phnom Penh 370, Cambodia; (S.R.); (I.-R.C.)
| | - Cheythyrith Chou
- General Directorate of Agriculture, Ministry of Agriculture, Forestry and Fisheries, Tuol Kork, Phnom Penh 370, Cambodia; (C.C.); (C.N.)
| | - Takao Oi
- Department of Plant Production Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan; (T.O.); (I.S.); (D.T.); (T.T.)
| | - Ikuo Sato
- Department of Plant Production Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan; (T.O.); (I.S.); (D.T.); (T.T.)
| | - Daigo Takemoto
- Department of Plant Production Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan; (T.O.); (I.S.); (D.T.); (T.T.)
| | - Toshiharu Tanaka
- Department of Plant Production Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan; (T.O.); (I.S.); (D.T.); (T.T.)
| | - Il-Ryong Choi
- Nagoya University Asian Satellite Campuses Institute—Cambodian Campus, Royal University of Agriculture, Dangkor District, Phnom Penh 370, Cambodia; (S.R.); (I.-R.C.)
- International Rice Research Institute—Korea Office, National Institute of Crop Science, Wanju-Gun 235, Jeollabuk-Do, Korea
| | - Chhay Nign
- General Directorate of Agriculture, Ministry of Agriculture, Forestry and Fisheries, Tuol Kork, Phnom Penh 370, Cambodia; (C.C.); (C.N.)
| | - Sotaro Chiba
- Department of Plant Production Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan; (T.O.); (I.S.); (D.T.); (T.T.)
- Correspondence:
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Cheng Y, Tang X, Gao C, Li Z, Chen J, Guo L, Wang T, Xu J. Molecular Diagnostics and Pathogenesis of Fungal Pathogens on Bast Fiber Crops. Pathogens 2020; 9:pathogens9030223. [PMID: 32197350 PMCID: PMC7157645 DOI: 10.3390/pathogens9030223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 11/16/2022] Open
Abstract
Bast fibers and products derived from them are undergoing a resurgence in demand in the global market. However, fungal diseases have become an important factor limiting their yield and quality, causing devastating consequences for the production of bast fiber crops in many parts of the world. Thus, there is a high demand for effective control and prevention strategies against fungal pathogens. Having rapid, specific, sensitive, and cost-effective tests that can be used for early and accurate diagnosis of disease agents is an essential step of such strategies. The objective of this study was to review the current status of research on molecular diagnosis of fungal pathogens on bast fiber crops. Our search of PubMed identified nearly 20 genera of fungal pathogens on bast fiber crops, among which the five most common genera were Colletotrichum, Pythium, Verticillium, Fusarium, and Golovinomyces. The gene regions that have been used for molecular identifications of these fungi include internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), ß-tubulin, calmodulin (CAL), histone subunit 3 (H3), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), etc. We summarize the molecular assays that have been used to identify these fungi and discuss potential areas of future development for fast, specific, and accurate diagnosis of fungal pathogens on bast fiber crops.
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Affiliation(s)
- Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Xiaoyu Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (Y.C.); (X.T.); (C.G.); (Z.L.); (J.C.); (L.G.); (T.W.)
- Department of Biology, McMaster University, Hamilton, L8S 4K1, Canada
- Correspondence:
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