296 results on '"Michael G. K. Jones"'
Search Results
2. Machine learning‐based LoRa localisation using multiple received signal features
- Author
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Khondoker Ziaul Islam, David Murray, Dean Diepeveen, Michael G. K. Jones, and Ferdous Sohel
- Subjects
internet of things ,sensors ,wireless sensor networks ,Telecommunication ,TK5101-6720 - Abstract
Abstract Low‐power localisation systems are crucial for machine‐to‐machine communication technologies. This article investigates LoRa technology for localisation using multiple features of the received signal, such as Received Signal Strength Indicator (RSSI), Spreading Factors (SF), and Signal to Noise Ratio (SNR). A novel range‐based technique to estimate the distance of a target node from a LoRa gateway using machine‐learning models that incorporates SF, SNR, and RSSI to train the models is proposed. A modified trilateration approach is then used to localise the target node from three gateways. Our experiment used three LoRaWAN gateways and two sensor nodes, on a sports oval with an approximate area coverage of 30,000 square metres. The authors also used a public LoRaWAN dataset to build a model test the proposed method and compare both range‐based distance mapping with trilateration and fingerprint‐based direct location estimation techniques. Our method achieved an average distance error of 43.97 m on our experimental dataset. The results show that the combination of RSSI, SNR, and SF‐based distance mapping provides ∼10% improvement on ranging accuracy and 26.58% higher accuracy for trilateration‐based localisation when compared with just using RSSI. Our method also achieved 50% superior localisation accuracy with fingerprint‐based direct location estimation approaches.
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- 2023
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- View/download PDF
3. RNA interference of an orthologue of Dicer of Meloidogyne incognita alludes to the gene’s importance in nematode development
- Author
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Sadia Iqbal, Michael G. K. Jones, and John Fosu-Nyarko
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Medicine ,Science - Abstract
Abstract Dicers and dicer-like enzymes play an essential role in small RNA processing in eukaryotes. Nematodes are thought to encode one dicer, DCR-1; only that for Caenorhabditis spp. is well-characterised. Using genomic sequences of eight root-knot nematodes (Meloidogyne spp.), we identified putative coding sequences typical of eukaryotic DICERS. We noted that the primary and secondary structures of DICERS they encode were different for different Meloidogyne species and even for isolates of the same species, suggesting paralogy for the gene. One of the genes for M. incognita (Midcr-1.1) expressed in eggs, juvenile stage 2 and adults, with the highest expression in the adult females. All the Meloidogyne DICERS had seven major domains typical of those for Caenorhabditis spp. and humans with very similar protein folding. RNAi of Midcr-1.1 in J2s using seven dsRNAs, each based on sequences encoding the domains, induced mild paralysis but measurable knockdown was detected in J2s treated with five of the dsRNAs. For four of the dsRNAs, the RNAi effect lasted and reduced the nematode’s infectivity. Also, host plant delivery of dsRNAs complementary to coding sequences of the Dicer Dimerisation domain impaired development, reducing nematode infection by 71%. These results confirm the importance of the gene to nematode health.
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- 2021
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4. Multiplex CRISPR-Cas9 Gene-Editing Can Deliver Potato Cultivars with Reduced Browning and Acrylamide
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Diem Nguyen Phuoc Ly, Sadia Iqbal, John Fosu-Nyarko, Stephen Milroy, and Michael G. K. Jones
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CRISPR-Cas9 ,gene-editing ,potato ,reducing sugars ,acrylamide formation ,vacuolar invertase ,Botany ,QK1-989 - Abstract
Storing potato tubers at cold temperatures, either for transport or continuity of supply, is associated with the conversion of sucrose to reducing sugars. When cold-stored cut tubers are processed at high temperatures, with endogenous asparagine, acrylamide is formed. Acrylamide is classified as a carcinogen. Potato processors prefer cultivars which accumulate fewer reducing sugars and thus less acrylamide on processing, and suitable processing cultivars may not be available. We used CRISPR-Cas9 to disrupt the genes encoding vacuolar invertase (VInv) and asparagine synthetase 1 (AS1) of cultivars Atlantic and Desiree to reduce the accumulation of reducing sugars and the production of asparagine after cold storage. Three of the four guide RNAs employed induced mutation frequencies of 17–98%, which resulted in deletions, insertions and substitutions at the targeted gene sites. Eight of ten edited events had mutations in at least one allele of both genes; for two, only the VInv was edited. No wild-type allele was detected in both genes of events DSpco7, DSpFN4 and DSpco12, suggesting full allelic mutations. Tubers of two Atlantic and two Desiree events had reduced fructose and glucose concentrations after cold storage. Crisps from these and four other Desiree events were lighter in colour and included those with 85% less acrylamide. These results demonstrate that multiplex CRISPR-Cas9 technology can generate improved potato cultivars for healthier processed potato products.
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- 2023
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5. Small RNA Analyses of a Ceratobasidium Isolate Infected with Three Endornaviruses
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Chi T. H. Cao, Mark C. Derbyshire, Roshan Regmi, Hua Li, Michael G. K. Jones, and Stephen J. Wylie
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Ceratobasidium ,Endornavirus ,symbiosis ,RNAi ,small RNA ,Microbiology ,QR1-502 - Abstract
Isolates of three endornavirus species were identified co-infecting an unidentified species of Ceratobasidium, itself identified as a symbiont from within the roots of a wild plant of the terrestrial orchid Pterostylis vittata in Western Australia. Isogenic lines of the fungal isolate lacking all three mycoviruses were derived from the virus-infected isolate. To observe how presence of endornaviruses influenced gene expression in the fungal host, we sequenced fungus-derived small RNA species from the virus-infected and virus-free isogenic lines and compared them. The presence of mycoviruses influenced expression of small RNAs. Of the 3272 fungus-derived small RNA species identified, the expression of 9.1% (300 of 3272) of them were up-regulated, and 0.6% (18 of 3272) were down-regulated in the presence of the viruses. Fourteen novel micro-RNA-like RNAs (Cer-milRNAs) were predicted. Gene target prediction of the differentially expressed Cer-milRNAs was quite ambiguous; however, fungal genes involved in transcriptional regulation, catalysis, molecular binding, and metabolic activities such as gene expression, DNA metabolic processes and regulation activities were differentially expressed in the presence of the mycoviruses.
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- 2022
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6. Enabling Trade in Gene-Edited Produce in Asia and Australasia: The Developing Regulatory Landscape and Future Perspectives
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Michael G. K. Jones, John Fosu-Nyarko, Sadia Iqbal, Muhammad Adeel, Rhodora Romero-Aldemita, Mahaletchumy Arujanan, Mieko Kasai, Xun Wei, Bambang Prasetya, Satya Nugroho, Osman Mewett, Shahid Mansoor, Muhammad J. A. Awan, Reynante L. Ordonio, S. R. Rao, Abhijit Poddar, Penny Hundleby, Nipon Iamsupasit, and Kay Khoo
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gene editing ,genome editing ,Cas9 ,GEd ,biosafety ,Asia ,Botany ,QK1-989 - Abstract
Genome- or gene-editing (abbreviated here as ‘GEd’) presents great opportunities for crop improvement. This is especially so for the countries in the Asia-Pacific region, which is home to more than half of the world’s growing population. A brief description of the science of gene-editing is provided with examples of GEd products. For the benefits of GEd technologies to be realized, international policy and regulatory environments must be clarified, otherwise non-tariff trade barriers will result. The status of regulations that relate to GEd crop products in Asian countries and Australasia are described, together with relevant definitions and responsible regulatory bodies. The regulatory landscape is changing rapidly: in some countries, the regulations are clear, in others they are developing, and some countries have yet to develop appropriate policies. There is clearly a need for the harmonization or alignment of GEd regulations in the region: this will promote the path-to-market and enable the benefits of GEd technologies to reach the end-users.
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- 2022
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7. Spillover of a Tobamovirus from the Australian Indigenous Flora to Invasive Weeds
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Weinan Xu, Hua Li, Krishnapillai Sivasithamparam, Dieu Thi Tran, Michael G. K. Jones, Xin Chen, and Stephen J. Wylie
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virus spillover ,emergence ,wild-plant virus ,tobamovirus ,virus transmission ,Microbiology ,QR1-502 - Abstract
The tobamovirus yellow tailflower mild mottle virus (YTMMV) was previously reported in wild plants of Anthocercis species (family Solanaceae) and other solanaceous indigenous species growing in natural habitats in Western Australia. Here, we undertook a survey of two introduced solanaceous weeds, namely Solanum nigrum (black nightshade) and Physalis peruviana (cape gooseberry) in the Perth metropolitan area and surrounds to determine if YTMMV has spread naturally to these species. At a remnant natural bushland site where both solanaceous weeds and indigenous Anthocercis hosts grew adjacent to one another, a proportion of S. nigrum and P. peruviana plants were asymptomatically-infected with YTMMV, confirming spillover had occurred. Populations of S. nigrum also grow as weeds in parts of the city isolated from remnant bushland and indigenous sources of YTMMV, and some of these populations were also infected with YTMMV. Fruit was harvested from virus-infected wild S. nigrum plants and the seed germinated under controlled conditions. Up to 80% of resultant seedlings derived from infected parent plants were infected with YTMMV, confirming that the virus is vertically-transmitted in S. nigrum, and therefore infection appears to be self-sustaining in this species. This is the first report of spillover of YTMMV to exotic weeds, and of vertical transmission of this tobamovirus. We discuss the roles of vertical and horizontal transmission in this spillover event, and its implications for biosecurity.
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- 2022
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8. Attempt to Silence Genes of the RNAi Pathways of the Root-Knot Nematode, Meloidogyne incognita Results in Diverse Responses Including Increase and No Change in Expression of Some Genes
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Sadia Iqbal, John Fosu-Nyarko, and Michael G. K. Jones
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in vitro RNAi ,host-induced gene silencing ,Meloidogyne incognita ,nematode control ,root-knot nematodes ,RNAi pathway ,Plant culture ,SB1-1110 - Abstract
Control of plant-parasitic nematodes (PPNs) via host-induced gene silencing (HIGS) involves rational selection of genes and detailed assessment of effects of a possible knockdown on the nematode. Some genes by nature may be very important for the survival of the nematode that knockdown may be resisted. Possible silencing and effects of 20 such genes involved in the RNA interference (RNAi) pathways of Meloidogyne incognita were investigated in this study using long double-stranded RNAs (dsRNAs) as triggers. Two of the genes, ego-1 and mes-2, could not be knocked down. Expression of six genes (xpo-1, pash-1, xpo-2, rha-1, ekl-4, and csr-1) were significantly upregulated after RNAi treatment whereas for 12 of the genes, significant knockdown was achieved and with the exception of mes-2 and mes-6, RNAi was accompanied by defective phenotypes in treated nematodes including various degrees of paralysis and abnormal behaviors and movement such as curling, extreme wavy movements, and twitching. These abnormalities resulted in up to 75% reduction in infectivity of a tomato host, the most affected being the J2s previously treated with dsRNA of the gfl-1 gene. For 10 of the genes, effects of silencing in the J2s persisted as the adult females isolated from galls were under-developed, elongated, and transparent compared to the normal saccate, white adult females. Following RNAi of ego-1, smg-2, smg-6, and eri-1, reduced expression and/or the immediate visible effects on the J2s were not permanent as the nematodes infected and developed normally in tomato hosts. Equally intriguing was the results of RNAi of the mes-2 gene where the insignificant change in gene expression and behavior of treated J2s did not mean the nematodes were not affected as they were less effective in infecting host plants. Attempt to silence drsh-1, mut-7, drh-3, rha-1, pash-1, and vig-1 through HIGS led to reduction in nematode infestation by up to 89%. Our results show that genes may respond to RNAi knockdown differently so an exhaustive assessment of target genes as targets for nematode control via RNAi is imperative.
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- 2020
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9. Co-Infection with Three Mycoviruses Stimulates Growth of a Monilinia fructicola Isolate on Nutrient Medium, but Does Not Induce Hypervirulence in a Natural Host
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Thao T. Tran, Hua Li, Duy Q. Nguyen, Michael G. K. Jones, and Stephen J. Wylie
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brown rot ,stone fruit ,Prunus ,mycovirus ,hypervirulence ,hypovirulence ,isogenic ,Microbiology ,QR1-502 - Abstract
Monilinia fructicola and Monilinia laxa are the most destructive fungal species infecting stone fruit (Prunus species). High-throughput cDNA sequencing of M. laxa and M. fructicola isolates collected from stone fruit orchards revealed that 14% of isolates were infected with one or more of three mycoviruses: Sclerotinia sclerotiorum hypovirus 2 (SsHV2, genus Hypovirus), Fusarium poae virus 1 (FPV1, genus Betapartitivirus), and Botrytis virus F (BVF, genus Mycoflexivirus). Isolate M196 of M. fructicola was co-infected with all three viruses, and this isolate was studied further. Several methods were applied to cure M196 of one or more mycoviruses. Of these treatments, hyphal tip culture either alone or in combination with antibiotic treatment generated isogenic lines free of one or more mycoviruses. When isogenic fungal lines were cultured on nutrient agar medium in vitro, the triple mycovirus-infected parent isolate M196 grew 10% faster than any of the virus-cured isogenic lines. BVF had a slight inhibitory effect on growth, and FPV1 did not influence growth. Surprisingly, after inoculation to fruits of sweet cherry, there were no significance differences in disease progression between isogenic lines, suggesting that these mycoviruses did not influence the virulence of M. fructicola on a natural host.
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- 2019
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10. LoRa localisation using single mobile gateway.
- Author
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Khondoker Ziaul Islam, David Murray, Dean Diepeveen, Michael G. K. Jones, and Ferdous Sohel
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- 2024
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11. Using Vital Dyes to Trace Uptake of dsRNA by Green Peach Aphid Allows Effective Assessment of Target Gene Knockdown
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Vineeta Bilgi, John Fosu-Nyarko, and Michael G. K. Jones
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RNA interference (RNAi) ,double stranded RNA (dsRNA) ,green peach aphid ,Myzus persicae ,vacuolar (H+)-ATPase (vha-8) ,vital dyes ,neutral red ,acridine orange ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
RNA interference (RNAi) is an effective tool to study gene function. For in vitro studies of RNAi in insects, microinjection of double-stranded (ds)RNA may cause stress. Non-persuasive oral delivery of dsRNA to trigger RNAi is a better mode of delivery for delicate insects such as aphids because it mimics natural feeding. However, when insects feed ad libitum, some individuals may not feed. For accurate measurement of gene knockdown, analysis should only include insects that have ingested dsRNA. The suitability of eleven dyes was assessed to trace ingestion of dsRNA in an artificial feeding system for green peach aphids (GPA, Myzus persicae). Non-toxic levels of neutral red and acridine orange were suitable tracers: they were visible in the stylet and gut after feeding for 24 h, and may also attract aphids to feed. Nymphs stained with neutral red (0.02%) were analysed for target gene expression after feeding on sucrose with dsRNA (V-ATPase, vha-8). There was a greater reduction in vha-8 expression and reproduction compared to nymphs fed the diet without dye. The results confirm the importance of identifying aphids that have ingested dsRNA, and also provide evidence that the vha-8 gene is a potential target for control of GPAs.
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- 2017
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12. LoRa-based outdoor localization and tracking using unsupervised symbolization.
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Khondoker Ziaul Islam, David Murray, Dean Diepeveen, Michael G. K. Jones, and Ferdous Sohel
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- 2024
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13. Early frost detection in wheat using machine learning from vertical temperature distributions.
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Sayma Shammi, Dean Diepeveen, Sebastian Zander, Michael G. K. Jones, and Ferdous Sohel
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- 2024
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14. Multi-task learning model for agricultural pest detection from crop-plant imagery: A Bayesian approach.
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Abderraouf Amrani, Dean Diepeveen, David Murray, Michael G. K. Jones, and Ferdous Sohel
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- 2024
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15. Plant disease recognition in a low data scenario using few-shot learning.
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Masoud Rezaei, Dean Diepeveen, Hamid Laga, Michael G. K. Jones, and Ferdous Sohel
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- 2024
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16. Deep learning-based detection of aphid colonies on plants from a reconstructed Brassica image dataset.
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Abderraouf Amrani, Ferdous Sohel, Dean Diepeveen, David Murray, and Michael G. K. Jones
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- 2023
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17. Image patch-based deep learning approach for crop and weed recognition.
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A. S. M. Mahmudul Hasan, Dean Diepeveen, Hamid Laga, Michael G. K. Jones, and Ferdous Sohel
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- 2023
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18. A Survey of Deep Learning Techniques for Weed Detection from Images.
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A. S. M. Mahmudul Hasan, Ferdous Sohel, Dean Diepeveen, Hamid Laga, and Michael G. K. Jones
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- 2021
19. Weed Recognition using Deep Learning Techniques on Class-imbalanced Imagery.
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A. S. M. Mahmudul Hasan, Ferdous Sohel, Dean Diepeveen, Hamid Laga, and Michael G. K. Jones
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- 2021
20. Machine learning-based detection of freezing events using infrared thermography.
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Sayma Shammi, Ferdous Sohel, Dean Diepeveen, Sebastian Zander, Michael G. K. Jones, Amanuel Bekuma, and Ben Biddulph
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- 2022
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21. Insect detection from imagery using YOLOv3-based adaptive feature fusion convolution network
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Abderraouf Amrani, Ferdous Sohel, Dean Diepeveen, David Murray, and Michael G. K. Jones
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Plant Science ,Agronomy and Crop Science - Abstract
Context Insects are a major threat to crop production. They can infect, damage, and reduce agricultural yields. Accurate and fast detection of insects will help insect control. From a computer algorithm point of view, insect detection from imagery is a tiny object detection problem. Handling detection of tiny objects in large datasets is challenging due to small resolution of the insects in an image, and other nuisances such as occlusion, noise, and lack of features. Aims Our aim was to achieve a high-performance agricultural insect detector using an enhanced artificial intelligence machine learning technique. Methods We used a YOLOv3 network-based framework, which is a high performing and computationally fast object detector. We further improved the original feature pyramidal network of YOLOv3 by integrating an adaptive feature fusion module. For training the network, we first applied data augmentation techniques to regularise the dataset. Then, we trained the network using the adaptive features and optimised the hyper-parameters. Finally, we tested the proposed network on a subset dataset of the multi-class insect pest dataset Pest24, which contains 25 878 images. Key results We achieved an accuracy of 72.10%, which is superior to existing techniques, while achieving a fast detection rate of 63.8 images per second. Conclusions We compared the results with several object detection models regarding detection accuracy and processing speed. The proposed method achieved superior performance both in terms of accuracy and computational speed. Implications The proposed method demonstrates that machine learning networks can provide a foundation for developing real-time systems that can help better pest control to reduce crop damage.
- Published
- 2022
22. Differential Symptom Development and Viral RNA Loads in 10 Nicotiana benthamiana Accessions Infected with the Tobamovirus Yellow Tailflower Mild Mottle Virus
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Xin Chen, Yuxia Guo, Michael G. K. Jones, Krishnapillai Sivasithamparam, Hua Li, Stephen J. Wylie, and Weinan Xu
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Genetic diversity ,biology ,Inoculation ,viruses ,fungi ,Mutant ,food and beverages ,Nicotiana benthamiana ,Tobamovirus ,Plant Science ,biology.organism_classification ,Virology ,Virus ,RNA polymerase I ,Agronomy and Crop Science ,Gene - Abstract
Yellow tailflower mild mottle virus (YTMMV, genus Tobamovirus) was identified from wild plants of solanaceous species in Australia. Nicotiana benthamiana is a species indigenous to the arid north of Australia. N. benthamiana accession RA-4 (the lab type), which has a mutant, functionally defective, RNA-dependent RNA polymerase 1 (Rdr1) gene (Nb-Rdr1m), has played a significant role in plant virology, but little study has been done regarding responses to virus infection by other accessions of N. benthamiana. All wild-collected N. benthamiana accessions used in this study harbored wild-type Rdr1 genes (Nb-Rdr1). We compared symptoms of YTMMV infection and viral RNA load on RA-4 and nine wild-collected accessions of N. benthamiana from mainland Western Australia, an island, and the Northern Territory. After inoculation with YTMMV, RA-4 plants responded with systemic hypersensitivity and all individuals were dead 35 days postinoculation (dpi). Plants of wild-collected accessions exhibited a range of symptoms, from mild to severe, and some, but not all, died in the same period. Quantitative reverse transcription PCR revealed that the Rdr1 mutation was not a predictor of viral RNA load or symptom severity. For example, wild-collected A019412 plants carried more than twice the viral RNA load of RA-4 plants, but symptom expression was moderate. For plants of most accessions, viral RNA load did not increase after 10 dpi. The exception was plants of accession Barrow-1, in which viral RNA load was low until 15 dpi, after which it increased more than 29-fold. This study revealed differential responses by N. benthamiana accessions to infection by an isolate of YTMMV. The Rdr1 gene, whether mutant or wild-type, did not appear to influence viral RNA load or disease expression. Genetic diversity of the 10 N. benthamiana accessions in some cases reflected geographical location, but in other accessions this was not so.
- Published
- 2022
23. In‐plant activation of root‐specific expression of a cytotoxic gene disrupts the development of the root‐knot nematode, Meloidogyne javanica
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Sadia Iqbal, Zhaohui Wang, Susan Mary Philip, John Fosu-Nyarko, and Michael G. K. Jones
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Barnase ,biology ,Plant Science ,Genetically modified crops ,Horticulture ,biology.organism_classification ,Cell biology ,Genetics ,biology.protein ,Root-knot nematode ,Cytotoxic T cell ,Barstar ,Agronomy and Crop Science ,Gene ,Meloidogyne javanica - Published
- 2021
24. Comparisons between sequenced and re-sequenced genomes of historical subterranean clover mottle virus isolates
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John Fosu-Nyarko, Ian P. Adams, Michael G. K. Jones, Adrian Fox, and Roger A. C. Jones
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Plant Science - Abstract
We report comparisons between the complete genomic sequences of five historical Western Australian isolates of subterranean clover mottle virus (SCMoV) from 1989–2000, and an infectious clone of its 1989 isolate. Sanger Sequencing (SS) and High Throughput Sequencing (HTS), or both, were used to obtain these genomes. Four of the SCMoV isolates were sequenced by SS in 1999–2002, but re-sequenced again by HTS in 2020. The pairs of sequences obtained from these four isolates differed by only 18–59 nucleotides. This small difference resulted from the different sequencing methods, the
- Published
- 2022
25. Fungal endophytes from salt-adapted plants confer salt tolerance and promote growth in wheat (
- Author
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Manjunatha, N, Nayana, Manjunatha, Hua, Li, Krishnapillai, Sivasithamparam, Michael G K, Jones, Ian, Edwards, Stephen J, Wylie, and Ruchi, Agarrwal
- Subjects
Seedlings ,Endophytes ,Humans ,Salt-Tolerant Plants ,Salt Tolerance ,Triticum - Abstract
With increasing human global population, increased yield under saline conditions is a desirable trait for major food crops. Use of endophytes, isolated from halophytic hosts, seems to be an exciting approach for conferring salt tolerance to a salt-sensitive crop. Therefore, in the current study, fungal endophytes were isolated from halophytic plants' roots and their ability to withstand
- Published
- 2022
26. RNA interference of an orthologue of Dicer of Meloidogyne incognita alludes to the gene’s importance in nematode development
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John Fosu-Nyarko, Sadia Iqbal, and Michael G. K. Jones
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0106 biological sciences ,0301 basic medicine ,Ribonuclease III ,Small RNA ,Science ,01 natural sciences ,Article ,03 medical and health sciences ,RNA interference ,medicine ,Meloidogyne incognita ,Animals ,Tylenchoidea ,Gene ,Genetics ,Multidisciplinary ,biology ,fungi ,food and beverages ,Functional genomics ,Helminth Proteins ,biology.organism_classification ,medicine.disease ,Caenorhabditis ,030104 developmental biology ,Nematode ,Nematode infection ,RNAi ,biology.protein ,Medicine ,RNA Interference ,010606 plant biology & botany ,Dicer ,Biotechnology - Abstract
Dicers and dicer-like enzymes play an essential role in small RNA processing in eukaryotes. Nematodes are thought to encode one dicer, DCR-1; only that for Caenorhabditis spp. is well-characterised. Using genomic sequences of eight root-knot nematodes (Meloidogyne spp.), we identified putative coding sequences typical of eukaryotic DICERS. We noted that the primary and secondary structures of DICERS they encode were different for different Meloidogyne species and even for isolates of the same species, suggesting paralogy for the gene. One of the genes for M. incognita (Midcr-1.1) expressed in eggs, juvenile stage 2 and adults, with the highest expression in the adult females. All the Meloidogyne DICERS had seven major domains typical of those for Caenorhabditis spp. and humans with very similar protein folding. RNAi of Midcr-1.1 in J2s using seven dsRNAs, each based on sequences encoding the domains, induced mild paralysis but measurable knockdown was detected in J2s treated with five of the dsRNAs. For four of the dsRNAs, the RNAi effect lasted and reduced the nematode’s infectivity. Also, host plant delivery of dsRNAs complementary to coding sequences of the Dicer Dimerisation domain impaired development, reducing nematode infection by 71%. These results confirm the importance of the gene to nematode health.
- Published
- 2021
27. Biochemical/Molecular Mechanisms Associated with Nematode Management Through Organic Amendments: A Critical Review
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John Fosu-Nyarko, Rhys G. R. Copeland, Sadia Iqbal, and Michael G. K. Jones
- Published
- 2022
28. Comparisons between genetic diversity, virulence and colony morphology of Monilinia fructicola and Monilinia laxa isolates
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Hua Li, T. T. Tran, Krishnapillai Sivasithamparam, Michael G. K. Jones, D. Q. Nguyen, and Stephen J. Wylie
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0106 biological sciences ,0301 basic medicine ,Genetic diversity ,biology ,Virulence ,Plant Science ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,Prunus ,Horticulture ,030104 developmental biology ,Monilinia fructicola ,Genetic variation ,Genotype ,Potato dextrose agar ,Monilinia laxa ,010606 plant biology & botany - Abstract
Monilinia fructicola and M. laxa, causing brown rot in stone fruit (Prunus species), were first described from Western Australia in 1997. Our previous work indicated that original invasive isolates of both species were each of a single genotype. This research aims to compare isolates from the region in the present day in terms of genetic diversity, colony morphology, and virulence on fruit. Genetic diversity of 68 M. laxa and 66 M. fructicola isolates collected in 2016-2017 from five populations was measured using ISSR markers. The genetic diversity within M. fructicola was greater than that of M. laxa, having Shannon’s diversity indices of 0.50 and 0.41, respectively. Most genetic variation was present within populations for both M. fructicola (77%) and M. laxa (76%), with the rest of the variation between geographically separated populations. Genotype did not correlate closely with virulence of isolates as measured by symptom severity index (SSI) on inoculated plum fruit and colony morphology on potato dextrose agar (PDA) medium. M. fructicola isolates with wide genetic variation exhibited closely similar SSIs and one morphotype on PDA, whereas M. laxa isolates exhibited a broad range of SSIs and four different morphotypes.
- Published
- 2020
29. Fungal endophytes from salt-adapted plants confer salt tolerance and promote growth in Wheat (Triticum aestivumL.) at early seedling stage
- Author
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Manjunatha Nanjundappa, Nayana Manjunatha, Hua Li, Krishnapillai Sivasithamparam, Michael G K Jones, Ian Edwards, Stephen J Wylie, and Ruchi Agarrwal
- Subjects
food and beverages - Abstract
With increasing human global population, increased yield under saline conditions is a desirable trait for major food crops. Use of endophytes, isolated from halophytic hosts, seems to be an exciting approach for conferring salt tolerance to a salt sensitive crop. Therefore, in the current study, fungal endophytes were isolated from halophytic plants’ roots and their ability to withstand in vitro salt stress was evaluated. They could withstand upto 1M NaCl concentrations and this tolerance was independent of their host or tissue source. When inoculated on salt sensitive wheat seeds/seedlings several of the endophytes showed a positive impact on germination and biomass related parameters upon salt stress, bothin vitroand under glasshouse conditions. One of the isolate from dicot plants (identified asMicrosphaeropsis arundinis) could successfully colonize wheat and promote its growth under salt and no salt conditions. Amongst the fungal isolates that are known to be natural endophytes of wheat, Chaetomium globosum was the best performing isolate which has been reported as an effective biocontrol agent earlier. Based on the results of our preliminary study, we suggest that these fungal endophytes could prove beneficial for salt stress tolerance enhancement of wheat crop.
- Published
- 2021
30. Differential Symptom Development and Viral RNA Loads in 10
- Author
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Weinan, Xu, Yuxia, Guo, Hua, Li, Krishnapillai, Sivasithamparam, Michael G K, Jones, Xin, Chen, and Stephen J, Wylie
- Subjects
Tobacco ,Tobamovirus ,RNA, Viral ,RNA-Dependent RNA Polymerase ,Plant Diseases - Abstract
Yellow tailflower mild mottle virus (YTMMV, genus
- Published
- 2021
31. Genome-Wide Identification and Validation of Target Genes Associated with Insecticide Treatment of the Green Peach Aphid, Myzus persicae
- Author
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Sadia, Iqbal, John, Fosu-Nyarko, Frances, Brigg, and Michael G K, Jones
- Subjects
Insecticide Resistance ,Prunus persica ,Insecticides ,Aphids ,Animals - Abstract
Next-generation sequencing and analyses of whole-genome transcripts can be used to identify genes and potential mechanisms that may be responsible for the development of resistance to insecticides. Such genes can be identified by isolating and sequencing high-quality messenger RNA and identifying differentially expressed genes (DEGs), and gene variants from insecticide-treated and untreated colonies of the Green peach aphid (GPA) or resistant and susceptible GPA populations. Datasets generated would reveal a set of genes whose expression may be associated with the insecticide treatment. The DEGs can then be validated using quantitative PCR assays.
- Published
- 2021
32. Functional Characterization of Target Genes Associated with Insecticide Resistance of the Green Peach Aphid, Myzus persicae
- Author
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John, Fosu-Nyarko, Sadia, Iqbal, Frances, Brigg, and Michael G K, Jones
- Subjects
Insecticide Resistance ,Prunus persica ,Insecticides ,Aphids ,Animals ,RNA Interference - Abstract
Identifying genes responsive to insecticide treatment is the first step towards understanding the mechanism(s) of insecticide resistance and the development of effective insecticides against economic insect pests such as the Green peach aphid (GPA). Functional and Reverse Genetics approaches such as the RNA interference (RNAi) technology can be used to assess the possible involvement of genes whose expression is associated with an insecticide treatment. For GPA, this can be done by comparing the behavior and development of the insect following RNAi of a putative gene associated with insecticide treatment and exposure of the RNAi-treated insects to lethal doses of insecticides. In a case where knockdown of a gene or genes increases the susceptibility of RNAi-treated populations compared to controls, the target gene may have a direct role in the development of resistance to the insecticide or the gene may be involved in other metabolic processes that may be required for resilience against the insecticide.
- Published
- 2021
33. Association of baseline hematoma and edema volumes with one-year outcome and long-term survival after spontaneous intracerebral hemorrhage: A community-based inception cohort study
- Author
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Jasmine Ng, Jerard Ross, Peter J. D. Andrews, Alan Jaap, Neil Turner, Helen Cook, Jon Stone, Michael G. K. Jones, Simon P. Hart, William Whiteley, Martin McKechnie, Billie Morrow, Graham McKillop, Laura Middleton, Sandra Dewar, Himanshu Shekhar, Susan Kealley, Laura Butler, Ashok Mathews, Donald Macleod, Neo Stavrinos, Andrew Elder, Ali Harmouche, Bethany Threlfall, Stuart McClellan, Frank Morrow, Ioannis P. Fouyas, Christopher P. Derry, Martin Dennis, Latana Munang, Peter Lange, Nicola L. Bell, David Summers, Judith Anderson, Robert Walker, Cathie Sudlow, Simon Leigh-Smith, Sarah Chambers, Robin Sellar, Patrick R. Taylor, Mark Hughes, Fiona Hughes, Jon Murchison, Richard Knight, Tim Russell, Moyra Masson, Donald Noble, Fiona Duncan, Claire Gordon, Ashok Jacob, M O Fitzpatrick, Randy Smith, Lynn McCallum, Belinda Weller, Katherine Jackson, Alasdair Gray, Angus B Gane, Siddharthan Chandran, Fiona Maxwell, Stanko Yordanov, Robert G. Will, Peter Foley, Patrick Statham, Henry Simms, Jon McCafferty, Colin Smith, Patricia Cantley, Alastair Crosswaite, Helen Spiers, Margarethe van Dijke, Yi Ng, Elizabeth Macdonald, Kate Enright, Gillian R. Kerr, Steven Makin, Katrina Dodds, Tom Fitzgerald, Simon Kerrigan, David Grant, Neil Hunter, Olayinka A Ogundipe, Claire Stirling, Astley Ainslie, Ian R. Whittle, Donald Farquhar, Jane Fothergill, Anne Knox, Andrew Jamieson, James M. Wilson, Alison Pollock, Andrew M. McIntosh, Andrew James Williams, Gillian Mead, Zoe Morris, Malcolm R. Macleod, Matthew J. Reed, Matthew Wilson, Colin B. Josephson, Brian Campbell, G. R. Nimmo, Brendan Sargent, Mark Rodrigues, Alastair Fitzgerald, Suvankar Pal, Colin J Mumford, Wendy Morley, Trish Elder-Gracie, Conor Maguire, Imran Liaquat, Sam Moultrie, James W. Dear, Peter Bodkin, Joanna M. Wardlaw, Johann R. Selvarajah, Antonia Torgersen, Iain Todd, Ralph Bouhaidar, Kristiina Rannikmäe, Syed Alhadad, Dilip Patel, Dave Caesar, Edinburgh Liberton Hospitals, Lynn M Myles, Fergus N. Doubal, Wendy Young, Kate Ahmad, Jonathan Rhodes, Anne Addison, Peter Sandercock, Rod Gibson, Seona Broadbent, Tim Morse, Gareth Clegg, Anant Kamat, Robin Henderson, Katherine Murray, Sudipto Ghosh, Sarah L. Keir, Joyce Stuart, Tom J Moullaali, Andrew J Coull, Rustam Al-Shahi Salman, Matthew King, Scott Ramsay, Linda Spence, Graham Mackay, Geraint Roberts, Mara Sittampalam, Laura Cunningham, Richard Davenport, Susan Duncan, Simon Dummer, Hamza Soleiman, Ross Murphy, James W. Ironside, Neshika Samarasekera, Paul Brennan, Peter Keston, Elaine Bisset, James J M Loan, Jonathan Carter, Brian Frier, David Hunt, Tracey Millar, Russell Hewett, Lewis Morrison, Mano Shanmuganathan, and Robin Grant
- Subjects
Adult ,Male ,peri-hematomal edema ,medicine.medical_specialty ,Brain Edema ,030204 cardiovascular system & hematology ,survival ,Cohort Studies ,03 medical and health sciences ,0302 clinical medicine ,Hematoma ,Edema ,Long term survival ,medicine ,Humans ,Spontaneous intracerebral hemorrhage ,Prospective Studies ,Aged ,Cerebral Hemorrhage ,Intracerebral hemorrhage ,Community based ,business.industry ,Research ,medicine.disease ,INCEPTION COHORT ,intracerebral hemorrhage ,radiology ,Surgery ,Stroke ,Neurology ,outcome ,Female ,medicine.symptom ,business ,Cohort study ,030217 neurology & neurosurgery - Abstract
Background Hospital-based studies have reported variable associations between outcome after spontaneous intracerebral hemorrhage and peri-hematomal edema volume. Aims In a community-based study, we aimed to investigate the existence, strength, direction, and independence of associations between intracerebral hemorrhage and peri-hematomal edema volumes on diagnostic brain CT and one-year functional outcome and long-term survival. Methods We identified all adults, resident in Lothian, diagnosed with first-ever, symptomatic spontaneous intracerebral hemorrhage between June 2010 and May 2013 in a community-based, prospective inception cohort study. We defined regions of interest manually and used a semi-automated approach to measure intracerebral hemorrhage volume, peri-hematomal edema volume, and the sum of these measurements (total lesion volume) on first diagnostic brain CT performed at ≤3 days after symptom onset. The primary outcome was death or dependence (scores 3–6 on the modified Rankin Scale) at one-year after intracerebral hemorrhage. Results Two hundred ninety-two (85%) of 342 patients (median age 77.5 y, IQR 68–83, 186 (54%) female, median time from onset to CT 6.5 h (IQR 2.9–21.7)) were dead or dependent one year after intracerebral hemorrhage. Peri-hematomal edema and intracerebral hemorrhage volumes were colinear ( R2 = 0.77). In models using both intracerebral hemorrhage and peri-hematomal edema, 10 mL increments in intracerebral hemorrhage (adjusted odds ratio (aOR) 1.72 (95% CI 1.08–2.87); p = 0.029) but not peri-hematomal edema volume (aOR 0.92 (0.63–1.45); p = 0.69) were independently associated with one-year death or dependence. 10 mL increments in total lesion volume were independently associated with one-year death or dependence (aOR 1.24 (1.11–1.42); p = 0.0004). Conclusion Total volume of intracerebral hemorrhage and peri-hematomal edema, and intracerebral hemorrhage volume alone on diagnostic brain CT, undertaken at three days or sooner, are independently associated with death or dependence one-year after intracerebral hemorrhage, but peri-hematomal edema volume is not. Data access statement Anonymized summary data may be requested from the corresponding author.
- Published
- 2021
34. IMPROVED HYPHAL GROWTH OF TWO SPECIES OF VESICULAR-ARBUSCULAR MYCORRHIZAL FUNGI IN THE PRESENCE OF SUSPENSION-CULTURED PLANT CELLS
- Author
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G. R. Carr, Michael G. K. Jones, M. A. Hinkley, F. Le Tacon, Christine M. Hepper, and E. Thomas
- Subjects
Hyphal growth ,biology ,Physiology ,Plant Sciences ,Plant Science ,Solanum tuberosum ,biology.organism_classification ,Plant cell ,Chlamydospore ,Botany ,Medicago sativa ,Mycorrhiza ,Phycomycetes ,Glomus - Abstract
Summary Conditions required for the combined culture of either Glomus caledonium (Nicol. &Gerd.) Trappe &Gerdemann or Glomus mosseae (Nicol. &Gerd.) Gerdemann &Trappe with suspension-cultured plant cells have been investigated. Sucrose levels (0.05 to 0.5%, w/v) lower than those used for growth of plant cells were optimal for hyphal growth of both G. caledonium and G. mosseae. In vitro hyphal growth from chlamydospores of G. caledonium was stimulated by addition of cells of wheat (Triticum aestivum L. cv. Maris Butler), lucerne (Medicago sativa L. cv. Europ) and potato (Solanum tuberosum L. cv. Maris Piper). The presence of wheat cells similarly stimulated hyphal growth from chlamydospores of G. mosseae. Further tests on the effect of lucerne cells on G. caledonium indicated that a volatile substance was involved in the improvement of hyphal growth.
- Published
- 2021
35. Biosafety of RNA silencing and genome editing technologies in crop plants: Malaysian and Australian research perspectives
- Author
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Muhammad Shakirin Mispan, Rofina Yasmin Othman, Sadia Iqbal, Yong Han, Michael G. K. Jones, and Jennifer Ann Harikrishna
- Subjects
0106 biological sciences ,0301 basic medicine ,Emerging technologies ,business.industry ,Biosecurity ,Timeline ,Agricultural biotechnology ,01 natural sciences ,Terminology ,03 medical and health sciences ,Biosafety ,030104 developmental biology ,Agriculture ,010608 biotechnology ,Mainstream ,Engineering ethics ,Business ,Molecular Biology ,Biotechnology - Abstract
Research in agricultural biotechnology can produce novel solutions to address the ever growing demand for food, feed, renewable materials and renewable energy using increasingly limited resources. Yet research is expensive with long timelines before implementation can disseminate the benefits to society, so there is a need to maximise co-operation and communication between scientists, stakeholders and their governments, to optimise research, its development and the implementation of research outcomes, into mainstream applications. Recognising the impacts of regulations on biosafety, biosecurity and intellectual property policy on strategies for research, senior and early career researchers from two research intensive universities in Malaysia and Australia, held a workshop to identify and to deliberate over two key areas of technology that offer much promise for agriculture, namely RNA silencing and genome editing. A major focus of the workshop was the regulation of new breeding technologies, and how the regulations need to take into account these new technologies. Themes discussed were the need for harmonisation of international legal frameworks and careful use of terminology, standards and guidelines; and the need for good communication and consensus within and between groups of stakeholders and law-makers. This mini-review highlights the deliberations and recommendations from the workshop.
- Published
- 2019
36. Genotypic structure of Monilinia populations in Western Australia two decades after incursion
- Author
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Hua Li, T. T. Tran, Krishnapillai Sivasithamparam, Michael G. K. Jones, D. Q. Nguyen, and Stephen J. Wylie
- Subjects
Germplasm ,biology ,food and beverages ,Plant Science ,Monilinia ,biology.organism_classification ,law.invention ,Horticulture ,Prunus ,Pome ,Monilinia fructicola ,law ,Genotype ,Quarantine ,Monilinia laxa - Abstract
In 1997, Monilinia fructicola and Monilinia laxa, fungi causing brown rot disease in stone fruit (Prunus species), were identified from Western Australia for the first time. Up until then, Monilinia were quarantine species, and importation of stone fruits to W.A. was prohibited. After Monilinia was identified in W.A., importation of stone fruit from sources outside W.A. was progressively permitted. Today, Monilinia is present in all stone fruit production regions in W.A. The aim of this study was to determine if the genotypes responsible for the first incursion subsequently spread, or if new genotypes have since become established. ISSR markers were used to identify the genotype of isolates collected during the initial incursion event in 1997, and compare them with isolates collected subsequently. Eight M. fructicola genotypes were identified, including a monotypic one on a fresh peach imported from the USA. M. fructicola isolates collected during the initial incursion in 1997 and an isolate from cherry collected in South Australia in the same year were all of the same genotype, suggesting fruit or germplasm from S.A. as the source of the W.A. incursion. However, this incursion genotype appears not have persisted, with different genotypes subsequently becoming widely or locally established. Four genotypes of M. laxa were identified. In contrast to M. fructicola, the 1997 incursion genotype of M. laxa has become widely established in W.A., infecting both stone fruits and pome fruits.
- Published
- 2019
37. Metabolic responses of endophytic Nicotiana benthamiana plants experiencing water stress
- Author
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Yonglin Ren, Michael G. K. Jones, Hua Li, Xin Du, Khondoker M. G. Dastogeer, Krishnapillai Sivasithamparam, and Stephen J. Wylie
- Subjects
0106 biological sciences ,0301 basic medicine ,biology ,fungi ,food and beverages ,Cladosporium cladosporioides ,Nicotiana benthamiana ,Plant Science ,Fungus ,biology.organism_classification ,01 natural sciences ,Endophyte ,Plant use of endophytic fungi in defense ,03 medical and health sciences ,030104 developmental biology ,Symbiosis ,Botany ,Colonization ,Sugar ,Agronomy and Crop Science ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
Endophytic fungal colonization may influence how plants respond to environmental stress. Two promising fungal isolates, one resembling Cladosporium cladosporioides and another unidentified ascomycetous fungus, isolated from wild N. benthamiana plants in northern Australia were inoculated to plants of the research accession of N. benthamiana (RA-4). Inoculated seedlings were grown under adequate or water deficit conditions. We examined leaf metabolites using gas chromatography-mass spectrometry (GC–MS) to compare levels of sugars, sugar alcohols, amino acids and other metabolites at various stages of plant growth and stress application. Ninety-three metabolites were detected in leaves, including 20 sugars, 13 sugar alcohols, 21 amino acids, 29 organic and fatty acids and ten other compounds. Endophyte colonization caused significantly differential accumulation of 17–21 metabolites when the plants were grown under well-watered condition. The presence of endophytes under water stress conditions caused differential accumulation of cytosine, diethylene glycol, galactinol, glycerol, heptadecanoate, mannose, oleic acid, proline, rhamnose, succinate, and urea. Accumulation of these metabolites suggests that fungal endophytes influence plants to accumulate certain metabolites under water-stress. Further, plants colonised by the two different endophytes tested, showed some differences in the metabolites they accumulated. Colonization with endophytic fungi significantly increased root dry mass and relative water content in plants under severe water stress condition, suggestive of a symbiotic relationship between these fungi and N. benthamiana plants, a species adapted to the hot and unpredictable soil moisture conditions of northern Australia. We reveal that endophyte colonization triggers reprogramming of host metabolism and indices changes in host development. This study sheds lights on the mechanisms underlying increased tolerance to water stress in plants conferred by fungal endophytes. Fungal endophytes have the potentials for application to increase the inherent water stress tolerance of crops.
- Published
- 2017
38. Cereal Cyst Nematodes: A Complex and Destructive Group of Heterodera Species
- Author
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De-liang Peng, Lieven Waeyenberge, Michael G. K. Jones, Abdelfattah A. Dababat, Sergei A. Subbotin, Zahra Tanha Maafi, Sadia Iqbal, and Richard W. Smiley
- Subjects
0106 biological sciences ,0301 basic medicine ,Calorie ,Animal feed ,Developing country ,Plant Science ,Biology ,Poaceae ,01 natural sciences ,03 medical and health sciences ,Animals ,Production (economics) ,Tylenchoidea ,Plant Diseases ,Consumption (economics) ,business.industry ,Heterodera ,Triticale ,biology.organism_classification ,030104 developmental biology ,Agronomy ,Livestock ,Edible Grain ,business ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Small grain cereals have served as the basis for staple foods, beverages, and animal feed for thousands of years. Wheat, barley, oats, rye, triticale, rice, and others are rich in calories, proteins, carbohydrates, vitamins, and minerals. These cereals supply 20% of the calories consumed by people worldwide and are therefore a primary source of energy for humans and play a vital role in global food and nutrition security. Global production of small grains increased linearly from 1960 to 2005, and then began to decline. Further decline in production is projected to continue through 2050 while global demand for these grains is projected to increase by 1% per annum. Currently, wheat, barley, and oat production exceeds consumption in developed countries, while in developing countries the consumption rate is higher than production. An increasing demand for meat and livestock products is likely to compound the demand for cereals in developing countries. Current production levels and trends will not be sufficient to fulfill the projected global demand generated by increased populations. For wheat, global production will need to be increased by 60% to fulfill the estimated demand in 2050. Until recently, global wheat production increased mostly in response to development of improved cultivars and farming practices and technologies. Production is now limited by biotic and abiotic constraints, including diseases, nematodes, insect pests, weeds, and climate. Among these constraints, plant-parasitic nematodes alone are estimated to reduce production of all world crops by 10%. Cereal cyst nematodes (CCNs) are among the most important nematode pests that limit production of small grain cereals. Heavily invaded young plants are stunted and their lower leaves are often chlorotic, forming pale green patches in the field. Mature plants are also stunted, have a reduced number of tillers, and the roots are shallow and have a “bushy-knotted” appearance. CCNs comprise a number of closely-related species and are found in most regions where cereals are produced.
- Published
- 2017
39. The challenges of using high-throughput sequencing to track multiple bipartite mycoviruses of wild orchid-fungus partnerships over consecutive years
- Author
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Krishnapillai Sivasithamparam, Jamie W.L. Ong, Stephen J. Wylie, Kingsley W. Dixon, Michael G. K. Jones, and Hua Li
- Subjects
0301 basic medicine ,food.ingredient ,Ceratobasidium ,Population ,Fungal Viruses ,DNA sequencing ,03 medical and health sciences ,food ,Virology ,Longitudinal Studies ,Orchidaceae ,education ,Phylogeny ,Genetics ,education.field_of_study ,biology ,Shotgun sequencing ,Basidiomycota ,Australia ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Partitiviridae ,biology.organism_classification ,Pterostylis sanguinea ,030104 developmental biology ,Mycovirus ,Pterostylis - Abstract
The bipartite alpha- and betapartitiviruses are recorded from a wide range of fungi and plants. Using a combination of dsRNA-enrichment, high-throughput shotgun sequencing and informatics, we report the occurrence of multiple new partitiviruses associated with mycorrhizal Ceratobasidium fungi, themselves symbiotically associated with a small wild population of Pterostylis sanguinea orchids in Australia, over two consecutive years. Twenty-one partial or near-complete sequences representing 16 definitive alpha- and betapartitivirus species, and further possible species, were detected from two fungal isolates. The majority of partitiviruses occurred in fungal isolates from both years. Two of the partitiviruses represent phylogenetically divergent forms of Alphapartitivirus, suggesting that they may have evolved under long geographical isolation there. We address the challenge of pairing the two genomic segments of partitiviruses to identify species when multiple partitiviruses co-infect a single host.
- Published
- 2017
40. 385 DEDIFFERENTIATION AND REPROGRAMMING OF EPITHELIAL CELLS DURING GASTRIC ULCER HEALING IS TRIGGERED BY HYPOXIA AND A WELL-COORDINATED, SEQUENTIAL ACTIVATION OF EGFR SIGNALING: CROSS TALK WITH IGF1 AND COX2
- Author
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Andrzej S. Tarnawski, Amrita Ahluwalia, and Michael G. K. Jones
- Subjects
Ulcer healing ,Hepatology ,business.industry ,Gastroenterology ,Cancer research ,Medicine ,Egfr signaling ,Hypoxia (medical) ,medicine.symptom ,business ,Reprogramming - Published
- 2021
41. Su292 IMPORTINS ARE CRITICAL FOR PANCREATIC CANCER GROWTH. UNDERLYING MECHANISMS INCLUDE INCREASED TRANSPORT OF TRANSCRIPTION FACTORS RESULTING IN ABERRANT, INCREASED VEGF EXPRESSION THAT DRIVES CANCER CELL GROWTH AND PROLIFERATION
- Author
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Michael G. K. Jones, Amrita Ahluwalia, Neil Hoa, and Andrzej S. Tamawski
- Subjects
Hepatology ,Pancreatic cancer ,Cancer cell ,Gastroenterology ,Cancer research ,medicine ,Vegf expression ,Importin ,Biology ,medicine.disease ,Transcription factor - Published
- 2021
42. Spatial distribution of Monilinia fructicola and M. laxa in stone fruit production areas in Western Australia
- Author
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Hua Li, Krishnapillai Sivasithamparam, D. Q. Nguyen, Stephen J. Wylie, T. T. Tran, and Michael G. K. Jones
- Subjects
0106 biological sciences ,0301 basic medicine ,Entomology ,biology ,Its region ,Plant Science ,Monilinia ,biology.organism_classification ,Spatial distribution ,01 natural sciences ,03 medical and health sciences ,Prunus ,030104 developmental biology ,Monilinia fructicola ,Botany ,Monilinia laxa ,010606 plant biology & botany - Abstract
In 2016 and 2017, 90 fungal isolates were collected from Prunus species exhibiting symptoms of brown rot disease at 12 sites in stone fruit production areas in Western Australia. ITS region analysis showed that 49 isolates belonged to Monilinia laxa and 34 to M. fructicola, species that cause brown rot in stone fruit. The two species were spatially separated to the south of the Perth Hills region, where only M. laxa was found, and to the north of Perth Hills where only M. fructicola was found. The two species co-existed only in the Perth Hills. The implications for control and trade are discussed, as is the need to implement biosecurity guidelines to prevent mixing of the two species where currently only one exists.
- Published
- 2017
43. Attempt to Silence Genes of the RNAi Pathways of the Root-Knot Nematode
- Author
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Sadia, Iqbal, John, Fosu-Nyarko, and Michael G K, Jones
- Subjects
nematode control ,host-induced gene silencing ,Plant Science ,transgenic plants ,root-knot nematodes ,in vitro RNAi ,Meloidogyne incognita ,Original Research ,RNAi pathway - Abstract
Control of plant-parasitic nematodes (PPNs) via host-induced gene silencing (HIGS) involves rational selection of genes and detailed assessment of effects of a possible knockdown on the nematode. Some genes by nature may be very important for the survival of the nematode that knockdown may be resisted. Possible silencing and effects of 20 such genes involved in the RNA interference (RNAi) pathways of Meloidogyne incognita were investigated in this study using long double-stranded RNAs (dsRNAs) as triggers. Two of the genes, ego-1 and mes-2, could not be knocked down. Expression of six genes (xpo-1, pash-1, xpo-2, rha-1, ekl-4, and csr-1) were significantly upregulated after RNAi treatment whereas for 12 of the genes, significant knockdown was achieved and with the exception of mes-2 and mes-6, RNAi was accompanied by defective phenotypes in treated nematodes including various degrees of paralysis and abnormal behaviors and movement such as curling, extreme wavy movements, and twitching. These abnormalities resulted in up to 75% reduction in infectivity of a tomato host, the most affected being the J2s previously treated with dsRNA of the gfl-1 gene. For 10 of the genes, effects of silencing in the J2s persisted as the adult females isolated from galls were under-developed, elongated, and transparent compared to the normal saccate, white adult females. Following RNAi of ego-1, smg-2, smg-6, and eri-1, reduced expression and/or the immediate visible effects on the J2s were not permanent as the nematodes infected and developed normally in tomato hosts. Equally intriguing was the results of RNAi of the mes-2 gene where the insignificant change in gene expression and behavior of treated J2s did not mean the nematodes were not affected as they were less effective in infecting host plants. Attempt to silence drsh-1, mut-7, drh-3, rha-1, pash-1, and vig-1 through HIGS led to reduction in nematode infestation by up to 89%. Our results show that genes may respond to RNAi knockdown differently so an exhaustive assessment of target genes as targets for nematode control via RNAi is imperative.
- Published
- 2019
44. Four Tulasnella taxa associated with populations of the Australian evergreen terrestrial orchid Cryptostylis ovata
- Author
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Hua Li, D. Q. Nguyen, Krishnapillai Sivasithamparam, Stephen J. Wylie, Michael G. K. Jones, and T. T. Tran
- Subjects
0106 biological sciences ,Tulasnella ,01 natural sciences ,Chiloglottis ,03 medical and health sciences ,Symbiosis ,Mycorrhizae ,Botany ,Genetics ,DNA, Fungal ,Orchidaceae ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,030304 developmental biology ,0303 health sciences ,Phylogenetic tree ,biology ,Cryptostylis ,Basidiomycota ,Genetic Variation ,Western Australia ,Evergreen ,biology.organism_classification ,Infectious Diseases ,Taxon ,Epiphyte ,Rhizome ,010606 plant biology & botany ,Microsatellite Repeats - Abstract
Of the more than 400 indigenous orchid species in Western Australia, Cryptostylis ovata is the only species that retains its leaves all year round. It exists as a terrestrial herb and occasionally as an epiphyte in forested areas. Like all terrestrial orchids, C. ovata plants associate with mycorrhizal fungi, but their identities have not previously been investigated. Fungi were isolated from pelotons in rhizomes collected from three southern and two northern populations of C. ovata on six occasions over two years. Phylogenetic analysis of ITS sequences temporally and spatially revealed that all the fungal isolates were of Tulasnella species of four distinct groups. One Tulasnella group was present only in the three southern orchid populations, and it closely resembled T. prima isolates previously described from Chiloglottis sp. orchids from eastern Australia. Isolates collected from plants in the two northern populations were of three undescribed Tulasnella groups. Analysis of intra-group diversity using inter-simple sequence repeat markers revealed that plants were usually colonised by a single genotype of Tulasnella at each sampling period, and this genotype usually, but not always, persisted with the host plant over both years tested.
- Published
- 2019
45. Serendipitous identification of Pratylenchus curvicauda from the grainbelt of Western Australia
- Author
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John Fosu-Nyarko, Shashi B. Sharma, S. Collins, Farhana Begum, Bill Macleod, and Michael G. K. Jones
- Subjects
Morphology ,biology ,Phylogenetic tree ,Internal transcribed spacer (ITS) ,Arts & Humanities ,Zoology ,Life Sciences ,Molecular phylogeny ,biology.organism_classification ,Monophyly ,Nematode ,lcsh:Biology (General) ,Pratylenchus spp ,Molecular phylogenetics ,Pratylenchus curvicauda ,Identification (biology) ,Taxonomy (biology) ,Scanning Electron Microscopy (SEM) ,PEST analysis ,Pratylenchus ,Root Lesion Nematodes ,lcsh:QH301-705.5 ,Nematode classification ,Taxonomy - Abstract
A Pratylenchus species identified during a survey of Pratylenchus quasitereoides incidence at four locations of the grainbelt of Western Australia is described. Morphological and morphometric features indicated the previously undescribed morphotypes in nematode mixtures encountered were conspecific to P. curvicauda, and were clearly distinguishable from nine common Pratylenchus spp. Typical features of P. curvicauda were its body length (415–540 µm), which was curved to a c-shaped with a maximum body diameter of 20 µm, and the nature of its tail; 34 µm long, 2.8 µm wide at the anus and a typical ventrally arcuate with a round terminus. Sequenced for the first time, the sequences of the partial 18S-ITS1-5.8S-ITS2-partial 28S (80 clones, 14 individual nematodes) and the 28S-D3 (17 clones) regions of the rDNA of P. curvicauda had overall mean distances of 0.013 and 0.085, respectively. Phylogenetic analyses with sequences of both segments of the rDNA clearly showed the P. curvicauda isolates as monophyletic, distinct from ca 40 Pratylenchus species. Notably, it was distinct from Pratylenchus species present in Australia including P. quasitereoides and a Western Australia isolate of P. thornei. Further research into the biology of P. curvicauda is needed to facilitate development of strategies for its management, if it is an important pest.
- Published
- 2019
46. Phylogenetic Analysis of Bean yellow mosaic virus Isolates from Four Continents: Relationship Between the Seven Groups Found and Their Hosts and Origins
- Author
-
Stephen J. Wylie, Michael G. K. Jones, Brenda A. Coutts, and Roger A. C. Jones
- Subjects
Genetic diversity ,Phylogenetic tree ,biology ,Host (biology) ,Potyviridae ,Potyvirus ,Plant Science ,Bean yellow mosaic virus ,biology.organism_classification ,Evolutionary biology ,Phylogenetics ,Botany ,Domestication ,Agronomy and Crop Science - Abstract
Genetic diversity of Bean yellow mosaic virus (BYMV) was studied by comparing sequences from the coat protein (CP) and genome-linked viral protein (VPg) genes of isolates from four continents. CP sequences compared were those of 17 new isolates and 47 others already on the database, while the VPg sequences used were from four new isolates and 10 from the database. Phylogenetic analysis of the CP sequences revealed seven distinct groups, six polytypic and one monotypic. The largest and most genetically diverse polytypic group, which had intragroup diversity of 0.061 nucleotide substitutions per site, contained isolates from natural infections in eight host species. These original isolation hosts included both wild (four) and domesticated (four) species and were from monocotyledonous and dicotyledonous plant families, indicating a generalized natural host range strategy. Only one of the other five polytypic groups spanned both monocotyledons and dicotyledons, and all contained isolates from fewer species (one to four), all of which were domesticated and had lower intragroup diversity (0.019 to 0.045 nucleotide substitutions per site), indicating host specialization. Phylogenetic analysis of the fewer VPg sequences revealed three polytypic and two monotypic groupings. These groups also correlated with original natural isolation hosts, but the branch topologies were sometimes incongruous with those formed by CPs. Also, intragroup diversity was generally higher for VPgs than for CPs. A plausible explanation for the groups found when the 64 different CP sequences were compared is that the generalized group represents the original ancestral type from which the specialist host groups evolved in response to domestication of plants after the advent of agriculture. Data on the geographical origins of the isolates within each group did not reveal whether the specialized groups might have coevolved with their principal natural hosts where these were first domesticated, but this seems plausible.
- Published
- 2019
47. Transgenic yellow lupin (Lupinus luteus)
- Author
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Michael G. K. Jones, Stephen J. Wylie, and Hua Li
- Subjects
fungi ,food and beverages ,Plant Science ,General Medicine ,Agrobacterium tumefaciens ,Biology ,Meristem ,biology.organism_classification ,food.food ,Lupinus luteus ,chemistry.chemical_compound ,Transformation (genetics) ,food ,Glufosinate ,chemistry ,Botany ,Subculture (biology) ,Agronomy and Crop Science ,Explant culture ,Transformation efficiency - Abstract
Transgenic yellow lupin (Lupinus luteus L.) plants have been generated by meristem co-cultivation with Agrobacterium tumefaciens. The binary plasmid pPZBNIa contains the bar gene under the control of a CaMV 35 S promoter. The transformation method involves inoculation of embryonic axis explants with A. tumefaciens, flooding the meristem with glufosinate, and initial culture on non-selective medium. Shoots were transferred to culture medium containing 20 mg/l glufosinate. Following subculture, shoots were grafted onto non-transgenic narrow-leafed lupin (L. angustifolius L.) seedling rootstocks, or rooted in vitro. The overall transformation efficiency, as determined at the T1 generation, was 0.05%–0.75%. The transgenic nature of plants grown to the T6 generation was confirmed by phosphinothricin acetyl transferase, PCR and Southern analyses.
- Published
- 2019
48. First Report of 'Candidatus Phytoplasma aurantifolia' Associated With Severe Stunting and Necrosis on the Invasive Weed Pelargonium capitatum in Western Australia
- Author
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Michael G. K. Jones, E. Lee, and Stephen J. Wylie
- Subjects
biology ,Ornamental plant ,Botany ,Plant Science ,Pelargonium ,biology.organism_classification ,Weed ,Endemism ,Agronomy and Crop Science ,Floristics ,Indigenous ,Invasive species ,Pelargonium capitatum - Abstract
Pelargonium capitatum (rose pelargonium) is a plant indigenous to southern Africa, originally brought to Western Australia for its ornamental qualities. It has since become naturalized in the Southwest Australian Floristic Region, recognized for its high level of species endemism, where it is a serious invasive weed in bushlands and coastal dunes. Since P. capitatum outcompetes native species it is listed among the top 10 most important coastal weeds of the region (3). In 2008, large patches of stunted, dying, and dead P. capitatum plants were observed within a population covering coastal dunes at Woodman Point, Western Australia (GPS coordinates 32°07′40.51″S, 115°45′28.39″E). Diseased plants had small misshapen leaves in clumps that were often chlorotic or pink, shortened internodes, and exhibited phylloidy typical of infection by a phytoplasma. From August 2009 to January 2010, samples from symptomatic and asymptomatic plants were collected from the site and from plants of an asymptomatic population at another site located on the Murdoch University campus nearby. DNA was extracted from 15 samples collected from symptomatic and asymptomatic plants at the dune site and from five at the campus site. Briefly, 2 to 5 g of leaf and stem tissue was cut into 5-mm pieces and shaken overnight in 30 ml of phosphate-buffered saline buffer. Supernatant was filtered and a pellet was collected by centrifugation. After resuspension in 500 μl of extraction buffer (200 mM Tris-HCl [pH 7.5] 250mM NaCl, 25mM ethylenediaminetetraacetic acid, 0.5% sodium dodecyl sulfate, and 2% polyvinylpyrrolidone), DNA was precipitated in 500 μl of cold isopropanol. Samples were tested for the presence of phytoplasma ribosomal 16S DNA by nested PCR using phytoplasma universal primers P1/P7 followed by amplification with primers Tint, R16mF2, and R16mR1 (1,2,4). Phytoplasma-specific DNA sequences were synthesized directly from amplicons using the above primers. Phytoplasma was detected from both symptomatic and asymptomatic plant samples collected from the dune site but not from the campus site. Analysis of the nine sequences obtained (GenBank Accession Nos. HM583339, HM583340, HM583341, HM583342, HM583343, HM583344, HM583345, HM583346, and HM583347) revealed high sequence identity between isolates (~99%) and with the ‘Candidatus Phytoplasma aurantifolia’ (16SrII) group of phytoplasmas (1,4). Presence of phytoplasma in symptomatic plants was confirmed by histological examination of stem sections stained with Dienes' stain. This finding is significant because there is potential for utilizing this phytoplasma to control P. capitatum where it has invaded ecologically significant sites, although its effect on indigenous plants must be determined first. Although phytoplasmas within the 16SrII group have been identified in Australia previously (1,4), to our knowledge, this is the first report of it infecting P. capitatum. References: (1) K. S. Gibb et al. Phytopathology 85:169, 1995. (2) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3) B. M. J. Hussey et al. Western Weeds. A Guide to the Weeds of Western Australia. 2nd ed. Plant Protection Society of Western Australia, Victoria Park, 2007. (4) M. Saqib et al. J. R. Soc. West. Aust. 90:175, 2007.
- Published
- 2019
49. Co-Infection with Three Mycoviruses Stimulates Growth of a Monilinia fructicola Isolate on Nutrient Medium, but Does Not Induce Hypervirulence in a Natural Host
- Author
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Hua Li, T. T. Tran, D. Q. Nguyen, Michael G. K. Jones, and Stephen J. Wylie
- Subjects
0301 basic medicine ,hypovirulence ,030106 microbiology ,Prunus ,Hyphal tip ,lcsh:QR1-502 ,lcsh:Microbiology ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,mycovirus ,Virology ,Hypovirus ,stone fruit ,biology ,Sclerotinia sclerotiorum ,hypervirulence ,brown rot ,biology.organism_classification ,isogenic ,030104 developmental biology ,Infectious Diseases ,chemistry ,Monilinia fructicola ,Mycovirus ,Monilinia laxa ,Nutrient agar - Abstract
Monilinia fructicola and Monilinia laxa are the most destructive fungal species infecting stone fruit (Prunus species). High-throughput cDNA sequencing of M. laxa and M. fructicola isolates collected from stone fruit orchards revealed that 14% of isolates were infected with one or more of three mycoviruses: Sclerotinia sclerotiorum hypovirus 2 (SsHV2, genus Hypovirus), Fusarium poae virus 1 (FPV1, genus Betapartitivirus), and Botrytis virus F (BVF, genus Mycoflexivirus). Isolate M196 of M. fructicola was co-infected with all three viruses, and this isolate was studied further. Several methods were applied to cure M196 of one or more mycoviruses. Of these treatments, hyphal tip culture either alone or in combination with antibiotic treatment generated isogenic lines free of one or more mycoviruses. When isogenic fungal lines were cultured on nutrient agar medium in vitro, the triple mycovirus-infected parent isolate M196 grew 10% faster than any of the virus-cured isogenic lines. BVF had a slight inhibitory effect on growth, and FPV1 did not influence growth. Surprisingly, after inoculation to fruits of sweet cherry, there were no significance differences in disease progression between isogenic lines, suggesting that these mycoviruses did not influence the virulence of M. fructicola on a natural host.
- Published
- 2019
50. Co-Infection with Three Mycoviruses Stimulates Growth of a
- Author
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Thao T, Tran, Hua, Li, Duy Q, Nguyen, Michael G K, Jones, and Stephen J, Wylie
- Subjects
Host Microbial Interactions ,Virulence ,Coinfection ,hypovirulence ,Communication ,hypervirulence ,brown rot ,Fungal Viruses ,isogenic ,Ascomycota ,mycovirus ,Fruit ,Prunus ,stone fruit ,Plant Diseases - Abstract
Monilinia fructicola and Monilinia laxa are the most destructive fungal species infecting stone fruit (Prunus species). High-throughput cDNA sequencing of M. laxa and M. fructicola isolates collected from stone fruit orchards revealed that 14% of isolates were infected with one or more of three mycoviruses: Sclerotinia sclerotiorum hypovirus 2 (SsHV2, genus Hypovirus), Fusarium poae virus 1 (FPV1, genus Betapartitivirus), and Botrytis virus F (BVF, genus Mycoflexivirus). Isolate M196 of M. fructicola was co-infected with all three viruses, and this isolate was studied further. Several methods were applied to cure M196 of one or more mycoviruses. Of these treatments, hyphal tip culture either alone or in combination with antibiotic treatment generated isogenic lines free of one or more mycoviruses. When isogenic fungal lines were cultured on nutrient agar medium in vitro, the triple mycovirus-infected parent isolate M196 grew 10% faster than any of the virus-cured isogenic lines. BVF had a slight inhibitory effect on growth, and FPV1 did not influence growth. Surprisingly, after inoculation to fruits of sweet cherry, there were no significance differences in disease progression between isogenic lines, suggesting that these mycoviruses did not influence the virulence of M. fructicola on a natural host.
- Published
- 2018
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