GANS-based data augmentation for citrus disease severity detection using deep learning

Recently, many Deep Learning models have been employed to classify different kinds of plant diseases, but very little work has been done for disease severity detection. However, it is more important to master the severities of plant diseases accurately and timely, as it helps to make effective decisions to protect the plants from being further infected and reduce financial loss. In this paper, based on the Huanglongbing (HLB)-infected leaf images obtained from PlantVillage and crowdAI, we created a dataset with 5,406 citrus leaf images infected by HLB. Then six different kinds of popular models were trained to perform the severity detection of citrus HLB with the goal to find which types of models are more suitable to detect HLB severity with the same training circumstance. The experimental results show that the Inception_v3 model with epochs=60 can achieve higher accuracy than that of other models for severity detection with an accuracy of 74.38% due to its highly computational efficiency and small number of parameters. Additionally, aiming for evaluating whether GANs-based data augmentation can contribute to improve the model learning performance, we adopted DCGANs (Deep Convolutional Generative Adversarial Networks) to augment the original training dataset up to two times itself. Finally, a new training dataset with 14,056 leaf images composed by the original training images and the augmented ones were used to train the Inception_v3 model. As a result, we achieved an accuracy of 92.60%, about 20% higher than that of the Inception_v3 model trained by the original training dataset, which suggested that the GANs-based data augmentation is very useful to improve the model learning performance

Proteomic study on growth promotion of PGPR inoculated aerobic rice (Oryza sativa L.) cultivar MR219-9

The plant growth promoting rhizobacteria (PGPR) perform substantial growth enhancement of aerobic rice. Study was conducted at Universiti Putra Malaysia using 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE) strategy to identify mechanisms for rice plant growth promotion by PGPR inoculation. In this study, diverse expressed proteins were determined by mass spectrometry (MS). Aerobic rice seedling (MR219-9) was grown in the soil and PGPR strains of Stenotrophomonas maltophilla and Bacillus spp. were inoculated separately and or as combined bacterial consortium. Leaf sheath and other plant parts were collected after 45 d of transplanting for the analysis of proteins. A total of 153 spots were found and from which 12 proteins were identified. All proteins were varied in MS analysis and exposed the differential expression. The identified proteins were tolerant to abiotic stresses (13.2%), disease resistance (10%), oxidation reduction process (10%), photosynthesis (16.62 μmol CO2 m–2 s–1), involved in the protein synthesis (23.28%), metabolism (13.6%) and related to internal plant physiological functions (13.29%). Beside protein identification, phenotypic characters, such as plant height and photosynthetic activity were measured. The highest plant height and length of root, tiller numbers and nutrients uptake were observed in PGPR inoculated treatments. PGPR inoculation increased leaf chlorophyll contents and net photosynthesis rate of inoculated aerobic rice. Hence, using plant proteomic approach it is proved that various designated proteins are responsible for the plant growth promotion of PGPR inoculated aerobic rice cultivar MR219-9

Diseases

This chapter describes the following diseases infecting longan and litchi (Litchi chinensis): soilborne diseases (rot caused by Armillaria mellea, litchi decline, and longan decline); diseases in nurseries (caused by Fusarium, Pythium and Rhizoctonia species); foliar, floral, fruit, stem and preharvest diseases (algal spot caused by Cephaleuros virescens, corky bark caused by F. decemcellulare [Nectria rigidiuscula], downy blight caused by Peronophythora litchii, branch blight and fruit rot caused by Lasiodiplodia theobromae, pepper spot caused by Colletotrichum gloeosporioides [Glomerella cingulata], leaf blight caused by Phomopsis species, Phytophthora-incited diseases, sooty mould and black mildew, witches' broom, and minor foliar and stem diseases); and postharvest diseases (anthracnose caused by Colletotrichum species, stem end rot, and other postharvest diseases). Information on symptoms, morphology of causal agents, vectors (insects and nematodes), and control strategies (mainly cultural and chemical) is provided

Genome Organizations and Functional Analyses of a Novel Gammapartitivirus from Rhizoctonia solani AG-1 IA Strain D122

Here, we describe a novel double-stranded (ds) RNA mycovirus designated Rhizoctonia solani dsRNA virus 5 (RsRV5) from strain D122 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight. The RsRV5 genome consists of two segments of dsRNA (dsRNA-1, 1894 bp and dsRNA-2, 1755 bp), each possessing a single open reading frame (ORF). Sequence alignments and phylogenetic analyses showed that RsRV5 is a new member of the genus Gammapartitivirus in the family Partitiviridae. Transmission electron microscope (TEM) images revealed that RsRV5 has isometric viral particles with a diameter of approximately 20 nm. The mycovirus RsRV5 was successfully removed from strain D122 by using the protoplast regeneration technique, thus resulting in derivative isogenic RsRV5-cured strain D122-P being obtained. RsRV5-cured strain D122-P possessed the traits of accelerated mycelial growth rate, increased sclerotia production and enhanced pathogenicity to rice leaves compared with wild type RsRV5-infection strain D122. Transcriptome analysis showed that three genes were differentially expressed between two isogenic strains, D122 and D122-P. These findings provided new insights into the molecular mechanism of the interaction between RsRV5 and its host, D122 of R. solani AG-1 IA

Diversity of dsRNA Viruses Infecting Rice Sheath Blight Fungus Rhizoctonia solani AG-1 IA

Rice sheath blight, caused by Rhizoctonia solani (Kühn), is a notorious soil-borne disease prevalent in many rice-growing regions. Although several sporadic studies of mycoviruses in R. solani AG-1 IA have been reported for single strain of R. solani AG-1 IA, there have been no reports describing the distribution and diversity of mycoviruses in natural populations. In this study, 43 R. solani AG-1 IA strains collected from different locations in China were examined for the presence of dsRNA elements to confirm the presence of viral infections. Electrophoretypes showed that 16 of the 43 fungal strains (37.2%) contained dsRNAs that can be characterized as viruses. Furthermore, the species-specific reverse transcription PCR (RT-PCR) showed dsRNA bands with similar sizes do not always contain the same virus but exist as mixed mycoviral infections. Thus, our findings indicate mycoviruses infecting R. solani AG-1 IA in China are diverse, widespread and universal

A novel mycovirus closely related to viruses in the genus Alphapartitivirus confers hypovirulence in the phytopathogenic fungus Rhizoctonia solani

AbstractWe report here the biological and molecular attributes of a novel dsRNA mycovirus designated Rhizoctonia solani partitivirus 2 (RsPV2) from strain GD-11 of R. solani AG-1 IA, the causal agent of rice sheath blight. The RsPV2 genome comprises two dsRNAs, each possessing a single ORF. Phylogenetic analyses indicated that this novel virus species RsPV2 showed a high sequence identity with the members of genus Alphapartitivirus in the family Partitiviridae, and formed a distinct clade distantly related to the other genera of Partitiviridae. Introduction of purified RsPV2 virus particles into protoplasts of a virus-free virulent strain GD-118 of R. solani AG-1 IA resulted in a derivative isogenic strain GD-118T with reduced mycelial growth and hypovirulence to rice leaves. Taken together, it is concluded that RsPV2 is a novel dsRNA virus belonging to Alphapartitivirus, with potential role in biological control of R. solani

Genome Organizations and Functional Analyses of a Novel Gammapartitivirus from <i>Rhizoctonia solani</i> AG-1 IA Strain D122

Here, we describe a novel double-stranded (ds) RNA mycovirus designated Rhizoctonia solani dsRNA virus 5 (RsRV5) from strain D122 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight. The RsRV5 genome consists of two segments of dsRNA (dsRNA-1, 1894 bp and dsRNA-2, 1755 bp), each possessing a single open reading frame (ORF). Sequence alignments and phylogenetic analyses showed that RsRV5 is a new member of the genus Gammapartitivirus in the family Partitiviridae. Transmission electron microscope (TEM) images revealed that RsRV5 has isometric viral particles with a diameter of approximately 20 nm. The mycovirus RsRV5 was successfully removed from strain D122 by using the protoplast regeneration technique, thus resulting in derivative isogenic RsRV5-cured strain D122-P being obtained. RsRV5-cured strain D122-P possessed the traits of accelerated mycelial growth rate, increased sclerotia production and enhanced pathogenicity to rice leaves compared with wild type RsRV5-infection strain D122. Transcriptome analysis showed that three genes were differentially expressed between two isogenic strains, D122 and D122-P. These findings provided new insights into the molecular mechanism of the interaction between RsRV5 and its host, D122 of R. solani AG-1 IA

Comparison of different methods for total RNA extraction from sclerotia of Rhizoctonia solani

Background: Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) is one of the most important pathogens of rice (Oryza sativa L.) that causes severe yield losses in all rice-growing regions. Sclerotia, formed from the aggregation of hyphae, are important structures in the life cycles of R. solani and contain a large quantity of polysaccharides, lipids, proteins and pigments. In order to extract high-quality total RNA from the sclerotia of R. solani, five methods, including E.Z.N.A.™ Fungal RNA Kit, sodium dodecyl sulfate (SDS)–sodium borate, SDS–polyvinylpyrrolidone (PVP), guanidinium thiocyanate (GTC) and modified Trizol, were compared in this study. Results: The electrophoresis results showed that it failed to extract total RNA from the sclerotia using modified Trizol method, whereas it could extract total RNA from the sclerotia using other four methods. Further experiments confirmed that the total RNA extracted using SDS–sodium borate, SDS–PVP and E.Z.N.A.™ Fungal RNA Kit methods could be used for RT-PCR of the specific amplification of GAPDH gene fragments, and that extracted using GTC method did not fulfill the requirement for above-mentioned RT-PCR experiment. Conclusion: It is concluded that SDS–sodium borate and SDS–PVP methods were the better ones for the extraction of high-quality total RNA that could be used for future gene cloning and expression studies, whereas E.Z.N.A.™ Fungal RNA Kit was not taken into consideration when deal with a large quantity of samples because it is expensive and relatively low yield

Molecular Characterization of a Novel <i>Endornavirus</i> Conferring Hypovirulence in Rice Sheath Blight Fungus <i>Rhizoctonia solani</i> AG-1 IA Strain GD-2

The complete sequence and genome organization of a novel Endornavirus from the hypovirulent strain GD-2 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight, were identified using a deep sequencing approach and it was tentatively named as Rhizoctonia solani endornavirus 1 (RsEV1). It was composed of only one segment that was 19,936 bp in length and was found to be the longest endornavirus genome that has been reported so far. The RsEV1 genome contained two open reading frames (ORFs): ORF1 and ORF2. ORF1 contained a glycosyltransferase 1 domain and a conserved RNA-dependent RNA polymerase domain, whereas ORF2 encoded a conserved hypothetical protein. Phylogenetic analysis revealed that RsEV1 was phylogenetically a new endogenous RNA virus. A horizontal transmission experiment indicated that RsEV1 could be transmitted from the host fungal strain GD-2 to a virulent strain GD-118P and resulted in hypovirulence in the derivative isogenic strain GD-118P-V1. Metabolomic analysis showed that 32 metabolites were differentially expressed between GD-118P and its isogenic hypovirulent strain GD-118P-V1. The differential metabolites were mainly classified as organic acids, amino acids, carbohydrates, and the intermediate products of energy metabolism. Pathway annotation revealed that these 32 metabolites were mainly involved in pentose and glucuronate interconversions and glyoxylate, dicarboxylate, starch, and sucrose metabolism, and so on. Taken together, our results showed that RsEV1 is a novel Endornavirus, and the infection of virulent strain GD-118P by RsEV1 caused metabolic disorders and resulted in hypovirulence. The results of this study lay a foundation for the biocontrol of rice sheath blight caused by R. solani AG1-IA