Multiomic approaches reveal novel lineage-specific effectors in the potato and tomato early blight pathogen Alternaria solani

Wang, Jinhui; Xiao, Siyu; Zheng, Lijia; Pan, Yang; Zhao, Dongmei; Zhang, Dai; Li, Qian; Zhu, Jun‐Jie; Yang, Zhihui

doi:10.1186/s42483-022-00135-z

Cited by 9 publications

(14 citation statements)

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“…A transcriptome analysis of the genes in potato and A. solani that exhibited interactions in the early infection stage showed that cell wall-degrading enzymes and metabolic processes may be important for early A. solani infection of potato [ 14 ]. In our previous study, we reported that the effector proteins AsCEP112, AsCEP19 and AsCEP20, and play important roles in late-stage A. solani infection of potato leaves [ 15 , 16 ]. In the current study, we inoculated potato leaves with A. solani and found that near the inoculation site, there were obvious whorl symptoms and tissue collapse within 72 h, and the disease spread rapidly between 96 and 120 h. Therefore, we focused on protein interaction in the late stage of infection, which was further investigated by genome-wide transcriptomic analyses.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, few reports have focused on the pathogenic effectors of A. solani in potato. In our previous study, the important effector proteins AsCEP112, AsCEP19 and AsCEP20 were identified [ 15 , 16 ]. AsCEP112 is an important effector protein that targets host cell membranes and regulates host senescence-related genes to control host leaf cell senescence and chlorosis, and contributes to pathogen virulence [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…AsCEP112 is an important effector protein that targets host cell membranes and regulates host senescence-related genes to control host leaf cell senescence and chlorosis, and contributes to pathogen virulence [ 15 ]. The deletion of AsCEP19 and AsCEP20 from A. solani HWC-168 led to reduced virulence in potato leaves [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome sequencing leads to an improved understanding of the infection mechanism of Alternaria solani in potato

et al. 2023

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Background Alternaria solani (A. solani), the main pathogen of potato early blight, causes serious yield reductions every year. The application of fungicides is the most common and effective method of controlling Alternaria-caused diseases. The differentially expressed transcripts of A. solani infecting potato were identified, revealing a group of valuable candidate genes for a systematic analysis to increase the understanding of the molecular pathogenesis of A. solani, and providing scientific data for formulating additional measures to prevent and control potato early blight. In this study, a deep RNA-sequencing approach was applied to gain insights into A. solani pathogenesis. At 3, 4, and 5 days post inoculation (dpi), RNA samples from the susceptible potato cultivar Favorita infected with A. solani strain HWC-168, were sequenced and utilized for transcriptome analysis, and compared to the transcriptome obtained 0 dpi. Results A total of 4430 (2167 upregulated, 2263 downregulated), 4736 (2312 upregulated, 2424 downregulated), and 5043 (2411 upregulated, 2632 downregulated) genes were differentially expressed 3, 4 and 5 dpi, respectively, compared with genes analysed at 0 dpi. KEGG enrichment analysis showed that genes involved in the pathways of amino acid metabolism, glucose metabolism, and enzyme activity were significantly differentially expressed at the late infection stage. Correspondingly, symptoms developed rapidly during the late stage of A. solani infection. In addition, a short time-series expression miner (STEM) assay was performed to analyse the gene expression patterns of A. solani and Profile 17 and 19 showed significant change trends 3, 4 and 5 dpi. Both profiles, but especially Profile 17, included enzymes, including transferases, oxidoreductases, hydrolases and carbohydrate-active enzymes (CAZYmes), which may play important roles in late fungal infection. Furthermore, possible candidate effectors were identified through the adopted pipelines, with 137 differentially expressed small secreted proteins identified, including some enzymes and proteins with unknown functions. Conclusions Collectively, the data presented in this study show that amino acid metabolism, and glucose metabolism pathways, and specific pathway-related enzymes may be key putative pathogenic factors, and play important roles in late stage A. solani infection. These results contribute to a broader base of knowledge of A. solani pathogenesis in potato, as indicated by the transcriptional level analysis, and provide clues for determining the effectors of A. solani infection.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptome sequencing leads to an improved understanding of the infection mechanism of Alternaria solani in potato

et al. 2023

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“…The amino acid sequences of βCA, SBP, and FBA in the examined plant species were separately subjected to multiple alignment using fast Fourier transform (MAFFT) ( Jasim et al., 2020 ) to generate multiple sequence alignments with default parameters for revealing the evolutionary history. ProtTest was used to estimate the best model in this analysis for finding the amino acid substitution model that best fitted our data ( Wang et al., 2022 ). The JTT+ Gamma model was the best-fit model for the βCA and SBP protein datasets, whereas the JTT model was the best amino acid substitution model for the FBA protein dataset.…”

Section: Methodsmentioning

confidence: 99%

Multigene manipulation of photosynthetic carbon metabolism enhances the photosynthetic capacity and biomass yield of cucumber under low-CO2 environment

Chen

Wang²,

Feng³

et al. 2022

Front. Plant Sci.

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Solar greenhouses are important in the vegetable production and widely used for the counter-season production in the world. However, the CO2 consumed by crops for photosynthesis after sunrise is not supplemented and becomes chronically deficient due to the airtight structure of solar greenhouses. Vegetable crops cannot effectively utilize light resources under low-CO2 environment, and this incapability results in reduced photosynthetic efficiency and crop yield. We used cucumber as a model plant and generated several sets of transgenic cucumber plants overexpressing individual genes, including β-carbonic anhydrase 1 (CsβCA1), β-carbonic anhydrase 4 (CsβCA4), and sedoheptulose-1,7-bisphosphatase (CsSBP); fructose-1,6-bisphosphate aldolase (CsFBA), and CsβCA1 co-expressing plants; CsβCA4, CsSBP, and CsFBA co-expressing plants (14SF). The results showed that the overexpression of CsβCA1, CsβCA4, and 14SF exhibited higher photosynthetic and biomass yield in transgenic cucumber plants under low-CO2 environment. Further enhancements in photosynthesis and biomass yield were observed in 14SF transgenic plants under low-CO2 environment. The net photosynthesis biomass yield and photosynthetic rate increased by 49% and 79% compared with those of the WT. However, the transgenic cucumbers of overexpressing CsFBA and CsSBP showed insignificant differences in photosynthesis and biomass yield compared with the WT under low-CO2.environment. Photosynthesis, fluorescence parameters, and enzymatic measurements indicated that CsβCA1, CsβCA4, CsSBP, and CsFBA had cumulative effects in photosynthetic carbon assimilation under low-CO2 environment. Co-expression of this four genes (CsβCA1, CsβCA4, CsSBP, and CsFBA) can increase the carboxylation activity of RuBisCO and promote the regeneration of RuBP. As a result, the 14SF transgenic plants showed a higher net photosynthetic rate and biomass yield even under low-CO2environment.These findings demonstrate the possibility of cultivating crops with high photosynthetic efficiency by manipulating genes involved in the photosynthetic carbon assimilation metabolic pathway.

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“…solani were cultured on potato dextrose agar (PDA) for strain activation and tomato juice agar medium (T4) to induce sporulation. The activated HWC-168 strain was transferred to a T4 medium plate, cultured in the dark at 25°C for 7 to 10 days, then scraped off the mycelia, UV irradiated for 10 minutes (Ultraviolet lamp power is 8 W), nally the plate was cultured in the dark at 25°C/20°C alternately for 3 days [15].…”

Section: Plant Growth and Infection Conditionsmentioning

confidence: 99%

Transcriptome Sequencing Provides Insights into Understanding the Infection Mechanism of Alternaria solani on Potato

Jiang

Guo

Tan

et al. 2022

Preprint

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Background Alternaria solani (A. solani), the main pathogen of potato early blight, causes serious yield reduction every year. However, the molecular interaction between A. solani and its host, potato, is largely unknown. In this study, a deep RNA-sequencing approach was applied to gain insights into the pathogenesis of A. solani. At 3, 4, and 5 days post inoculation (dpi), RNA samples from the susceptible potato cultivar Favorita infected by A. solani strain HWC-168, were sequenced and utilized for transcriptome analysis. Results A total of 4430 (2167 up-regulated, 2263 down-regulated), 4736 (2312 up-regulated, 2424 down-regulated), and 5043 (2411 up-regulated, 2632 down-regulated) genes were differentially expressed at 3, 4 and 5 dpi, respectively. KEGG enrichment analysis showed that the genes of amino acid metabolism, glucose metabolism, and enzyme activity were significantly expressed at the late infection stage. Correspondingly, the symptoms developed rapidly during the late stage infection of A. solani. In addition, the short time-series expression miner (STEM) assay was conducted to analyze the gene expression patterns of A. solani and it was found that profile 17 and 19 showed significant changing trends at 3, 4 and 5 dpi. Both profiles especially profile 17 contained a large number of enzymatic proteins, including transferases, oxidoreductases, hydrolases and carbohydrate-active enzymes (CAZYmes), which may play important roles in the late process of fungal infection. Furthermore, we screened possible candidate effectors by an adopted pipeline and found 137 differentially expressed small secreted proteins, which included some enzymes and unknown function proteins. Conclusions Collectively, the data presented in this study showed that amino acid metabolism, and glucose metabolism pathways may be the key metabolic pathways and these specific enzymes were important at the late stage of A. solani infection. These results contributed to the establishment of a broader knowledge of the pathogenesis of A. solani to potato at the transcriptional level and provided clues for determining the effectors of A. solani.

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Multiomic approaches reveal novel lineage-specific effectors in the potato and tomato early blight pathogen Alternaria solani

Cited by 9 publications

References 70 publications

Transcriptome sequencing leads to an improved understanding of the infection mechanism of Alternaria solani in potato

Transcriptome sequencing leads to an improved understanding of the infection mechanism of Alternaria solani in potato

Multigene manipulation of photosynthetic carbon metabolism enhances the photosynthetic capacity and biomass yield of cucumber under low-CO2 environment

Transcriptome Sequencing Provides Insights into Understanding the Infection Mechanism of Alternaria solani on Potato

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