Comparative NGS Transcriptomics Unravels Molecular Components Associated with Mosaic Virus Infection in a Bioenergy Plant Species, Jatropha curcas L.

Sood, Archit; Chauhan, Rajinder Singh

doi:10.1007/s12155-016-9783-6

Cited by 11 publications

(7 citation statements)

References 75 publications

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“…Plants produce chemically diverse secondary metabolites and every plant species has its own characteristic set [ 50 ]. In our study, most of the maize transcripts related to metabolic processes were up-regulated in response to MIMV infection similar to what has been reported following virus infection in rice, jatropha, capsicum and tobacco [ 8 , 21 , 51 , 52 ] and also similar to maize infected by B . zeicola [ 16 ].…”

Section: Resultssupporting

confidence: 88%

Changes in maize transcriptome in response to maize Iranian mosaic virus infection

2018

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BackgroundMaize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated.Methodology/Principal findingsComplementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR.Conclusion/SignificanceApproximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.

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Section: Resultssupporting

confidence: 88%

Changes in maize transcriptome in response to maize Iranian mosaic virus infection

2018

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“…Genes involved in photosynthesis were down-regulated in both PSV-G and PSV-G + satRNA infected plants, but in the latter case the number of DEGs and their fold-change were much bigger. Similar observations have been reported in numerous plant–virus pathosystems [ 19 , 24 , 47 , 48 , 49 ], which suggests that this is a relatively common phenomenon and that cellular photosynthetic components participate in plant immunity signaling [ 50 ]. This finding is directly associated with another observation; that is, the cellular component severely affected during PSV infection was chloroplast, involving DEGs that encode proteins that are components of the chloroplast thylakoid membrane, chloroplast envelope, stroma, and photosystem.…”

Section: Discussionsupporting

confidence: 78%

The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA

Obrępalska‐Stęplowska

Żmieńko

Wrzesińska

et al. 2018

Viruses

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Peanut stunt virus (PSV) is a widespread pathogen infecting legumes. The PSV strains are classified into four subgroups and some are defined by the association of satellite RNAs (satRNAs). In the case of PSV, the presence of satRNAs alters the symptoms of disease in infected plants. In this study, we elucidated the plant response to PSV-G strain, which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA, which exacerbated pathogenesis in Nicotiana benthamiana. To explain the mechanisms underlying PSV infection and symptoms exacerbation caused by satRNA, we carried out transcriptome profiling of N. benthamiana challenged by PSV-G and satRNA using species-specific microarrays. Co-infection of plants with PSV-G + satRNA increased the number of identified differentially expressed genes (DEGs) compared with the number identified in PSV-G-infected plants. In both treatments, the majority of up-regulated DEGs were engaged in translation, ribosome biogenesis, RNA metabolism, and response to stimuli, while the down-regulated DEGs were required for photosynthesis. The presence of satRNA in PSV-G-infected plants caused different trends in expression of DEGs associated with phosphorylation, ATP binding, and plasma membrane.

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“…RBCL ribulose-bisphosphate carboxylase large chain; PGK phosphoglycerate kinase; GAPDH glyceraldehyde 3-phosphate dehydrogenase; ALDO aldolase, class I; FBP fructose-1,6-bisphosphatase I; TK transketolase; SBP sedoheptulose-bisphosphatase; PRK phosphoribulokinase; RPIA ribose 5-phosphate isomerase A; GPI glucose-6-phosphate isomerase; PGM phosphoglucomutase; GLGC glucose-1-phosphate adenylyltransferase; GLGA starch synthase; GLGB 1,4-alpha-glucan branching enzyme; AMYA alpha-amylase; AMYB beta-amylase; HK hexokinase; GPI glucose-6-phosphate isomerase; PFK 6-phosphofructokinase 1; PDH pyruvate dehydrogenase 2002). As per our observations, the decreased transcript abundance of gene-encoding enzyme NADP+ reductase in TR30 is associated with reduced photosynthetic electron flow further limits ATPs required for carbon fixation (Kramer and Evans 2011;Sood and Chauhan 2017). Thus, from our findings, it is inferred that the reduced biomass in TR30 might be due to decrease in overall photosynthetic capacity or availability of photosynthates required for the proper development of increased number of flowers and subsequent formation of fruits and seeds (Wang et al 1996).…”

Section: Effect Of Cytokinin Application On Photosynthesissupporting

confidence: 75%

Comparative transcriptomics reveals a reduction in carbon capture and flux between source and sink in cytokinin-treated inflorescences of Jatropha curcas L.

et al. 2018

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The low seed yield of has been a stumbling block in realizing its full potential as an ideal bioenergy crop. Low female to male flower ratio is considered as a major limiting factor responsible for low seed yield in Jatropha. An exogenous cytokinin application was performed on floral meristems to increase the seed yield. This resulted in an increase of total flowers count with a higher female to male flower ratio. However, the seed biomass did not increase in the same proportion. The possible reason for this was hypothesized to be the lack of increased photosynthesis efficiency at source tissues which could fulfil the increased demand of photosynthates and primary metabolites in maturing seeds. After cytokinin application, possible molecular mechanisms underlying carbon capture and flux affected between the source and sink in developing flowers, fruits and seeds were investigated. Comparative transcriptome analysis was performed on inflorescence meristems (treated with cytokinin) and control (untreated inflorescence meristems) at time intervals of 15 and 30 days, respectively. KEGG-based functional annotation identified various metabolic pathways associated with carbon capture and flux. Pathways such as photosynthesis, carbon fixation, carbohydrate metabolism and nitrogen metabolism were upregulated after 15 days of cytokinin treatment; however, those were downregulated after 30 days. Five genes, ,, and showed significant increase in transcript abundance after 15 days of treatment but showed a significant decrease after 30 days. These genes, after functional validation, can be suitable targets in designing a suitable genetic intervention strategy to increase overall seed yield in Jatropha.

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Comparative NGS Transcriptomics Unravels Molecular Components Associated with Mosaic Virus Infection in a Bioenergy Plant Species, Jatropha curcas L.

Cited by 11 publications

References 75 publications

Changes in maize transcriptome in response to maize Iranian mosaic virus infection

Changes in maize transcriptome in response to maize Iranian mosaic virus infection

The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA

Comparative transcriptomics reveals a reduction in carbon capture and flux between source and sink in cytokinin-treated inflorescences of Jatropha curcas L.

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