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Phloem-specific transcriptome profiling links gene expression, physiological characterization with phloem function in the pedicle and fruit of cucumber (Cucumis sativus L.)

ABSTRACT: Phloem is essential for higher plant development and survival by transporting photosynthetic products and systemic signals from source to sink organs. To date, most phloem studies were performed with the phloem exudate for physiological, transcriptomic or proteomic analyses. However, as yet, no transcriptomic profiling was performed to the phloem tissue itself, probably due to the technique difficulties to access the phloem tissue inside the plant body. In this study, laser microdissection combined with RNA-Seq technology was used to gain phloem-specific transcript profiling in three different organs (pedicle, stalk and fruit) of cucumber, a model plant species for phloem research. We found that transcription factors and biotic/abiotic stress related genes are highly enriched in the sink organs, while cell growth via calcium ion, hormone actions and cell cycle control was largely restricted in the pedicle and stalk, and genes implicated in transporting amino acids and sugars are mostly up-regulated in the pedicle. Further, we found excellent corroboration between phloem-specific gene expression, and physiological characterization with phloem function. In addition, we identified 432 cucumber-unique genes and several phloem-specific markers for future functional studies. This study provides new insights into the molecular genetics of the function of phloem tissue in cucumber, rather than the conventional phloem sap analyses.

ORGANISM(S): Cucumis sativus

PROVIDER: GSE62338 | GEO | 2015/10/15

SECONDARY ACCESSION(S): PRJNA263870

REPOSITORIES: GEO

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Project description:Phloem is the primary conduit through which photosynthates, hormones, and other biologically important molecules are distributed from aerial plant organs downward and throughout the plant. Increasing evidence suggests that phloem contents are diverse and play a critical role in biotic and abiotic stress adaptation. Drought causes the greatest decreases in agricultural crop productivity among all biotic and abiotic stresses, and the link between water deficiency and phloem protein contents is relatively unexplored. Here we employed the EDTA-facilitated phloem exudate collection method from Solanum lycopersicum leaves during a period of drought stress and recovery. Our analysis resulted in the confident identification and quantification of 2,558 proteins. Comparing our data with previous findings confirms that our exudate collection strategy enriched for known phloem proteins. Independent of drought, enrichment analysis of the total phloem exudate protein profiles from all samples suggest that the exchange of proteins into the phloem is more complex than previously thought, including additional protein chaperone systems, branched-chain amino acid synthesis proteins, trehalose metabolism, and RNA silencing proteins. During the experiment we observed 169 proteins whose abundance changed significantly within the phloem sap, the majority of which were impacted specifically in response to drought. Among these were proteins involved in lipid metabolism, chaperone-mediated protein folding, carboxylic acid metabolism, abscisic acid signaling, cytokinin biosynthesis, and amino acid metabolism are significantly upregulated during drought. Conversely, proteins involved in lipid signaling, sphingolipid metabolism, cell wall organization, carbohydrate metabolism, and a mitogen-activated protein kinase are downregulated in response to drought. Many of these observations are consistent with previous literature findings at the whole plant level but have not been localized to the vasculature in tomato, suggesting phloem plays a critical role in adaptation to drought stress in tomato .

Dataset Information

Phloem-specific transcriptome profiling links gene expression, physiological characterization with phloem function in the pedicle and fruit of cucumber (Cucumis sativus L.)

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