Cucurbit Expression Atlas

Phloem-specific transcriptome profiling links gene expression, physiological characterization with phloem function in the pedicle and fruit of cucumber (Cucumis sativus L.) (cucumber). 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. Overall design: Transcriptome profiling by laser microdissection combined with RNA sequencing analysis was employed to discover critical genes that are expressed and regulated in phloem tissue in three different organs (pedicle, stalk and fruit) of cucumber. Two biological replicates were generated for each sample.

sample
fruit
pedicle
stalk
# fruit: Phloem of fruit at 3 days post anthesis
# pedicle: Phloem of pedicle at 3 days post anthesis
# stalk: Phloem of stalk at 3 days post anthesis