Transcriptome profiling of cucumber genome expression in response to long-term low nitrogen stress

The present study aimed to delineate the genes mediating nitrogen metabolism in cucumber ( Cucumis sativus L.) and elucidate the mechanisms underlying the response to long-term nitrogen limitation. As an economically important crop, cucumber is strongly nitrogen dependent. The mechanisms underlying nitrogen metabolism in cucumber are not fully known. This study found that cucumber developed to a 3.5-leaf stage with reduced plant size and biomass under chronic low nitrogen stress condition. Gene expression profiling and analysis of cucumber roots and leaves under nitrogen-starved condition identified a total of 2991 unigenes as reliable differentially expressed genes (DEGs). A comprehensive analysis of the transcriptome revealed that the mechanisms underlying the response of cucumber roots to nitrogen-deficient stress were considerably different from those of its leaves. Importantly, the DEGs involved in the photosynthesis were almost downregulated, suggesting that the photosystem was sensitive to nitrogen starvation. Otherwise, the nitrate metabolic pathway of cucumber was suppressed by nitrogen deficiency, which was further confirmed by quantitative reverse transcription–polymerase chain reaction. This study represents a comparative analysis of the transcriptome levels of roots and leaves of cucumber, which possibly provides a valuable resource for further investigating the mechanism underlying plant response to long-term nitrogen limitation stress along with the candidate genes controlling the nitrogen metabolism.