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Rehmannia glutinosa Libosch (R.glutinosa), a perennial herbaceous medicinal plant,belongs to the Scrophulariaceae family.R.glutinosa is rich in medicinal value and has a long history of cultivation.However, its productivity and quality declines seriously when it replanted on the soil that the preceding crops being themselves, which described as "continuous cropping problem".Since there is very little known about the molecular mechanism of replanting disease, we aimed to investigate transcriptional changes in replanted R.glutinosa roots and identify genes responding to the disease.Here,we sampled roots from first year (FP) and second year (SP) planting R.glutinosa, respectively, at the five representative periods at 20-day intervals.We constructed a cDNA library from total RNA isolated from the mixture of roots and leaves of the above ten samples.We generated 24,000 million raw reads by using deep sequencing and obtained 66,960 distinct sequences by de novo assembly.Based on this resource, we screened differentially expressed genes in the five stages (SP1/FP1, SP2/FP2, SP3/FP3,SP4/FP4 and SP5/FP5) by RNA-Seq technique.There are respectively 7,653, 602, 2,092, 3,676 and 8,435 differentially expressed genes screened between continuous cropping and first cropping R.glutinosa in the seedling stage (SP1/FP1);the root stretch stage (SP2/FP2);the initial stage of tuber root enlargement(SP3/FP3);the mid stage of tuber enlargement (SP4/FP4) and the maturity stage (SP5/FP5).Function analysis revealed that, the modification mechanism of chromatin was inhibited,the key process blocked cell division, and the plant growth and development related processes being completely broken in SP1;hormone metabolism was disordered, the salicylic acid-related genes being significantly up-regulated, growth of root was inhibited in SP2;the perception of R.glutinosa to light being affected in SP3;salicylic acid signaling pathway is extremely significant increasing in SP4;The above ground part of continuous cropping R.glutinosa being basically dead, part of the root re-developing into seedlings in SP5.This study outlines the "poison" mechanism of replanting R.glutinosa, which laid a theoretical foundation to reveal the molecular mechanism of replanting problems.