| Panax ginseng C. A. Meyer belongs to the Araliaceae family and is one of the most valuable traditional Chinese herbal medicines. Ginseng has the characteristic that cannot continuous cropping, and the effect can last up to several years. The sustainable development of ginseng industry was seriously restricted by ginseng continuous cropping obstacle. Autotoxicity is one of the most important factors that causing continuous cropping obstacles, and so far, the mechanism of differential expression of ginseng gene to response the autotoxicity stress has not been reported yet. In the present study, with the help of high-throughput sequencing platform, we focuse on the differential expression, the signal transduction pathways and gene expression regulation model of ginseng functional gene under the benzoic acid stress at the transcriptome level, and find the autotoxicity stress related functional gene based on the annotation information. Thus reveal the molecular mechanism of ginseng response to autotoxicity stress, and which will be helpful for the interpretation of the developing process of continuous cropping obstacle of ginseng. Specific results are as follows:1. Taken seven allelopathic phenolic acids reported in the old ginseng soil as sample, we researched the effects of them on the ginseng seed growth and morphology of ginseng roots. And primarily confirmed that these phenolic acids had allelopathic effects on growth radicle and plumule of ginseng seeds under the certain concentrations.2. Based on the results of previous study, we researched the effects of benzoic acid on micro-and ultra-structures of ginseng root tip cells. And investigated allelopathic effects by pot experiment. As a result, we confirmed that the autotoxicity critical concentration of benzoic acid were about 25 mg·L-1.3. RNA samples were collected from roots, stems and leaves at 0,1,3,5,7 and 9 d after 25 mg·kg-1 benzoic acid treatment used Trizol method. In total,18 RNA-Seq libraries generated approximately 996,000000 clean reads of 100 nt in length. The reads were pooled together and assembled into reference sequences by Trinity, yielding 72,732 contigs. The GC content was 38.55%. The N50 and average length of assembled sequences were 1794 bp and 1428 bp, respectively. A total of 3697 and 2828 genes were identified with significantly up- and down-regulated expression, respectively, compared with control. A total of 11,838,15,469, and 21,807 genes were annotated in the UniProt, NR and NT databases, respectively. A total of 2783 genes in 262 pathways were identified according to the KEGG database. The results of GO enrichment analysis showed that the up-regulated genes were enriched for’Enzyme inhibitor activity’, ’Carboxylesterase activity’,’Pectinesterase activity’,’Centrosome cycle and duplication’and’Mitotic spindle elongation’, and the up-regulated genes were enriched for’Cell wall organization or biogenesis’,’Ion binding’,’Stress response’and ’Secondary metabolic process’4. The allelopathic effects of benzoic acid on proline, MDA and root activity of ginseng were researched. Compared with the result of RNA-Seq, ten differential expression gene including one P5CS gene, one PC5R gene, one APX gene, and seven ROS-related genes were obtained from the transcriptome.5. The differential expression of ginseng saponin synthesis pathways related genes under the benzoic acid stress were investigated, and seven related genes including two FPS genes, two GPS genes, one HMGS gene and two UGT genes were obtained from the transcriptome.6. The differential expression of ginseng transcription factor related genes under the benzoic acid stress were investigated, and fifteen related genes including twoAP2/ERF genes, four MYB genes and nine WRKY genes were obtained from the transcriptome.
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