title: Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq.
abstract: BACKGROUND
  As a valuable medicinal plant, the yield of Panax ginseng is seriously affected by autotoxicity, which is a common phenomenon due to continuous cropping. However, the mechanism of autotoxicity in P. ginseng is still unknown.
  
  
  RESULTS
  In total, high throughput sequencing of 18 RNA-Seq libraries produced 996,000,000 100-nt reads that were assembled into 72,732 contigs. Compared with control, 3697 and 2828 genes were significantly up- and down-regulated across different tissues and time points, respectively. Gene Ontology enrichment analysis showed that 'enzyme inhibitor activity', 'carboxylesterase activity', 'pectinesterase activity', 'centrosome cycle and duplication' and 'mitotic spindle elongation' were enriched for the up-regulated genes. Transcription factors including AP2s/ERFs, MYBs, and WRKYs were up-regulated in roots after benzoic acid treatment. Moreover, reactive oxygen species, peroxidases and superoxide dismutase contigs were up-regulated in roots after benzoic acid treatment. Physiological and biochemical indexes showed that the proline and malondialdehyde content were restored to lower levels at a later stage after benzoic acid treatment. Benzoic acid inhibited the root hair development in a dose-dependent manner, and several differential expressed genes potentially involved in hair development were identified. Several key contigs in the flavonoid and ginsenoside biosynthesis pathways were repressed. Finally, 58,518 alternative splicing (AS) events from 12,950 genes were found after benzoic acid treatment. Interestingly, contigs in the ginsenoside biosynthetic pathway underwent AS, providing useful information about post-transcriptional regulation in P. ginseng.
  
  
  CONCLUSIONS
  This study revealed the stress-response molecular mechanisms in P. ginseng induced by benzoic acid.
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. bwu@implad.ac.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. longqiliangok@163.com.
authors.forename: Qiliang
authors.initials: Q
authors.lastname: Long
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. gao131yuan@163.com.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. hebe668@sina.com.
authors.forename: Zi
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. sweetsnow1991@163.com.
authors.forename: Tianwei
authors.initials: T
authors.lastname: Shao
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. liuyanan0120@126.com.
authors.forename: Yanan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. liyong@implad.ac.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. wlding@implad.ac.cn.
authors.forename: Wanlong
authors.initials: W
authors.lastname: Ding
mesh_terms: D017398:Alternative Splicing; D019817:Benzoic Acid / Q000494:pharmacology; D053898:Biosynthetic Pathways / Q000187:drug effects; D016000:Cluster Analysis; D019295:Computational Biology; D005419:Flavonoids / Q000096:biosynthesis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D063990:Gene Ontology; D036145:Ginsenosides / Q000096:biosynthesis; D059014:High-Throughput Nucleotide Sequencing; D008315:Malondialdehyde / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D005894:Panax / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D011392:Proline / Q000378:metabolism; D017382:Reactive Oxygen Species / Q000378:metabolism; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D005419:Flavonoids; D036145:Ginsenosides; D017382:Reactive Oxygen Species; D014157:Transcription Factors; D008315:Malondialdehyde; D019817:Benzoic Acid; D011392:Proline