Abstract
BackgroundAs 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.ResultsIn 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.ConclusionsThis study revealed the stress-response molecular mechanisms in P. ginseng induced by benzoic acid.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2151-7) contains supplementary material, which is available to authorized users.
Highlights
As a valuable medicinal plant, the yield of Panax ginseng is seriously affected by autotoxicity, which is a common phenomenon due to continuous cropping
RNA sequencing and de novo assembly RNA samples were collected from roots, stems and leaves at 0 days post treatment (DPT), 1 DPT, 3 DPT, 5 DPT, 7 DPT and 9 DPT after benzoic acid treatment
We investigated the effect of benzoic acid on gene expression profiles using RNASeq technology and identified the differentially expressed genes that directly respond to autotoxins and the enriched gene ontology (GO) terms that were involved in multiple biological processes
Summary
As a valuable medicinal plant, the yield of Panax ginseng is seriously affected by autotoxicity, which is a common phenomenon due to continuous cropping. Autotoxicity indicates that one plant releases allelochemicals into the adjacent environment, which directly or indirectly inhibit their own normal growth or that of their relatives in continuous cropping or short rotation [1,2,3]. Autotoxicity commonly occurs both in nature and cultivation and affects the yield and quality of plants [4,5,6]. Other types of autotoxins including phenolic compounds, flavones and terpenoids, and phenolic compounds are the main types of autotoxins
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