Illumina-based transcriptomic profiling of Panax notoginseng in response to arsenic stress

BACKGROUND: Panax notoginseng, a famous herbal medicine, has recently attracted great attention on its safety and quality since P. notoginseng can accumulate and tolerate As from growing environment. For the purpose of understanding As damage to the quality of P. notoginseng as well as corresponding tolerance mechanisms, genes involved in As stress response were identified using Illumina sequencing. RESULTS: Totally 91,979,946 clean reads were generated and were de novo assembled into 172,355 unigenes. A total of 81,575 unigenes were annotated in at least one database for their functions, accounting for 47.34 %. By comparative analysis, 1725 differentially expressed genes (DEGs, 763 up-regulated/962 down-regulated) were identified between As stressed plant (HAs) and control plant (CK), among which 20 DEGs were further validated by real-time quantitative PCR (qRT-PCR). In the upstream and downstream steps of biosynthesis pathways of ginsenosides and flavonoids, 7 genes encoding key enzymes were down-regulated in HAs. Such down-regulations were also revealed in pathway enrichment analysis. Genes encoding transporters (transporters of ABC, MATE, sugar, oligopeptide, nitrate), genes related to hormone metabolism (ethylene, ABA, cytokinin) and genes related to arsenic accumulation (HXT, NRAMP, MT and GRX) were differentially expressed. The up-regulated genes included those of oxidative stress-related protein (GSTs, thioredoxin), transcription factors (HSFs, MYBs) and molecular chaperones (HSP). CONCLUSIONS: The down-regulation of biosynthesis of ginsenoside and flavonoid indicated that As accumulation in P. notoginseng can cause not only safety hazard, but also qualitative losses. Aside from the results of arsenic content of seedling roots, the ability of P. notoginseng to over-accumulate arsenic can also be explained by the differential expression of genes of HXT, NRAMP, MT and GRX. To illustrate the detoxification mechanism of P. notoginseng, differential expression of genes encoding oxidative-related proteins, transcription factors, molecular chaperones, transporters and hormone were revealed in our study, which agreed with those reported in Arabidopsis to a certain extent, indicating P. notoginseng and Arabidopsis shared some common detoxification mechanisms in response to As stress. The longer As treatment in our study may account for the smaller quantity of related DEGs and smaller degree of expression differences of certain DEGs compared with those of Arabidopsis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40529-016-0128-8) contains supplementary material, which is available to authorized users.