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. 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). 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.

Sampling for DUS test of flower colors should be fixed at the stages and sites that petals are fully colored, and besides, flower colorations are uniform among individuals and stable for a period of time to allow testers to get consistent results. It remains a problem since spatial and temporal flower colorations are reported a lot but their change traits are little discussed. In this study, expression state, uniformity and stability of color phenotypes, anthocyanin contents, and gene expression levels were taken into account based on measurements at 12 development stages and three layers (inner, middle, and outer petals) of two varieties of Ranunculus asiaticus L. to get their best sampling. Our results showed that, outer petals of L9–L10 (stage 9–stage 10 of variety ‘Jiaoyan zhuanhong’) and C5–C6 (stage 5–stage 6 of variety ‘Jiaoyan yanghong’) were the best sampling, respectively. For DUS test, it is suggested to track flower colorations continuously to get the best sampling as well as representative colors since different cultivars had different change traits, and moreover, full expression of color phenotypes came later and lasted for a shorter duration than those of anthocyanin contents and gene expressions. Our innovation exists in following two points. Firstly, a model of change dynamic was introduced to illustrate the change traits of flower colorations, anthocyanin contents, and gene expressions. Secondly, genes used for expression analysis were screened on account of tentative anthocyanins, which were identified based on comparison between liquid chromatography–mass spectrometry (LC–MS) results and molecular mass and mass fragment pattern (M²) of each putative anthocyanin and their fragments deduced in our previous study. Gene screening in this regard may also be interest for other non-model plant genera with little molecular background.