Transcriptomic Study Of Erigeron Breviscapus Under Low Nitrogen Stress

Erigeron breviscapus (vant.) Hand. Mazz.[Deng-zhan-hua in Chinese] is a wellknown traditional Chinese medicinal plant for heart disease. The main medicinalactive ingredients are flavonoids, such as scutellarin, and phenolic acids. However,the wild resources of E. breviacapus are nearly exhausted due to excessive diggingfrom wild field. For meeting its demand in pharmacy, currently artificial cultivationtake the place of wild resources in supply E. breviscapus to the macket. The existingstudies on E. Breviacapus mainly focus on its habitat ecological, chemicalconstituents, pharmacological effects and the technique of artificial cultivation, etc..By comparison, there is rare report about genetic background and secondarymetabolic pathways of E. breviscapus.A number of studies have shown that low-nitrogen stress is one of the greatestenvironmental impact factors inducing active ingredient content of E. breviacapus. Inthis study, by using of tissue culture and Illumina sequencing technology, two cDNAlibraries prepared from low-nitrogen stress (LD) and normal control (CK) weresequenced to obtain the transcriptome information of E. breviacapus, and toinvestigate changes in the transcriptome of the species in response to low-nitrogenstress, and flavonoids compounds biosynthesis pathways. In addition, SSR (SimpleSequence Repeat) locis were identified. The results of the present study are asfollows:1. By the Illumina high-throughput transcriptome sequencing technique, in total,35.87million and25.82million pieces of short sequences(Raw Reads) weregenerated from LD and CK libraries, respectively. The overall sequencing outputswere over6Gb. Among all the raw reads, more than98.37%and98.67%hadPhred-like quality scores at Q20level(an error probability of1%), respectively. Afterfiltered to remove low quality reads, the high quality sequencing sequence were usedfor de novo assembly.101,156pieces Unigenes with average length of768bp(N501290bp) were obtained, and the length of44,908pieces(44.39%) is more than500bp. Accordingly, a high-quality and comprehensive transcriptome database of E.Breviacapus was constructed successfully.2. Among101,156Unigenes,59,538(58.86%) showed significant BLAST hitsin the public databases.43,392Unigenes were categorized into57GO(GeneOntology) terms,22,462Unigenes were subjected to25COG(Clusters ofOrthologous Groups) families, and22,391Unigenes were mapped to183canonicalpathways in the KEGG (Kyoto Encyclopedia of Genes and Genomes). We selectedsome key genes and transcription factors related to the synthesis of flavonoids, andfound that most of these genes belong to multi-gene family.3. Digital gene expression annotation and expression pattern of the differentiallyexpressed genes showed that, among101,156Unigenes,22,088were up-regulatedand69,820were down-regulated upon treatment of E. breviacapus with low-nitrogensolution. But only63Unigenes were identifed as Differentially Expressed genes(DEGs), including36up-and27down-regulated DEGs.4.15,311SSRs were searched in the transcriptome database of E. Breviacapus.Single nucleotide repeat have the most frequency, accounted for40.87%, followed bytri-nucleotides and di-nucleotide repeat, accounted for33.98%and23.60%,respectively. The length of SSRs rang from10bp to261bp. Length distributiongravely deviates from the normal distribution.