| Cistanche deserticola is a completely non-photosynthetic parasitic plant with great medicinal value and mainly distributed in desert of Northwest China. Its dried fleshy stem is a crucial tonic in traditional Chinese medicine with roles of mainly improving male sexual function and strengthening immunity, but few genomic and transcriptomic resources are available. In this study, we performed deep transcriptome sequencing in fleshy stem of C. deserticola, and about 80 million reads were generated using Illumina pair-end sequencing technology. Using trinity assembler, we obtained 95,787 transcript sequences with lengths ranging from 200bp to 15,698bp, having an average length of 950 bases.63,957 transcripts were identified as actively expressed transcripts with FPKM≥ 0.5, in which 30,098 transcripts were annotated with gene descriptions or gene ontology terms by sequence similarity analyses against several public databases (Uniprot, NR and Nt at NCBI, and KEGG). Furthermore, we identified enzymes involved in biosynthesis of lignin by comparison with KEGG database. At least four phenylalanine ammonia-lyase (PAL) genes, the first key enzyme in lignin and phenylethanoid glycosides (PhGs) biosynthesis, were identified based on sequences comparison and phylogenetic analysis. PhGs are known to be the primary active ingredients and two potential biosynthesis pathways of PhGs in C. deserticola were also proposed for the first time.To further research difference of primary active ingredients and gene transcription among various C. deserticola resources, samples were collected from different sites to quantify medical composition and perform mRNA sequencing. Fleshy stem of samples obviously varied in length and diameter; In term of weight, samples from ZuoQi had small variances, while samples from YouQi had much difference. We used HPLC to quantify echinacoside, acteoside and total glycosides, PhGs content of samples from YouQi was more than that from ZuoQi. We performed deep transcriptome sequencing in those six samples using Illumina pair-end sequencing technology, clean reads were mixed into a reads pool. Using Trinity software, we obtained 337,132 transcript sequences with average length 1,125 bases.156,877 transcripts were actively expressed with FPKM≥ 0.5, in which 72,186 transcripts were annotated with gene descriptions by sequence similarity analyses against Genbank nt/nr database. Transcripts co-expressed among samples were more than that specific-expressed in one sample. Results of differential expressed transcripts analysis showed that expression change among samples from YouQi was less than that from ZuoQi. Ten transcripts whose FPKM value changed concerted with PhGs content change among samples were selected as molecular marker. Moreover, SSR tags were detected based on transcripts sequence.1/3 transcripts contained SSR, and most SSR were one-nucleotide repeat motif. A public database (CISTANCHE DESERTICOLA Genome Database) was built based on our transcriptome dataset. Our study will accelerate understanding of physiological process and great medicinal value of C. deserticola in molecular level, also given the potential for quality evaluation and cultivars selection of C. deserticola. |
