1. College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xi��an 712046, China; 2. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; 3. Penghui Prosperity Agriculture & Animal Husbandry Co., Ltd. in Xinglong Town, Zhenba 723601, China; 4. Science and Technology Bureau of Zhenba County, Zhenba 723600, China)
Abstract��OBJECTIVE To obtain the transcriptomic characteristics of Rheum officinale Baill. and screen anthraquinone biosynthesis genes.METHODSR. officinale Baill. seedlings were subjected to high-throughput transcriptomic sequencing via Illumina HiSeqTM 2000 150PE platform, followed by systemic bioinformatics analyses. Then the anthraquinone biosynthesis genes were uncovered based on previously published studies. RESULTS The transcriptome sequencing analyses produced a total of 9.34 Gb clean data, resulting in 62 240 114 clean reads (SRA acc. SRP160030). Using trinity assembling, a total of 82 229 unigenes were finally obtained, with an average length of 1 082 nt. BLAST analyses showed that 64 361 unigenes (78.23%) were successfully annotated against the NR, NT, Swiss-port, PFAM, and KOG databases. GO classification of biological process, cellular component, and molecular function further contained 57 subgroups. KEGG analysis revealed that 1 253 unigenes were involved in 17 secondary metabolic standard pathways. Totally 195 unigenes were found to encode key enzymes of MVA, MEP, shikimic acid, and polyketide pathways that were mostly correlated to the anthraquinone biosynthesis. It was found that 166 and 66 unigenes, encoding cytochrome P450s and UDP-glycosyltransferases respectively, were related with the modification of secondary metabolites in R. officinale Baill. Meantime, MISA prediction produced a number of 16 378 simple sequence repeats (SSRs). CONCLUTION The transcriptomic characteristics of R. officinale Baill. seedlings are revealed by high-throughput sequencing technology along with bioinformatics analyses, better for further functional gene characterization, secondary metabolism pathway dissections, and their regulatory mechanisms in this species.
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2019, Vol. 54 
