High-throughput transcriptomic sequencing of Rheum palmatum L. seedlings and elucidation of genes in anthraquinone biosynthesis
10.16438/j.0513-4870.2018-0547
- VernacularTitle:利用转录组测序挖掘掌叶大黄蒽醌类生物合成相关基因
- Author:
Huan LI
1
;
Na ZHANG
1
;
Yi-min LI
1
;
Xiao-bin HEI
1
;
Yuan-min LI
1
;
Chong DENG
1
;
Yong-gang YAN
1
;
Meng-meng LIU
2
;
Gang ZHANG
1
Author Information
1. College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an 712046, China
2. Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
- Publication Type:ORIGINAL ARTICLES
- Keywords:
Rheum palmatum L.;
transcriptome;
anthraquinone;
gene;
metabolism pathway
- From:
Acta Pharmaceutica Sinica
2018;53(11):1908-1917
- CountryChina
- Language:Chinese
-
Abstract:
Anthraquinones are not only the main active constituents but also the index components for the quality control of Rhei Radix et Rhizoma. To study the anthraquinone biosynthesis, Rheum palmatum L. seedlings were subjected to a high-throughput transcriptomic sequencing analysis by Illumina HiSeqTM 2000 150PE. The Illumina sequencing generated a total of 11.04 G clean data resulting in 736 309 74 clean reads, deposited in the sequence read archive (SRA accession SRP160030). Trinity do novo assembly yielded 93 646 unigenes, with an average of 1 108 nt. Functional annotation revealed that all unigenes were successfully annotated in the NR, NT, Swiss-port, PFAM, and KOG databases. GO enrichments showed that 57 subgroups were involved in biological process, cellular component, and molecular function. KEGG analysis indicated that 1 107 unigenes were implicated in 19 standard secondary metabolic pathways. 172 unigenes were analyzed to encode 28 key enzymes during the MVA, MEP, shikimic acid, and polyketide pathways related to anthraquinone biosynthesis. 125 CYP450 and 73 UGTs unigenes were related the modification of secondary metabolites in R. palmatum L. Furthermore, seven unigenes with full length cDNAs were successfully verified by RT-PCR and sequencing analyses. Then, MISA prediction produced a number of 18 885 simple sequence repeats (SSRs). Herein, the transcriptomic gene expression profiles of R. palmatum L. and candidate genes during the anthraquinone biosynthesis pathway were obtained for the first time. The results provided basic information for subsequent gene function characterization, secondary metabolic pathway analysis, and anthraquinone biosynthesis and regulation elucidation in R. palmatum L.
