Transcriptomic analyses of Chloranthus japonicus by RNA-seq / 中草药

ABSTRACT

Objective To obtain the transcriptome dataset of Chloranthus japonicas. Methods Using the Illumina HiSeqTM 2000 150PE, a rhizome transcriptome of C. japonicus was generated, followed by systemic bioinformatics analyses. Results A total of 68 458 750 high quality clean reads were produced by the transcriptome sequencing. Trinity de novo assembling resulted in a total of 56 096 unigenes with an average length of 801 nt. BLAST analysis indicated that 25 773 (45.94%), 17 801 (31.73%), 16 082 (28.67%), and 9 649 (17.20%) unigenes were successfully annotated in the NR, Swiss-port, KOG, and KEGG databases, respectively. All unigenes were classified into three major groups by GO, including biological process, cellular component, and molecular function, and then, grouped into 40 subgroups. And 131 KEGG standard pathways were designated, 16 of which were defied as the secondary metabolism. Further analysis revealed that a total of 170 unigenes were involved in the biosynthesis of mono-, di-, sesqui-, or triterpene. Meantime, 1 887 unigenes were predicted to contain protein coding sequences. Totally 54 families of transcription factors of higher plant were identified. Using MISA prediction, 8 987 simple sequence repeats (SSRs) were obtained, among which the di-nucleotide SSRs were abundant with 5 948 (66.2%), whereas the penta-nucleotide SSRs were relatively less, accounting for 1.3%. Conclusion The transcriptome of C. japonicus rhizome was generated by RNA-seq along with the identification of unigenes implicated in various terpenes biosynthesis, which will provide a fundamental basis for secondary metabolism pathway dissections and their regulatory mechanisms in this plant species.