Transcriptome characterization of Stellera chamaejasme with Illumina sequencing technology / 中草药

ABSTRACT

Objective To obtain the transcriptome database and gene sequence, SSR as well as transposon information of Stellera chamaejasme. Methods Using the high-throughput sequencing platform (Illumina HiSeq 2000), a root transcriptome dataset of S. chamaejasme was obtained, and the sequencing results were analyzed with the bioinformatic way. Results With a total of 26 785 872 clean reads, 47 053 unigenes were assembled. All these unigenes were then blasted with Nr, Swiss-Prot, KEGG, COG, and GO databases. There were 11 138 and 24 744 unigenes were annotated with Nr and Swiss-Prot databases, respectively. The unigenes were involved in 36 GO-terms and 119 metabolic pathways. Further analysis showed that 15 unigenes were involved in terpenoids biosynthesis. Using MISA software, the results showed that there were 3 480 SSR from the 47 053 unigenes, and the most type of SSR was mononucleotide (1 986) with the frequency of 57.07%. Moreover, the hexanucleotide only had five repeat SSR and the frequency was only 0.14%. With RepeatMasker online tools to analyze the transposon of the transcriptome sequences, the results indicated that there were 1 497 transposons, and the number of transposons with E < 1×10-5 was 827. All the transposons were grouped into 22 types, and the LINE/L1 type (405) had the highest frequency (48.97%). The DNA/Ginger, DNA/hAT, DNA/PIF-ISL2EU, and LINE/Jockey as well as LTR/Lenti were the least type since each of them has only one transposon. Conclusion In this study, rich sequence information of gene, SSR as well as transposon information of Stellera chamaejasme is helpful to carry out the research of the molecular mechanism of phorbol ester biosynthesis in S. chamaejasme in the future.