High-throughput transcriptome sequencing of roots of Dictamnus dasycarpus and data analyses / 中草药

ABSTRACT

Objective To obtain the transcriptome dataset of roots of Dictamnus dasycarpus. Methods The root transcriptome dataset of D. dasycarpus was obtained using the high-throughput sequencing platform Illumina HiSeqTM 2000 150PE, followed by systemic bioinformatics analyses. Results A great number of 69 643 286 high quality clean reads were obtained by the transcriptome sequencing analyses. Using Trinity de novo assembling, a total of 49 050 unigenes were finally obtained, with an average length of 841 nt. BLAST analysis indicated that 31 636 (accounting 64.49% of the total unigenes), 22 367 (45.60%), 19 246 (39.23%), 12 595 (25.68%) unigenes were successfully annotated in the NR, Swiss-port, KOG, and KEGG databases, respectively. And GO classification contained the basic three major groups, including biological process, cellular component, and molecular function with 42 subgroups. A total of 132 KEGG standard metabolic pathways were designated, 18 of which were defied as the secondary metabolism. Further analysis revealed that a total of 90 unigenes were involved in the biosynthesis of various alkaloids. Of all unigenes, 1 908 were predicted to have CDS, and 55 families of plant transcription factors were also identified. Using MISA prediction, 4 579 simple sequence repeats (SSRs) were obtained, among which the tri-nucleotide SSRs were abundant with 2 021 (44.1%), whereas the penta-nucleotide SSRs accounted for 3.5%. Conclusion The root transcriptome of D. dasycarpus revealed by the high-throughput sequencing technology will be important for gene functional characterization, secondary metabolism pathway exploration, and regulation mechanism research in this species.