Transcriptomic data analyses of Melicope pteleifolia via Illumina high-throughput sequencing technology / 中草药

ABSTRACT

Objective: To obtain the transcriptome sequence database of Melicope pteleifolia. Methods: The transcriptome sequencing and systematic bioinformatics analysis were carried out using the second generation high-throughput sequencing platform Illumina HiSeqTM 2000 with mixed root, stem and leaf samples of M. pteleifolia. Results: A total of 47 045 040 high quality sequences (clean reads) were obtained by transcriptome sequencing analysis. A total of 67 956 unigenes were assembled by Trinity de novo, with an average length of 787 nt. BLAST analysis showed that 42 749 (61.92%), 31 152 (45.84%), 26 563 (39.09%), and 17 481 (25.72%) unigenes were annotated in NR, Swiss port, KOG and KEGG databases respectively, and 47 groups were involved in three GO classification biological process, cellular component and molecular function. A total of 9807 unigenes were annotated to 130 KEGG metabolic pathways, 19 secondary metabolic pathways were screened. Twenty-five different KOG functional groups were obtained by the analysis of KOG functional classification. It was predicted that there were 56 families of higher plant transcription factors. A total of 7 748 simple sequence repeats (SSRs) were found by MISA software. The number (4 117) of the tri-nucleotide SSRs was the richest, with a frequency of 53.1%, and the number of the penta-nucleotide SSRs was relatively small, accounting for 2.2%. Conclusion: The transcriptome information characteristics of root, stem, and leaf of M. pteleifolia can be obtained by high-throughput Illumina sequencing technology and bioinformatics analysis, which will lay a foundation for further research on functional gene mining, secondary metabolic pathway analysis and regulation mechanism of M. pteleifolia.