Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species

Abstract

BackgroundTaxol is an efficient anticancer drug; however, the accumulation of taxoids can vary hugely among Taxus species. The mechanism underlying differential accumulation of taxoids is largely unknown. Thus, comparative analysis of the transcriptomes in three Taxus species, including T. media, T. mairei and T. cuspidata, was performed.ResultsKEGG enrichment analysis revealed that the diterpenoid biosynthesis and cytochrome P450 pathways were significantly enriched in different comparisons. Differential expressions of these taxol biosynthesis related genes might be a potential explanation for the interspecific differential accumulation of taxol and its derivatives. Besides, the sequences of several MEP pathway-associated genes, such as DXS, DXR, MCT, CMK, MDS, HDS, HDR, IPPI, and GGPPS, were re-assembled based on independent transcriptomes from the three Taxus species. Phylogenetic analysis of these MEP pathway-associated enzymes also showed a high sequence similarity between T. media and T. cuspidata. Moreover, 48 JA-related transcription factor (TF) genes, including 10 MYBs, 5 ERFs, 4 RAPs, 3 VTCs, and 26 other TFs, were analyzed. Differential expression of these JA-related TF genes suggested distinct responses to exogenous JA applications in the three Taxus species.ConclusionsOur results provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species. The data give us an opportunity to reveal the mechanism underlying the variations in the taxoid contents and to select the highest-yielding Taxus species.Electronic supplementary materialThe online version of this article (10.1186/s12870-019-1645-x) contains supplementary material, which is available to authorized users.

Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes

“…Transcriptome analysis is currently the most widely used and cost effective way to screen target gene(s) rapidly in functional genomic studies (Ali et al, 2018;Ma et al, 2019;Zhou et al, 2019). In this study, a total of 100,218 unigenes were generated by transtomic sequencing of three chemotypes of C. burmannii.…”

Biochemical characterization of acyl activating enzymes for side chain moieties of Taxol and its analogs

“…We previously performed metabolite analyses as part of a capacity building project for medicinal plants, which also included samples from T. media cell suspension cultures (16). Since these cultures were available to us as a source for candidate genes, we downloaded publicly available whole transcriptome shotgun sequencing (RNA-Seq) data sets acquired with this species (National Center for Biotechnology Information (NCBI) Bioproject numbers PRNJA169654, PRJNA341288, and PRNJA497542) (17,18), with an emphasis on suspension cells treated with the elicitor methyl jasmonate, which is commonly used to upregulate the formation of taxoids (19). We then searched in these publicly available data sets for gene sequences with homology to previously characterized AAEs of varying specificity (for details see Experimental procedures).…”

“…First-strand cDNA was prepared from RNA with the SuperScript III First Strand Synthesis kit (Invitrogen, Carlsbad, CA, USA) with random hexamer oligonucleotides. Open reading frames for CoA ligases were amplified using gene-specific primers (Table S3) designed based on AAE sequences identified in publicly available T. media transcriptome data sets (NCBI Bioproject numbers PRNJA169654, PRJNA341288, and PRNJA497542) (17,18). Amplicons were ligated into the pET-32b vector featuring an encoded 6 x histidine tag (EMD Millipore, Burlington, MA, USA) and, following sequence confirmation, transformed into E. coli BL21(DE3) cells (New England Biolabs, Ipswich, MA, USA).…”

Comparative analysis of transcriptome and metabolome uncovers the metabolic differences between Dendrobium officinale protocorms and mature stems

“…In addition, DEGs were mapped to the KEGG database in order to elucidate their biological functions (Liang et al 2019;Miao et al 2019;Zhou et al 2019). The top 20 most enriched pathways are shown in Figure 5B and Table A7.…”