Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation

Abstract

BachgroundEuscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candidate genes involved in flavonoid biosynthesis and accumulation, we analyzed transcriptome data from three E. konishii tissues (leaf, branch and capsule) using Illumina Hiseq 2000 platform.ResultsA total of 91.7, 100.3 and 100.1million clean reads were acquired for the leaf, branch and capsule, respectively; and 85,342 unigenes with a mean length of 893.60 bp and N50 length of 1307 nt were assembled using Trinity program. BLASTx analysis allowed to annotate 40,218 unigenes using public protein databases, including NR, KOG/COG/eggNOG, Swiss-Prot, KEGG and GO. A total of 14,291 (16.75%) unigenes were assigned to 128 KEGG pathways, and 900 unigenes were annotated into 22 KEGG secondary metabolites, including flavonoid biosynthesis. The structure enzymes involved in flavonoid biosynthesis, such as phenylalanine ammonia lyase, cinnamate 4-hydroxylase, 4-coumarate CoA ligase, shikimate O-hydroxycinnamoyltransferase, coumaroylquinate 3′-monooxygenase, caffeoyl-CoA O-methyltransferase, chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, flavonoid 3′-hydroxylase, flavonoid 3′,5′-hydroxylase, flavonolsynthese, dihydroflavonol 4-reductase, anthocyanidinreductase, leucoanthocyanidin dioxygenase, leucoanthocyanidin reductase, were identified in the transcriptome data, 40 UDP-glycosyltransferase (UGT), 122 Cytochrome P450 (CYP) and 25 O-methyltransferase (OMT) unigenes were also found. A total of 295 unigenes involved in flavonoid transport and 220 transcription factors (97 MYB, 84 bHLH and 39 WD40) were identified. Furthermore, their expression patterns among different tissues were analyzed by DESeq, the differentially expressed genes may play important roles in tissues-specific synthesis, accumulation and modification of flavonoids.ConclusionWe present here the de novo transcriptome analysis of E. konishii and the identification of candidate genes involved in biosynthesis and accumulation of flavonoid. In general, these results are an important resource for further research on gene expression, genomic and functional genomics in E. konishii and other related species.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5354-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

“…In detail, 45,485 unigenes (45.38%) succeeded in functional annotation against several public databases. However, the annotation rate of unigene assembled in this study appear to be quite low, compared to other species, which may be due to the variable splicing of transcripts and the deficient of genomic sequences (Liang et al, 2019).…”

Comprehensive transcriptome analysis of reference genes for fruit development ofEuscaphis konishii

“…GAPDH shows stable expression in Citrus sinensis (Wu et al, 2014) and Lycopersicon esculentum (Mascia et al, 2010), but it did not perform well in S. viridis (Martins et al, 2016) and Panicum virgatum (Jiang et al, 2014). In previous study, our colleague Liang revealed EkGSTU1 performed better than EkGAPDH2 in root, leaf, branch and seed samples (Liang et al, 2019). However, in our study, EkGAPDH2 and EkUBC23 performed well in different stages of fruit ripening.…”

“…Yuan et al (2018) identified a large number of differentially expressed genes associated with endocarp colouration based on the transcriptome database, but it is unknown which genes are suitable as reference genes related to fruit development. Huang et al (2019) revealed that the total triterpenes of Euscaphis konishii pericarp showed the immune boosting effect and hepatic protective activity against inflammation, oxidative stress and apoptosis in BCG/LPS-induced liver injury. These findings suggest that pericarp of E. konishii might be a promising natural food for immunological hepatic injury.…”

“…The fruit of E. konishii has various chemical compounds, including flavonoid compounds (Liang et al, 2018a), triterpene compounds (Cheng et al, 2010;Li et al, 2016), and phenolic acid compounds (Huang et al, 2014), which have both anti-inflammatory and anticancer effects according to traditional and modern medical research. Moreover, in order to study the gene regulation mechanisms of medicinal compounds in E. konishii, several reference genes in E. konishii were selected by Liang et al (2019) based on transcriptome data (Liang et al, 2018b). However, the data being studied from Liang et al lack the transcriptome of the fruit at different developmental stages.…”

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.…”