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.
Highlights
The major active ingredients of medicinal plants are secondary metabolites, which their biosynthesis and accumulation are different among development stages, organs [1], environment [2], artificial tending measures and even different lineages [3]
The information provided from transcriptome studies of different experimental conditions or tissues can help in the characterization of important traits related to secondary metabolite formation and to test the molecular mechanisms associated to these metabolites [4,5,6]
In the biosynthesis of secondary metabolites category, 900 unigenes were annotated into 22 KEGG secondary metabolites, “phenylpropanoid biosynthesis pathway” was the largest group, followed by “terpenoid backbone biosynthesis”, “steroid
Summary
The major active ingredients of medicinal plants are secondary metabolites, which their biosynthesis and accumulation are different among development stages, organs [1], environment [2], artificial tending measures and even different lineages [3]. Several kinds of compounds have been isolated from Euscaphis, such as triterpene compounds [7,8,9,10], phenolic acid compounds [11, 12], flavonoid compounds [9, 11] and others [11, 13, 14]. Anti-cancer, anti-inflammatory and antifibrotic activities have been demonstrated from Euscaphis extracts from different organs by modern pharmacological research, showing that the major active ingredients were triterpenes, flavonoids and phenolic acid [7,8,9, 11]. The molecular mechanism of active ingredients biosynthesis and accumulation was still unclear because of the lack of E. konishiii genomic data
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