Transcriptome analysis of Panax vietnamensis var. fuscidicus discovers putative ocotillol-type ginsenosides biosynthesis genes and genetic markers

Abstract

BackgroundP. vietnamensis var. fuscidiscus, called “Yesanqi” in Chinese, is a new variety of P. vietnamensis, which was first found in Jinping County, the southern part of Yunnan Province, China. Compared with other Panax plants, this species contains higher content of ocotillol-type saponin, majonoside R2. Despite the pharmacological importance of ocotillol-type saponins, little is known about their biosynthesis in plants. Hence, P. vietnamensis var. fuscidiscus is a suitable medicinal herbal plant species to study biosynthesis of ocotillol-type saponins. In addition, the available genomic information of this important herbal plant is lacking.ResultsTo investigate the P. vietnamensis var. fuscidiscus transcriptome, Illumina HiSeq™ 2000 sequencing platform was employed. We produced 114,703,210 clean reads, assembled into 126,758 unigenes, with an average length of 1,304 bp and N50 of 2,108 bp. Among these 126,758 unigenes, 85,214 unigenes (67.23%) were annotated based on the information available from the public databases. The transcripts encoding the known enzymes involved in triterpenoid saponins biosynthesis were identified in our Illumina dataset. A full-length cDNA of three Squalene epoxidase (SE) genes were obtained using reverse transcription PCR (RT-PCR) and the expression patterns of ten unigenes were analyzed by reverse transcription quantitative real-time PCR (RT-qPCR). Furthermore, 15 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely to involve in triterpenoid saponins biosynthesis pathway were discovered from transcriptome sequencing of P. vietnamensis var. fuscidiscus. We further analyzed the data and found 21,320 simple sequence repeats (SSRs), 30 primer pairs for SSRs were randomly selected for validation of the amplification and polymorphism in 13 P. vietnamensis var. fuscidiscus accessions. Meanwhile, five major triterpene saponins in roots of P. vietnamensis var. fuscidicus were determined using high performance liquid chromatography (HPLC) and evaporative light scattering detector (ELSD).ConclusionsThe genomic resources generated from P. vietnamensis var. fuscidiscus provide new insights into the identification of putative genes involved in triterpenoid saponins biosynthesis pathway. This will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level. The SSR markers identified and developed in this study show genetic diversity for this important crop and will contribute to marker-assisted breeding for P. vietnamensis var. fuscidiscus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1332-8) contains supplementary material, which is available to authorized users.

The complete chloroplast genome sequence of Panax vietnamensis Ha et Grushv (Araliaceae)

“…Some studies revealed the diversity of secondary metabolites and pharmacological effects of P. vietnamensis (Court, 2006;Le et al, 2015). Although several studies performed phylogenetic analysis and transcriptomics in P. vietnamensis and related natural variant (Komatsu et al, 2001;Zhang et al, 2015;Zhu et al, 2003), current genomic resource for P. vietnamensis is very limited. On this account, we characterized the complete chloroplast genome sequence of P. vietnamensis to facilitate molecular study of this species together with other Panax species.…”

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

“…fuscidiscus (43.25%), indicating better quality sequencing. In the sequence assembly 89,271 unigenes (average length = 598.32 bp, N50 = 942 bp) were recorded, which was shorter than the results of Cao et al [47] in P. ginseng (average length = 690-698 bp, N50 = 1130-1161 bp) and Zhang et al [2] in P. vietnamensis var. fuscidiscus (average length = 1,304 bp, N50 = 2,018 bp).…”

“…From 8,927 unigenes, 11,343 EST-SSR molecular markers were identi ed by RNA sequencing, while 2,763 unigenes have EST-SSR locus more than one. Zhang et al [2] also identi ed 21,320 SSRs in P. vietnamensis var. fuscidiscus with 2,918 containing more than one SSR.…”

“…The results are in line with GO functional categories of P. vietnamensis var. fuscidiscus [2] and P. ginseng [47]. The predicted unigenes 5,838 (5.42%) through KEGG pathways were mapped into 118 biological pathways and majority of pathways were related to metabolism.…”

“…Panax species (Araliaceae) are medicinally important plants of North America and eastern Asia [1,2]. In 19 species of the Panax genus [3,4], three known species, Panax vietnamensis, P. stipuleanatus and P. bipinati dus are related to the high mountains of Vietnam [5,6].…”