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

Zhang GH, Ma CH, Zhang JJ, Chen JW, Tang QY, He MH, Xu XZ, Jiang NH, Yang SC - BMC Genomics (2015)

Bottom Line: P. 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. zgh73107310@163.com.

ABSTRACT

Background: P. 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.

Results: To 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).

Conclusions: The 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.

Show MeSH
UPGMA dendrogram of 13 accessions ofP. vienamensisvar.fuscidiscus. Dendrogram constructed with UPGMA clustering method among 13 different accessions of P. vienamensis var. fuscidiscus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4355973&req=5

Fig6: UPGMA dendrogram of 13 accessions ofP. vienamensisvar.fuscidiscus. Dendrogram constructed with UPGMA clustering method among 13 different accessions of P. vienamensis var. fuscidiscus.

Mentions: The dendrogram constructed based on UPGMA (un-weighted pair group method with arithmetic average) clustering method was used to perform genetic correlation analysis among the 13 P. vietnamensis var. fuscidiscus accessions (Figure 6). The coefficients of genetic similarity among the 13 P. vietnamensis var. fuscidiscus accessions ranged from 0.82 to 0.94, indicating a high genetic similarity among them. UPGMA cluster analysis grouped these individuals into two groups at the similarity level of 0.836. According to the dendrogram, all the 3 accessions from Laos were clustered into cluster I. In cluster II, all the 10 accession of P. vietnamensis var. fuscidiscus from China were clustered into one group. The results of the cluster analysis showed that the individuals from the same area tend to clustered together. Therefore, the UPGMA cluster analysis based on SSR data was closely related to the geographical origins. Meanwhile, these results demonstrate that SSRs primer pairs derived from P. vietnamensis var. fuscidiscus unigenes can distinguish varieties without morphological diversities, and will be a powerful tool for genetic applications in this herb crop.Figure 6


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

Zhang GH, Ma CH, Zhang JJ, Chen JW, Tang QY, He MH, Xu XZ, Jiang NH, Yang SC - BMC Genomics (2015)

UPGMA dendrogram of 13 accessions ofP. vienamensisvar.fuscidiscus. Dendrogram constructed with UPGMA clustering method among 13 different accessions of P. vienamensis var. fuscidiscus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4355973&req=5

Fig6: UPGMA dendrogram of 13 accessions ofP. vienamensisvar.fuscidiscus. Dendrogram constructed with UPGMA clustering method among 13 different accessions of P. vienamensis var. fuscidiscus.
Mentions: The dendrogram constructed based on UPGMA (un-weighted pair group method with arithmetic average) clustering method was used to perform genetic correlation analysis among the 13 P. vietnamensis var. fuscidiscus accessions (Figure 6). The coefficients of genetic similarity among the 13 P. vietnamensis var. fuscidiscus accessions ranged from 0.82 to 0.94, indicating a high genetic similarity among them. UPGMA cluster analysis grouped these individuals into two groups at the similarity level of 0.836. According to the dendrogram, all the 3 accessions from Laos were clustered into cluster I. In cluster II, all the 10 accession of P. vietnamensis var. fuscidiscus from China were clustered into one group. The results of the cluster analysis showed that the individuals from the same area tend to clustered together. Therefore, the UPGMA cluster analysis based on SSR data was closely related to the geographical origins. Meanwhile, these results demonstrate that SSRs primer pairs derived from P. vietnamensis var. fuscidiscus unigenes can distinguish varieties without morphological diversities, and will be a powerful tool for genetic applications in this herb crop.Figure 6

Bottom Line: P. 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. zgh73107310@163.com.

ABSTRACT

Background: P. 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.

Results: To 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).

Conclusions: The 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.

Show MeSH