This article is part of the supplement: The 2010 International Conference on Bioinformatics and Computational Biology (BIOCOMP 2010): Genomics

Open Access Research article

Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers

Hongmei Luo1, Chao Sun1, Yongzhen Sun1, Qiong Wu2, Ying Li1, Jingyuan Song1, Yunyun Niu1, Xianglin Cheng3, Hongxi Xu4, Chuyuan Li5, Juyan Liu5, André Steinmetz6 and Shilin Chen1*

Author Affiliations

1 The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China

2 School of Pharmacy, Guilin Medical University, Guilin 541004, China

3 China National Center for Biotechnology Development, Beijing 100036, China

4 Shanghai University of Traditional Chinese Medicine, Shanghai, China

5 Guanzhou Pharmaceutical Holding Limited, Guangzhou, China

6 Centre de Recherche Public-Santé, Luxembourg, L-1526 Luxembourg, Belgium

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BMC Genomics 2011, 12(Suppl 5):S5  doi:10.1186/1471-2164-12-S5-S5

Published: 23 December 2011

Additional files

Additional file 1:

Summary of the annotation percentage of P. notoginseng 454-ESTs as compared to public databases. The annotation for P. notoginseng unique sequences was based on sequence similarity searches against public databases including SwissProt, KEGG, TAIR, NCBI non-redundant protein (Nr), and NCBI non-redundant nucleotide (Nt) database. A total of 70.2% of P. notoginseng unique sequences were annotated by BLAST searches against the above public databases.

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Additional file 2:

Mapping of P. notoginseng unique sequences to KEGG biochemical pathways. List of the number of P. notoginseng unique sequences involved in metabolism, genetic information processing, environmental information processing, cellular processes, human diseases, unclassified and unassigned in the 454-EST dataset.

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Additional file 3:

The P. notoginseng unique sequences involved in the biosynthesis of secondary metabolites. The number of unique sequences involved in the biosynthesis of alkaloid, brassinosteroid, caffeine, carotenoid, diterpenoid, flavone and flavonol, flavonoid, limonene and pinene, monoterpenoid, novobiocin, phenylpropanoid, streptomycin, terpenoid, tetracycline and zeatin.

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Additional file 4:

The detection of SSR motifs in the unique sequences of P. notoginseng. The list of unique sequences (including contigs and singletons) containing potential microsatellite loci including the name of unique sequence, motif (SSR-repeat type), number of repeat, SSR start, SSR end and sequence length from P. notoginseng 454-EST dataset.

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Additional file 5:

The discovery of SSR motifs in the putative triterpene saponin-biosynthetic genes. The SSR motifs were detected in the putative triterpene saponin-biosynthetic genes including AACT (acetyl-CoA acetyltransferase), HMGR (HMG-CoA reductase), SS (squalene synthase), SE (squalene epoxidase) and DS (dammarenediol-II synthase).

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Additional file 6:

The P. notoginseng unique sequences encoding putative transcription factors based on Inter-Pro searches. The 906 unique sequences of P. notoginseng containing transcription factor domains using Inter-Pro searches.

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Additional file 7:

Major transcription factor families identified from P. notoginseng using Inter-Pro. The unique sequences from P. notoginseng with similarities to genes encoding transcription factors.

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Additional file 8:

Cytochrome P450 discovery. The unique sequences from P. notoginseng with sequence similarities to cytochrome P450s.

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Additional file 9:

Glycosyltransferase discovery. The unique sequences from P. notoginseng with sequence similarities to glycosyltransferase.

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Additional file 10:

The primers used for RACE in this study. The primers used in 5'-RACE for the amplification of unique sequences including Pn01024, Pn02132, Pn03717, and Pn00788.

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