Open Access Research article

Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins

Chun Sui, Jie Zhang, Jianhe Wei*, Shilin Chen, Ying Li, Jiesen Xu, Yue Jin, Caixiang Xie, Zhihui Gao, Hongjiang Chen, Chengmin Yang, Zheng Zhang and Yanhong Xu

Author Affiliations

Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China

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BMC Genomics 2011, 12:539  doi:10.1186/1471-2164-12-539

Published: 2 November 2011

Additional files

Additional file 1:

Summary of the annotation of the 454 assembled unique B. chinense sequences. The annotations were obtained by comparing the assembled sequences with sequences from KEGG, Nr, and UniProt (E < 1 × 10-10).

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Additional file 2:

Functional annotations of the 454 unique sequences of B. chinense based on GO categories. The annotations were obtained by assigning the 454 assembled unique sequences to the GO categories of molecular function, biological process, and cellular component based on their similarities with A. thaliana protein sequences (TAIR9, http://www.arabidopsis.org webcite). A cut-off value of E < 1.0-10 was used.

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Additional file 3:

Summary of metabolic pathway assignments of the 454 assembled unique sequences based on KEGG. The numbers of 454 assembled unique sequences that were assigned into different metabolism categories based on KEGG are shown in a bar chart.

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Additional file 4:

Putative P450 and GT genes in the 454 dataset. The 454 assembled unique sequences that were annotated as P450 and GT genes by comparing the assembled sequences with sequences from KEGG, Nr, and UniProt (E < 1 × 10-10) were manual identified and listed.

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Additional file 5:

Summary of family classification of the annotated P450s from the 454 assembled unique sequences. The number of annotated 454 unique sequences and reads of B. chinense encoding P450s that belong to different families and subfamilies are listed. Families belong to the CYP71 clan are shown in red, and families belong to the CYP85 clan are shown in blue.

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Additional file 6:

Classification of the candidate glycosyltransferase/glucosyltransferase genes. The assembled 454 unique sequences that were annotated as genes with various glycosyltransferase/glucosyltransferase activities were classified and listed. The classification was obtained by comparing annotated glycosyltransferase/glucosyltransferase genes from the 454 dataset with A. thaliana protein sequences (TAIR9, http://www.arabidopsis.org webcite).

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Additional file 7:

Screening of internal reference genes for real-time PCR analysis of MeJA inducibility. The RNA transcription levels of actin, β-tubulin, and EF1α in the MeJA-treated and control adventitious roots of B. chinense were assayed by real-time PCR and are presented as Ct values.

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Additional file 8:

The primers used in the present study. All primers used for full-length cDNA cloning and real-time PCR analysis of P450s and UGTs in the present study are listed.

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