Open Access Highly Accessed Research article

Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids

Hyun Jo Koo16, Eric T McDowell1, Xiaoqiang Ma17, Kevin A Greer28, Jeremy Kapteyn1, Zhengzhi Xie139, Anne Descour2, HyeRan Kim1104, Yeisoo Yu14, David Kudrna14, Rod A Wing14, Carol A Soderlund2 and David R Gang1115*

  • * Corresponding author: David R Gang gangd@wsu.edu

  • † Equal contributors

Author Affiliations

1 School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson, AZ, 85721, USA

2 Arizona Genomics Computational Laboratory and BIO5 Institute, The University of Arizona, Tucson, AZ, 85721, USA

3 Department of Pharmaceutical Sciences, The University of Arizona, Tucson, AZ, 85721, USA

4 Arizona Genomics Institute, The University of Arizona, Tucson, AZ, 85721, USA

5 Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA

6 Present address: Salk Institute for Biological Studies, PO Box 85800, San Diego, CA, 92186, USA

7 Present address: XenoBiotic Laboratories, Inc., Morgan Ln 107, Plainsboro, NJ, 08536, USA

8 Present address: Department of Surgery, College of Medicine, The University of Arizona, Tucson, AZ, 85724, USA

9 Present address: Division of Cardiovascular Medicine, University of Louisville, Louisville, KY, 40202, USA

10 Present address: Plant Genome Research Center, KRIBB, Daejeon, 305-803, South Korea

11 Institute of Biological Chemistry, Washington State University, P.O. Box 646340, Pullman, WA, 99164-6340, USA

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BMC Plant Biology 2013, 13:27  doi:10.1186/1471-2229-13-27

Published: 15 February 2013

Additional files

Additional file 1: Table S1:

cDNA library sources for sequences and unigene sets described in this study. Table S2. The most abundantly represented transcripts in the ArREST database (EST number ≥ 40). Table S3. The most abundantly represented transcripts in specific ginger and turmeric rhizome libraries (EST number ≥ 10 per library). Table S4. Normalized EST expression levels for selected enzymes in ginger and turmeric metabolic pathways. Table S5. Normalized EST expression levels for selected gene families. Table S6. Normalized EST expression levels for cytochrome P450 monooxygenases. Table S7. Normalized percentage of ArREST ESTs with GO associations. Table S8. Probable transcriptional regulator classes within ArREST associated with GO:0003677.

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Additional file 2: Figure S1:

Distribution of EST sequence length. The average EST sequence length was 817 bp, with unitrans (unique transcripts, a.k.a. contigs) lengths ranging from 151 to 4021 bp, with the greatest number of unitrans having between 701 and 800 bp, and with 95% exceeding 300 bp. Figure S2. Gene Ontology (GO) annotations of ArREST unitrans. 87.6% of the ArREST unitrans could be annotated by GO classification. Eight GO categories had EST abundances greater than 5%, including protein modification (10.5%), transport (9.2%), metabolism (9.0%), transcription (8.6%), cellular process (8.0%), protein biosynthesis (6.9%), electron transport (5.6%), and biological process unknown (5.3%). In contrast, the GO category secondary metabolism contained relatively few ESTs (0.3%). Figure S3. Proposed metabolic map showing how the curcuminoids, gingerols and terpenoids are produced from sucrose in a large interconnected network. Names of enzymes identified in the ArREST database are colored blue; % values indicate fraction of unitrans in the database that are represented by genes encoding each protein. Figure S4. Phylogenetic tree of P450 monooxygenases. A neighbor joining tree was generated with 1136 P450s including 170 ginger and turmeric P450s from the ArREST database (indicated by black diamonds), 247 Arabidopsis P450s, 350 rice P450s and 369 P450s from other plants. P450 subfamily classifications are indicated. Additional file1: Table S6 contains a summary of these data for ginger and turmeric. As the tree is so large, it was impossible to display it at readable scale on a page size that is typical. Thus, details of tree can been seen by zooming in on this page of the PDF file. Figure S5. Overall gene expression in rhizomes is similar to but distinct from that observed for other plant tissues. Total ArREST ESTs, ESTs with shared expression in ginger or turmeric rhizomes and at least one other ginger or turmeric tissue, and ESTs found exclusively in ginger or turmeric rhizomes are represented as light grey, dark grey and black bars, respectively. Values used to generate this graph are presented in Additional file1 :Table S7.

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Additional file 3:

GenBank Accessions for Rhizome-specific Transcripts from Sorghum.

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Additional file 4:

Microarray experimental methods, oligonucleotide probe design, microarray design (interwoven design).

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