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Next-Generation Sequencing-Based Transcriptional Profiling of Sacred Lotus “China Antique”

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Abstract

Rhizomes are underground stems that serve various purposes including vegetative propagation, invasion of new territory, and bioactive compound synthesis and storage. An important rhizomatous plant is sacred lotus (Nelumbo nucifera), which is prized in Asia as a medicine and a food. RNA-seq and total transcriptome analysis of rhizomes and other lotus tissues was applied to identify genes involved in rhizome growth, development and metabolism. Root, petiole, rhizome internode, and leaf tissues were used for single-read RNA-seq analysis. Two whole transcriptome paired-end read libraries from rhizome apical tip and elongation zone tissues were also generated in order to survey gene expression profiles. In this analysis, 22,803 genes were expressed: 20,476 in rhizome apical meristem and elongation zone, 17,171 in rhizome internode, 16,656 in leaf, 19,457 in root, and 16,845 in petiole. Gene ontology (GO) analysis indicated that “other membrane”, “nucleotide binding”, and “other cellular processes” were highly represented in the expressed genes. A total of 231 genes displayed rhizome-specific expression including several transcription factors, protein kinases, cytochromes P450 and a sulfate transporter. GOseq analysis showed that genes in the “molecular function” GO category and several genes related to cell proliferation based on KEGG IDs were preferentially up-regulated in rhizome tissue. In addition, 1,251 possible exon-skipping events were observed in 1,149 gene models. These results provide valuable insight into gene expression profiles and regulation in sacred lotus, and the identified rhizome-specific genes provide insight into important processes involved in the biology and development of sacred lotus rhizomes.

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Acknowledgments

We gratefully acknowledge the US National Science Foundation (Grant IOS-1044821) for financial support of this research and Dr. Ray Ming for growth of the sacred lotus plants.

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Authors and Affiliations

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

    Min-Jeong Kim & David R. Gang

  2. BIO5 Institute, The University of Arizona, Tucson, AZ, 85721, USA

    William Nelson & Carol A. Soderlund

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  1. Min-Jeong Kim
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  2. William Nelson
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  3. Carol A. Soderlund
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  4. David R. Gang
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Corresponding author

Correspondence to David R. Gang.

Additional information

Communicated by Marcelo C. Dornelas

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Additional file 1

Classification of the lotus genes at the second level of the generic gene ontology (GO) categories (XLSX 12 kb)

Additional file 2

Genes highly enriched or specifically expressed in rhizome apical meristem, elongation zone, and internode. (XLSX 348 kb)

Additional file 3

Genes highly enriched or specifically expressed in leaf. (XLSX 45 kb)

Additional file 4

Genes highly enriched or specifically expressed in root. (XLSX 120 kb)

Additional file 5

Genes highly enriched or specifically expressed in petiole. (XLSX 23 kb)

Additional file 6

Potential novel genes enriched in lotus rhizome. (XLSX 50 kb)

Additional file 7

Probability Weighting Function (PWF) for quantifying the bias of the length (A) and number of reads (B). (PDF 468 kb)

Additional file 8

Highly expressed genes in rhizome apical tip and elongation zone of lotus. (XLSX 1090 kb)

Additional file 9

Highly expressed genes in rhizome apical tip and elongation zone of common reed. (XLSX 2114 kb)

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Kim, MJ., Nelson, W., Soderlund, C.A. et al. Next-Generation Sequencing-Based Transcriptional Profiling of Sacred Lotus “China Antique”. Tropical Plant Biol. 6, 161–179 (2013). https://doi.org/10.1007/s12042-013-9130-4

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  • DOI: https://doi.org/10.1007/s12042-013-9130-4

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