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Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags

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Abstract

Gene and genome duplication events have long been accepted as driving forces in the evolution of angiosperms. Panax ginseng C. A. Meyer and Panax quinquefolius L., which inhabit eastern Asia and eastern North America, respectively, are famous medicinal herbs and are similar in growth condition, morphological and genetic characteristics. However, no molecular data regarding their evolution has been available. In this study, expressed sequence tags (ESTs) were generated from a cDNA library of P. ginseng and comparative analyses were conducted to reveal genome-level duplication and speciation of P. ginseng and P. quinquefolius by in-depth comparison of paralog and orthlog ESTs. Sequencing and assembly of 5,760 clones from the cDNA library resulted in 4,552 uniESTs of P. ginseng and these were subjected to initial annotation steps. Comparative analysis was conducted with the uniESTs and transcriptome data of P. quinquefolius retrieved from the public database. Paralog pairing and analysis of the distribution of synonymous substitutions per synonymous site (Ks) showed two coincident peaks in both Panax species, implying two rounds of genome duplication in their common ancestor. Comparison of orthologs revealed one Ks peak that is younger than the two peaks identified from the analysis of paralogs. However, absolute dating of genome duplication and speciation events is needed to address caveats related to their long generation times, speculated to be more than 8–10 years in the wild. This is the first report regarding the evolutionary relationship of Panax species at the genome-wide level, and will provide a foundation to unravel the genome structure of the enigmatic genus Panax and the family Araliaceae.

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Acknowledgments

This study was supported by the Mid-career Researcher Program through a National Research Foundation of Korea (NRF) grant funded by the Ministry of Education, Science and Technology (MEST) (No. R01-2007-000-20823-0) and a grant from the Next-Generation BioGreen 21 Program (No. PJ008202), Rural Development Administration, Republic of Korea, and partially supported by grant 2007-04269 from the MEST.

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  1. Department of Plant Science, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Republic of Korea

    Hong-Il Choi, Nam-Hoon Kim, Junki Lee, Jee Young Park, Sang-Choon Lee & Tae-Jin Yang

  2. Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea

    Hong-Il Choi, Nam-Hoon Kim, Junki Lee, Jee Young Park, Sang-Choon Lee & Tae-Jin Yang

  3. National Instrumentation Center for Environmental Management, Seoul National University College of Agriculture and Life Sciences, Seoul, 151-742, Republic of Korea

    Beom Soon Choi

  4. Institute of Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA

    Kyung Do Kim

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  1. Hong-Il Choi
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Choi, HI., Kim, NH., Lee, J. et al. Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags. Genet Resour Crop Evol 60, 1377–1387 (2013). https://doi.org/10.1007/s10722-012-9926-3

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