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Diversity and evolution of major Panax species revealed by scanning the entire chloroplast intergenic spacer sequences

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Abstract

Ginseng is an important medicinal plant, but almost no genomic information is known for it. For the primary step to understand the Panax genome, we inspected the chloroplast genome sequence diversity and used that to infer the evolution of Panax species using them. We inspected a total of 101 intergenic spacers (IGS) covering 44,563 bp (96.8 % of the total IGS) from four Panax species. Diversity was inspected by three steps: gel electrophoresis, high resolution melting (HRM) analysis, and further confirmation by sequencing. Even though low levels of InDel polymorphism were detected by gel electrophoresis, high levels of reproducible polymorphisms were identified by HRM analysis. Sequencing of the HRM-polymorphic spaces and pair-wise multiple sequence alignments revealed up to 247 sequence variations between species. We have identified 62 IGS showing polymorphism between species. Among them, the trnE-trnT, trnT-psbD, ndhF-rpl32, and rpl14-rpl16 spaces are more informative for studying the diversity of Panax relatives. Phylogenetic analysis and molecular evolution studies revealed that P. notoginseng is most diverged from the other Panax species, with a nucleotide substitution rate of 0.0039. P. quinquefolius shows a close relationship with P. ginseng and P. japonicus, with a nucleotide substitution rate of 0.0009. Meanwhile, no sequence variation was detected between P. ginseng and P. japonicus. Calculation of molecular clocks revealed that P. notoginseng diverged more than 1.30 million years ago from the other Panax species and then, P. quinquefolius diverged from P. ginseng by migration in the American continent more than 0.29 million years ago.

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Acknowledgments

This study was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ008202) and the Mid-career Researcher Program through a National Research Foundation of Korea grant funded by the Ministry of Education, Science and Technology (No. 2007-0056122) of the Republic of Korea.

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Authors and Affiliations

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

    Jun Ha Kim, Ju-Yeon Jung, Hong-Il Choi, Nam-Hoon Kim, Jee Young Park & Tae-Jin Yang

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

    Jun Ha Kim, Ju-Yeon Jung, Hong-Il Choi, Nam-Hoon Kim, Jee Young Park & Tae-Jin Yang

  3. Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 361-763, Korea

    Yi Lee

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  1. Jun Ha Kim
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Correspondence to Tae-Jin Yang.

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Jun Ha Kim and Ju-Yeon Jung authors contributed equally to this work.

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Kim, J.H., Jung, JY., Choi, HI. et al. Diversity and evolution of major Panax species revealed by scanning the entire chloroplast intergenic spacer sequences. Genet Resour Crop Evol 60, 413–425 (2013). https://doi.org/10.1007/s10722-012-9844-4

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