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Molecular Genetics and Genomics

, Volume 271, Issue 6, pp 709–716 | Cite as

Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences

  • C. P. Hong
  • S. J. Lee
  • J. Y. Park
  • P. Plaha
  • Y. S. Park
  • Y. K. Lee
  • J. E. Choi
  • K. Y. Kim
  • J. H. Lee
  • J. Lee
  • H. Jin
  • S. R. Choi
  • Y. P. LimEmail author
Original Paper

Abstract

We estimated the genome size of Korean ginseng ( Panax ginseng C.A. Meyer), a medicinal herb, constructed a Hin dIII BAC library, and analyzed BAC-end sequences to provide an initial characterization of the library. The 1C nuclear DNA content of Korean ginseng was estimated to be 3.33 pg (3.12×103 Mb). The BAC library consists of 106,368 clones with an average size of 98.61 kb, amounting to 3.34 genome equivalents. Sequencing of 2167 BAC clones generated 2492 BAC-end sequences with an average length of 400 bp. Analysis using BLAST and motif searches revealed that 10.2%, 20.9% and 3.8% of the BAC-end sequences contained protein-coding regions, transposable elements and microsatellites, respectively. A comparison of the functional categories represented by the protein-coding regions found in BAC-end sequences with those of Arabidopsis revealed that proteins pertaining to energy metabolism, subcellular localization, cofactor requirement and transport facilitation were more highly represented in the P. ginseng sample. In addition, a sequence encoding a glucosyltransferase-like protein implicated in the ginsenoside biosynthesis pathway was also found. The majority of the transposable element sequences found belonged to the gypsy type (67.6%), followed by copia (11.7%) and LINE (8.0%) retrotransposons, whereas DNA transposons accounted for only 2.1% of the total in our sequence sample. Higher levels of transposable elements than protein-coding regions suggest that mobile elements have played an important role in the evolution of the genome of Korean ginseng, and contributed significantly to its complexity. We also identified 103 microsatellites with 3–38 repeats in their motifs. The BAC library and BAC-end sequences will serve as a useful resource for physical mapping, positional cloning and genome sequencing of P. ginseng.

Keywords

Panax ginseng BAC (bacterial artificial chromosome) library BAC-end sequences Transposable elements Microsatellites 

Notes

Acknowledgement

This research was supported by Plant Diversity Research Center (PDRC) Grant No. PF003101-01

Supplementary material

supp.pdf (535 kb)
(PDF 536 KB)

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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • C. P. Hong
    • 1
  • S. J. Lee
    • 1
  • J. Y. Park
    • 1
  • P. Plaha
    • 2
  • Y. S. Park
    • 1
  • Y. K. Lee
    • 1
  • J. E. Choi
    • 3
  • K. Y. Kim
    • 4
  • J. H. Lee
    • 4
  • J. Lee
    • 5
  • H. Jin
    • 1
  • S. R. Choi
    • 1
  • Y. P. Lim
    • 1
    Email author
  1. 1.Department of Horticulture, and Genome Research CenterChungnam National UniversityDaejeonKorea
  2. 2.Advanced Centre of Hill Bioresources and BiotechnologyHP Agricultural UniversityPalampurIndia
  3. 3.Department of AgronomyChungnam National UniversityDaejeonKorea
  4. 4.Department of Plant BiotechnologyDong-A UniversityBusanKorea
  5. 5.School of Biological Sciences, College of Natural SciencesSeoul National UniversitySeoulKorea

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