title: Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag-simple sequence repeat bands in Panax ginseng Meyer.
abstract: BACKGROUND
  Panax ginseng, the most famous medicinal herb, has a highly duplicated genome structure. However, the genome duplication of P. ginseng has not been characterized at the sequence level. Multiple band patterns have been consistently observed during the development of DNA markers using unique sequences in P. ginseng.
  
  
  METHODS
  We compared the sequences of multiple bands derived from unique expressed sequence tag-simple sequence repeat (EST-SSR) markers to investigate the sequence level genome duplication.
  
  
  RESULTS
  Reamplification and sequencing of the individual bands revealed that, for each marker, two bands around the expected size were genuine amplicons derived from two paralogous loci. In each case, one of the two bands was polymorphic, showing different allelic forms among nine ginseng cultivars, whereas the other band was usually monomorphic. Sequences derived from the two loci showed a high similarity, including the same primer-binding site, but each locus could be distinguished based on SSR number variations and additional single nucleotide polymorphisms (SNPs) or InDels. A locus-specific marker designed from the SNP site between the paralogous loci produced a single band that also showed clear polymorphism among ginseng cultivars.
  
  
  CONCLUSIONS
  Our data imply that the recent genome duplication has resulted in two highly similar paralogous regions in the ginseng genome. The two paralogous sequences could be differentiated by large SSR number variations and one or two additional SNPs or InDels in every 100 bp of genic region, which can serve as a reliable identifier for each locus.
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Nam-Hoon
authors.initials: NH
authors.lastname: Kim
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Hong-Il
authors.initials: HI
authors.lastname: Choi
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Kyung Hee
authors.initials: KH
authors.lastname: Kim
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Woojong
authors.initials: W
authors.lastname: Jang
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
keywords: Panax ginseng; SSR marker; genome duplication; multi-band pattern; paralogs
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