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.
J Ginseng Res. 2014 Apr;38(2):130-5. doi: 10.1016/j.jgr.2013.12.005. Epub 2014 Jan 18.
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.
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.
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.
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.
人参是最著名的药用植物，具有高度重复的基因组结构。然而，人参的基因组复制尚未在序列水平上得到描述。在使用人参独特序列开发 DNA 标记的过程中，一直观察到多带模式。
我们比较了从独特表达序列标签简单重复序列（EST-SSR）标记获得的多个带的序列，以研究序列水平的基因组复制。
对单个条带的再扩增和测序表明，对于每个标记，预期大小周围的两条带是真正的来自两个同源基因座的扩增子。在每种情况下，两条带之一是多态的，在 9 个人参品种中显示出不同的等位形式，而另一条带通常是单态的。两条基因座的序列高度相似，包括相同的引物结合位点，但每个基因座都可以通过 SSR 数量变化以及额外的单核苷酸多态性（SNP）或插入缺失来区分。从同源基因座之间的 SNP 位点设计的基因座特异性标记产生了一个单带，该单带在人参品种之间也表现出明显的多态性。
我们的数据表明，人参基因组最近发生了基因组复制，产生了两个高度相似的同源基因区域。这两个同源序列可以通过较大的 SSR 数量变化以及每个基因区域 100bp 内的一个或两个额外 SNP 或插入缺失来区分，这可以作为每个基因座的可靠标识符。
