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, 151-921, Korea.
Plant J. 2014 Mar;77(6):906-16. doi: 10.1111/tpj.12441. Epub 2014 Feb 24.
Ginseng (Panax ginseng) is a famous medicinal herb, but the composition and structure of its genome are largely unknown. Here we characterized the major repeat components and inspected their distribution in the ginseng genome. By analyzing three repeat-rich bacterial artificial chromosome (BAC) sequences from ginseng, we identified complex insertion patterns of 34 long terminal repeat retrotransposons (LTR-RTs) and 11 LTR-RT derivatives accounting for more than 80% of the BAC sequences. The LTR-RTs were classified into three Ty3/gypsy (PgDel, PgTat and PgAthila) and two Ty1/Copia (PgTork and PgOryco) families. Mapping of 30-Gbp Illumina whole-genome shotgun reads to the BAC sequences revealed that these five LTR-RT families occupy at least 34% of the ginseng genome. The Ty3/Gypsy families were predominant, comprising 74 and 33% of the BAC sequences and the genome, respectively. In particular, the PgDel family accounted for 29% of the genome and presumably played major roles in enlargement of the size of the ginseng genome. Fluorescence in situ hybridization (FISH) revealed that the PgDel1 elements are distributed throughout the chromosomes along dispersed heterochromatic regions except for ribosomal DNA blocks. The intensity of the PgDel2 FISH signals was biased toward 24 out of 48 chromosomes. Unique gene probes showed two pairs of signals with different locations, one pair in subtelomeric regions on PgDel2-rich chromosomes and the other in interstitial regions on PgDel2-poor chromosomes, demonstrating allotetraploidy in ginseng. Our findings promote understanding of the evolution of the ginseng genome and of that of related species in the Araliaceae.
人参（Panax ginseng）是一种著名的药用植物，但它的基因组组成和结构在很大程度上是未知的。在这里，我们描述了主要的重复成分，并检查了它们在人参基因组中的分布。通过分析人参的三个富含重复序列的细菌人工染色体（BAC）序列，我们鉴定了 34 个长末端重复反转录转座子（LTR-RTs）和 11 个 LTR-RT 衍生物的复杂插入模式，这些重复序列占 BAC 序列的 80%以上。LTR-RTs 被分为三个 Ty3/gypsy（PgDel、PgTat 和 PgAthila）和两个 Ty1/Copia（PgTork 和 PgOryco）家族。将 30-Gbp Illumina 全基因组鸟枪法测序reads 映射到 BAC 序列上，结果表明这五个 LTR-RT 家族至少占据了人参基因组的 34%。Ty3/Gypsy 家族占主导地位，分别占 BAC 序列和基因组的 74%和 33%。特别是，PgDel 家族占基因组的 29%，可能在人参基因组大小的扩大中发挥了主要作用。荧光原位杂交（FISH）显示，PgDel1 元件分布在染色体上，除了核糖体 DNA 块外，还分布在分散的异染色质区域。PgDel2 的 FISH 信号强度偏向于 48 条染色体中的 24 条。独特的基因探针显示出两对具有不同位置的信号，一对位于 PgDel2 丰富染色体的端粒区域，另一对位于 PgDel2 贫乏染色体的间质区域，表明人参是同源四倍体。我们的研究结果促进了对人参基因组和伞形科相关物种进化的理解。
