Genome structure and evolution of Panax ginseng C. A. Meyer

Abstract

Ginseng (Panax ginseng C. A. Meyer) has been known as a valuable medicinal herb for thousands of years in East Asia. Although medicinal components and their functions of ginseng have been widely investigated, it could be regarded as an underdeveloped crop in genetics and genomics research areas. This study was conducted to elucidate genome structure and evolution in ginseng by analyses of expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) sequences. The EST analysis based on the calculation of synonymous substitutions per synonymous site (Ks) in paralog and ortholog pairs revealed that two rounds of polyploidy events occurred in the common ancestor of ginseng and American ginseng (P. quinquefolius L.) and subsequent divergence of the two species. The sequence analysis of repeat-rich BAC clones characterized the major component of the ginseng genome, long terminal repeat retrotransposons (LTR-RTs). Ty3/Gypsy-like elements were more predominant than Ty1/Copia. High abundance of the LTR-RTs were revealed by whole genome shotgun (WGS) read mapping and fluorescence in situ hybridization (FISH) analysis. Particularly, the PgDel1 elements played major roles in expanding heterochromatic regions as well as remodeling euchromatic regions. The PgDel2 elements showed biased intensity of FISH signals on half the total chromosomes, which demonstrate the alloploidy-like nature of ginseng. Insertion time of the LTR-RTs indicated that LTR-RTs may proliferate after the recent polyploidy event in the ginseng genome. These results suggest that the ginseng genome of the present day has been expanded and evolved by two rounds of polyploidy events and accumulation of LTR-RTs.