Micro-Collinearity within Panax Ginseng Genome Sequences Resulted from Two Rounds of Whole Genome Duplication

Korean ginseng (Panax ginseng C.A. Meyer) has been used as medicinal plant for several centuries. Even though its medicinal effect was well studied, the genomic study of this plant species is at the initial stage. Therefore generation and analysis of genomic resources information are essential to understand genomic features of this plant species. Since ginseng genome has been considered to undergo two rounds of whole genome duplication (WGD), we investigate micro-collinearity with ginseng genomes to find an evidence for WGD as well as to understand current ginseng genome structure. Four paralogous gene-rich genome blocks were found, consisted by eight scaffolds using zig-zag extension within scaffold sequences recently duplicated, using about 3.0 Gb whole genome draft sequence and 48,821 unigenes of P. ginseng generated by whole genome shotgun sequencing. Paralogous scaffold pairs that were recently duplicated showed high sequence conservation in genic and non-genic regions. However, old duplicated paralogue scaffold sequences showed little conservation only in genic regions. Finally, a total of 110 paralogous gene pairs and its expression were identified from recently and old duplicated scaffold pairs, which were co-linear among four genomic blocks. This study provides the first insight into duplicated genome structure of ginseng and will be a valuable information for further ginseng genomics including improvement of draft sequence quality, chromosome anchoring of scaffolds, and genetic mapping. This research was supported by   “Next-Generation BioGreen21 Program for Agriculture & Technology Development (Project No. PJ01100801)” Rural Development Administration, Republic of Korea.