Sequence Characterization of 382-kb Sequences Revealed Major Repeat Components and Structure of Ginseng (Panax ginseng C. A. Meyer) Genome

Ginseng is a highly valuable medicinal plant having a large genome, which is estimated more than 3-Gb on a haploid chromosomes equivalent. The two factors, polyploidy and repetitive DNAs, have long been generally accepted as major force of genome size variation and evolution. In this study, we report the in-depth analysis of 382-kb sequences regarding three bacterial artificial chromosome (BAC) clones to find major repeat constituents and catch a glimpse of genome structure in ginseng. Total 10.7 Mb of sequences were generated by using Sanger and 454 technologies, and then assembled into 4 contigs of 381,613 bp in length. Sequence annotation revealed that more than 90 % of the BAC clones consisted of repetitive elements with complex insertion patterns, and long terminal repeat (LTR) retrotransposons were the major repeat components. The clades of PgDel, PgTat, and PgAthila belonging to the Ty3/Gypsy family and PgTork and PgOryco belonging to the Ty1/Copia were identified by similarity search against GyDB 2.0. Mapping of thirty-Gb whole genome shotgun reads to the BAC sequences showed that more than 30% of the genome has been occupied by the repetitive elements characterized on the BAC sequences, and the copy numbers of LTR retrotransposons were estimated more than 50,000. Estimation showed some differences between the copy numbers and genome proportion in the clade level of LTR retrotransposons, which may indicate differential proliferation and loss of the elements. This study was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ008202), Rural Development Administration, Republic of Korea.