A Glimpse of Panax ginseng Genome Structure Revealed from Ten BAC Clone Sequences Obtained by SMRT Sequencing Platform

Abstract

Korean ginseng (Panax ginseng) is a well-known valuable medicinal plant with excellent therapeutic effects, however its complex genome structure has not been elucidated yet. To understand its genome structure, we obtained ten ginseng bacterial artificial chromosome (BAC) clone sequences by single-molecule real-time (SMRT) sequencing platform using a pooled DNA of the BAC clones. Out of the ten BAC clones, nine were completely assembled without any gap and one remained a single gap. The total length of BAC clone sequences was 1,163,364 bp. Sophisticated sequence analysis revealed that the 89.7% of the sequences are high copy repeat regions and the remaining 10.3% are non-repeat regions. Eleven protein-coding genes were identified in the non-repeat regions. Most of the repeat regions show more than 1,000 copies and complex structure of various repetitive elements. Ty3/Gypsy family long terminal repeat retrotransposons (LTR-RTs) are predominant repeats occupying 46.9% of the 1,163-kbp sequence. We identified six novel LTR-RTs and their insertion time. Fluorescence in situ hybridization (FISH) analysis demonstrated that PgDel2 and PgDel5 elements had a subgenome-biased distribution. Collectively, our analysis reveals that ginseng genome has very complex genome structure with abundant repetitive elements and rare gene frequency.

Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng

“…Studies on ginseng have focused primarily on its pharmacological effects in humans; however, its unique physiological and developmental characteristics have rarely been explored thoroughly due to its perennial heterozygous nature [3]. The application of functional genomic approaches in ginseng has been challenging because of its unique physiological and ecological characteristics and the lack of genomic information [4,5], which could be attributed to its relatively large genome (3.2 Gbp), heterozygous allotetraploid nature (2n = 4x = 48), and significant amounts of repetitive DNA [6,7].…”

Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

“…Ginseng seeds need a dormant period for maturity that enables germination [9]. In addition, ginseng is sensitive to environmental factors such as light and soil moisture, so maintaining individual plants requires considerable effort [8].…”

Cytokinin signaling promotes root secondary growth and bud formation in Panax ginseng

“…Furthermore, CK plays an important role in controlling cambial stem cell maintenance and vascular tissue differentiation in plants [ [9] , [10] , [11] , [12] , 15 ]. However, given the complex structure and polyploid nature of its genome, the functional genomic analysis of P. ginseng has been challenging [ 6 , 7 ]. In this study, we performed a functional genomic analysis of exogenous CK-induced physiological changes in P. ginseng , and examined their genetic regulation by integrating in silico RNA-seq analysis.…”

“…Progress has recently been made in understanding the physiological properties and the primary and secondary growth of P. ginseng storage roots. However, the implementation of functional genomic approaches in P. ginseng is challenging because of its allotetraploid character (2n = 4x = 48) and its relatively large genome size (3.2 Gb) with high quantities of repetitive DNA [ 6 , 7 ]. To shed light on the mechanism of secondary growth of storage roots, the main endogenous signaling components governing the growth and developmental features of P. ginseng should be characterized.…”