Major repeat components covering one‐third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy

Abstract

SUMMARYGinseng (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.

Self-microemulsifying Drug Delivery System Improved Oral Bioavailability of 20(<i>S</i>)-Protopanaxadiol: From Preparation to Evaluation

“…The dissolution flasks were immersed in a water bath at 37°C, filled with 900 mL of 1 M HCl, distilled water or phosphate-buffered saline (pH 6.8). At different time intervals (1,3,5,10,20,30,45, 60 min), 1 mL of dissolution media were withdrawn and filtered using 0.45 µm polyether sulfone membrane filters. One milliliter of fresh media was supplemented into the corresponding flasks.…”

“…1) is one of aglycones of ginsenosides and has a wide range of pharmacological activities, especially in antitumor and neurological function recovery. [4][5][6][7][8] However, the low bioavailability of ginsenosides (1% for Rb 1 , 3.4% for Rb 2 , 1.9% for Rg 1 ) after oral administration restricts their clinical applications. [9][10][11] Importantly, PPD is the final active component after the absorption of ginsenosides in intestine.…”

Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in Panax ginseng

“…Numerous studies have shown the indispensable roles of repeats in a genome which include genotypic and phenotypic variations, heterochromatin formation and environmental adaptation (Kalendar et al 2000;Lippman et al 2004;Wei et al 2014). Because repeat amplification or elimination could happen before or after species divergence, repeats can be an excellent tool in studying evolution of genomes (Choi et al 2014;Mehrotra and Goyal 2014;Wei et al 2014). Although different repeats follow different evolutionary pathways, tandem repeats have been evolutionarily associated with other repetitive DNA like transposable elements and the intergenic spacers (IGSs) of the 45S rDNA genes in several plant species (Cheng and Murata 2003;Macas et al 2003).…”

“…Panax ginseng (Korean ginseng or Asian ginseng) is an important allotetraploid (2n = 4x = 48) perennial crop (Choi et al 2014;Jang et al 2017), highly priced for its ginsenoside, which is known to have a wide range of therapeutic effects (Court 2000;Park et al 2012). In addition, its sensitivity to light, slow growth (∼four years/generation) and low seed yield (∼40 seeds/plant) have contributed to its high price and a multi-billion USD market (Baeg and So 2013).…”

“…Tandem repeats are also excellent cytogenetic markers because they are often distributed in unique chromosomal regions, allowing easy discrimination of chromosomes (Mendes et al 2011;Choi et al 2014).…”