Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences

Hong, Chang Pyo; Lee, S. J.; Park, J. Y.; Plaha, P.; Park, Y. S.; Lee, Y. K.; Choi, Jae-Hun; Kim, K. Y.; Lee, J. H.; Lee, J.; Jin, Hua; Choi, Su Ryun; Lim, Yong Pyo

doi:10.1007/s00438-004-1021-9

Cited by 62 publications

(48 citation statements)

References 51 publications

(51 reference statements)

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“…The size of the ginseng genome is estimated to be 3.12 Gbp per haploid chromosome equivalent (Hong et al, 2004), whereas American ginseng, which recently diverged from ginseng , has an estimated genome size of 4.91 Gbp (Obae and West, 2012). However, details of the ginseng genome structure remain unknown due to the lack of genomic sequence data.…”

Section: Introductionmentioning

confidence: 99%

“…Research on ginseng has historically focused mainly on its medicinal components and their efficacy (Shibata et al, 1966;Lee and Huemer, 1971;Coon and Ernst, 2002;Park et al, 2012a). Genetic and genomic studies, such as functional analyses of genes (Tansakul et al, 2006;Kim et al, 2008Kim et al, , 2011, marker development Jo et al, 2011;Sun et al, 2011;Kim et al, 2012), construction of DNA libraries (Hong et al, 2004;Bang et al, 2010) and transcriptome sequencing (Chen et al, 2011;Wu et al, 2012) have been initiated only recently.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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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.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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“…Chunpoong (Hong et al 2004). The selected BAC clones were cultured in 500 mL 2xYT medium for 20 hours at 38 o C and harvested by centrifugation.…”

Section: Bac Clone Selection and Dna Extractionmentioning

confidence: 99%

“…ginseng has an estimated genome size of over 3.5 Gbp for haploid genome equivalent (Hong et al 2004;Waminal et al 2012) and is regarded as an allotetraploid (2n=4x=48) . A previous study illustrated that P. ginseng genome had experienced two rounds of whole genome duplication (WGD) , and recent WGD occurring 2-3 million years ago (MYA), which made its genome much bigger than those of other diploid Panax species (Yi et al 2004;Choi et al 2013).…”

Section: Introductionmentioning

confidence: 99%

“…Despite its excellent pharmacological effects and many studies on efficacy of their medicinal components, breeding or genetic studies are still limited in this plant species. With increasing interests in the genome in recent years, various efforts have been made for marker development (Choi et al 2011;Kim et al 2012;Kim et al 2013;Jung et al 2014), DNA library construction (Bang et al 2010;Hong et al 2004) and complete assembly of 45S nuclear ribosomal DNA and chloroplast genome (Kim et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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

Jang

Kim

Lee

et al. 2017

Plant Breed. Biotech.

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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.

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Genomics-Assisted Crop Improvement

Varshney¹,

Tuberosa²

2007

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Who would have believed only two decades ago that plant scientists would have access to nearly the complete genetic code of numerous plant species, including major crop species. The idea of having ready access to whole genome sequences encompassing 140 million bases of the model plant Arabidopsis seemed like science fiction, let alone having available even larger genomes such as rice at 430 Mb or maize at 2500 Mb (the same size as the human genome). And then proceeding to identify variation beyond what was anticipated, such as the 2.6 SNPs (Single Nucleotide Polymorphisms) per kb in rice. The number of strains of various species with literally hundreds of thousands of inserts, allowing the association of sequence and trait, increased at an unanticipated rate. Who would have believed only a decade ago that we would be capable of analyzing the expression of genes across the whole genome and matching that profile with traits of interest. And now the area of metabolomics is allowing even more meaningful explanations of the genetic control of important traits.This book brings all of these advances in genomics to the forefront and prepares the plant scientists for the next decade. Important technologies are discussed such as association mapping, simulation modeling, and development of appropriate populations including the advanced backcross and introgression-lines for incorporating traits into useful genetic materials. Such approaches are facilitating the identification of traits that are not obvious simply from observing the plant phenotype, and they provide ways to extract new and useful traits from wild related species. Comparing the genomic information across broadly-related species has generated important evolutionary information. In addition, the common occurrence of duplicated segments and large gene families with partially redundant or tissue-and developmentally-specific expression will lead to information fundamental to plant performance.Methods for the identification of genes underlying traits are improving every day. The association of allelic variation in a candidate gene and a trait is leading to much greater understanding of the genetic control of traits. Numerous transcription factors and even non-coding sequences are being implicated as the basis of considerable genetic variation. Forward and reverse genetics are both found to be very useful in revealing gene-trait associations.The tremendous expansion of genomic analytical approaches along with efforts to reduce the cost, together with appropriate statistical designs and analyses, are xi xii FOREWORD making it easier and more expeditious to use the ever-increasing sequence information to identify useful genes. This body of knowledge in plant genomics and its myriad of applications are nicely reflected in this book.

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Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences

Cited by 62 publications

References 51 publications

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

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

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

Genomics-Assisted Crop Improvement

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