Cytogenomic evaluation of regenerated Aralia elata using PLOP-FISH and flow cytometry.

Aralia elata is closely related to Panax ginseng and contains high levels of saponins and other medicinal compounds. Successful A. elata micropropagation is commercially significant; however, the genomic stability of tissue culture-derived regenerants is unclear.

Engineering homoeologs provide a fine scale for quantitative traits in polyploid.

Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement.

Disentangling Series and Its Polyploids.

Spring crocuses, the eleven species within series (Iridaceae), consist of di- and tetraploid cytotypes. Among them is a group of polyploids from southeastern Europe with yet-unclear taxonomic affiliation. Crocuses are generally characterized by complex dysploid chromosome number changes, preventing a clear correlation between these numbers and ploidy levels.

Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna.

Background: DNA tandem repeats (TRs) are often abundant and occupy discrete regions in eukaryotic genomes. These TRs often cause or generate chromosomal rearrangements, which, in turn, drive chromosome evolution and speciation. Tracing the chromosomal distribution of TRs could therefore provide insights into the chromosome dynamics and speciation among closely related taxa.

Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Dysploidy.

Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the genome and compared the chromosomal distribution of these repeats between and a closely related euploid, . Using a read clustering algorithm, we identified the major tandem repeats and visualized their chromosomal distribution by fluorescence hybridization.

Dynamic evolution of Panax species.

Background: Panax ginseng is one of the most valuable medicinal plants in Korea. However, deciphering its full genome sequence information for crop improvement has been hampered due to its complex genomic, genetic, and growth characteristics. Many efforts have been made in the past decade to overcome these limitations and understand the genome structure and the evolutionary history of P.

Genetic diversity among cultivated and wild populations revealed by high-resolution microsatellite markers.

Background: Ginseng ( Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood.

Comprehensive comparative analysis of chloroplast genomes from seven species and development of an authentication system based on species-unique single nucleotide polymorphism markers.

Background: species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven species, two ( and ) from North America and five ( , , , , and ) from Asia.

Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven whole chloroplast genomes.

In silico mining and FISH mapping of a chromosome-specific satellite DNA in Capsicum annuum L.

Background: A large proportion of eukaryote nuclear genomes is composed of repetitive DNA. Tracing the dynamics of repetitive elements in the genomes of related taxa can reveal important information about their phylogenic relationships as well as traits that have become distinct to a lineage.

Objective: Study the genomic abundance and chromosomal location of repetitive DNA in Capsicum annuum L.

Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat.

Background: The family Araliaceae contains many medicinal species including ginseng of which the whole genome sequencing analyses have been going on these days.

Objective: To characterize the chromosomal distribution of 5S and 45S rDNAs and telomeric repeat in four ginseng related species of Aralia elata (Miq.) Seem.

Rapid and Efficient FISH using Pre-Labeled Oligomer Probes.

Fluorescence in situ hybridization (FISH) is used to visualize the distribution of DNA elements within a genome. Conventional methods for FISH take 1-2 days. Here, we developed a simplified, rapid FISH technique using pre-labeled oligonucleotide probes (PLOPs) and tested the procedure using 18 PLOPs from 45S and 5S rDNA, Arabidopsis-type telomere, and newly-identified Panax ginseng-specific tandem repeats.

Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences.

The concept of U's triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B.

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study.

Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution.

Decoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences of Brassica rapa (A genome), B. oleracea (C) and B.

A refined karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs.

Background: Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes.

Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax.

Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution.

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

Ginseng (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.

Randomly detected genetically modified (GM) maize (Zea mays L.) near a transport route revealed a fragile 45S rDNA phenotype.

Monitoring of genetically modified (GM) crops has been emphasized to prevent their potential effects on the environment and human health. Monitoring of the inadvertent dispersal of transgenic maize in several fields and transport routes in Korea was carried out by qualitative multiplex PCR, and molecular analyses were conducted to identify the events of the collected GM maize. Cytogenetic investigations through fluorescence in situ hybridization (FISH) of the GM maize were performed to check for possible changes in the 45S rDNA cluster because this cluster was reported to be sensitive to replication and transcription stress.

Karyotype analysis of Panax ginseng C.A.Meyer, 1843 (Araliaceae) based on rDNA loci and DAPI band distribution.

Ginseng has long been considered a valuable plant owing to its medicinal properties; however, genomic information based on chromosome characterization and physical mapping of cytogenetic markers has been very limited. Dual-color FISH karyotype and DAPI banding analyses of Panax ginseng C. A.