Genome sequencing has been going on major medicinal plants, including Platycodon grandiflorus, which is commonly used as a functional food and medicinal resource in Korea. Molecular cytogenetic studies using fluorescence in situ hybridization (FISH) show the chromosomal organization of specific DNA sequences. We analyzed the FISH karyotypes of P. grandiflorus ‘Jangbaek’ and a colchicine-induced tetraploid cultivar ‘Etteumbaek’ using 5S and 45S rDNA probes. As a result, ‘Jangbaek’ had chromosome length ranging from 2.34 ± 0.13 to 3.99 ± 0.197 μm with its karyotypic formula of 2n = 2x = 18 = 16m + 2sm (two satellites) whereas ‘Etteumbaek’ had chromosome length of 2.37 ± 0.08 to 4.20 ± 0.16 μm and a karyotypic formula of 2n = 4x = 36 = 24m + 12sm (four satellites). A pair of 5S rDNA signals observed interstitially in chromosome 3 and the co-localization of 5S and 45S rDNA signals occupying the nucleolar-organizing region (NOR) of chromosome 6 was observed in the diploid cultivar ‘Jangbaek’. Doubling of both signals co-localized in the NOR of chromosome 6 were observed in the colchicine induced tetraploid cultivar. However, the tetraploid revealed a modified positioning of 5S rDNA signals on chromosome 3 interstitially, with observable vague dispersed signals in one chromosome of chromosomes 1 and 5. This result will be useful for further breeding program and chromosomal backbone for the Platycodon genome analysis.

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• Cytogenomic evaluation of regenerated Aralia elata using PLOP-FISH and flow cytometry
  Eliazar Alumbro Peniton, Hong Thi Nguyen, Nomar Espinosa Waminal, Tae-Jin Yang, Hyun Hee Kim
  Scientific Reports.2024;[Epub]     CrossRef
• Cell cycle synchronization in Panax ginseng roots for cytogenomics research
  Eliazar Alumbro Peniton, Nomar Espinosa Waminal, Tae-Jin Yang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2022; 63(1): 137.     CrossRef

Perilla species (Lamiaceae) have been used as a resource for oilseeds and vegetables, and medicinal purposes. Cytogenetic studies based on chromosomal composition are essential to understand the basic genome structure of a species and to provide vital information for crop improvements. However, only a few studies have assessed the cytogenetic aspects of Perilla species. Fluorescence in situ hybridization (FISH) karyotypes using 5S and 45S rDNA probes were analyzed for the wild and cultivated species of Perilla: P. citriodora and P. frutescens. Chromosome complements were diploid in P. citriodora and allotetraploid in P. frutescens. The chromosome length ranged from 3.07 to 4.92 μm and 2.41 to 5.73 μm in the diploid and allotetraploid variants, respectively. The karyotypic formula was 2n = 12m + 8sm (2 satellites) for P. citriodora and 2n = 20m + 20sm (2 satellites) for P. frutescens. A pair of 5S signals was detected in the telomeric region of chromosome pair 7, while a pair of 45S rDNA signals was detected in the telomeric region extending through the satellite region of chromosome 2 of P. citriodora. However, two pairs of 5S signals were detected from the interstitial to the telomeric regions of chromosome 7 and 17, and a pair of 45S rDNA signals was located on the satellite region of chromosome 20 of P. frutescens. This result will provide useful information to develop a breeding program and to construct the chromosomal backbone for the ongoing genome sequence assembly project.

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• Cytogenomic profiling of Panax ginseng cultivars and in vitro root cultures through multi-color PLOP-FISH and flow cytometry reveals somaclonal variations
  Eliazar A. Peniton Jr., Hong T. Nguyen, Nomar E. Waminal, Tae-Jin Yang, Hyun Hee Kim
  Journal of Ginseng Research.2026; 50(4): 101058.     CrossRef
• Cytogenomic evaluation of regenerated Aralia elata using PLOP-FISH and flow cytometry
  Eliazar Alumbro Peniton, Hong Thi Nguyen, Nomar Espinosa Waminal, Tae-Jin Yang, Hyun Hee Kim
  Scientific Reports.2024;[Epub]     CrossRef
• Comparative triple-color FISH mapping and genome size advances understanding of the cytogenetic diversity in wild Solanum species
  Hong Thi Nguyen, Soon Ju Park, Byung Yong Kang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2023; 64(5): 811.     CrossRef
• Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna
  Thanh Dat Ta, Nomar Espinosa Waminal, Thi Hong Nguyen, Remnyl Joyce Pellerin, Hyun Hee Kim
  Genes & Genomics.2021; 43(3): 237.     CrossRef
• Comparative triple-color FISH mapping in eleven Senna species using rDNA and telomeric repeat probes
  Thi Hong Nguyen, Nomar Espinosa Waminal, Do Sin Lee, Remnyl Joyce Pellerin, Thanh Dat Ta, Nicole Bon Campomayor, Byung Yong Kang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2021; 62(6): 927.     CrossRef
• FISH Karyotype Comparison ofPlatycodon grandiflorus(Jacq.) A. DC. ‘Jangbaek’ and Its Colchicine-Induced Tetraploid ‘Etteumbaek
  Eliazar Alumbro Peniton Jr., Yurry Um, Hyun Hee Kim
  Plant Breeding and Biotechnology.2020; 8(4): 389.     CrossRef

×Brassicoraphanus (AARR, 2n = 38) is a synthetic intergeneric allopolyploid between Brassica rapa L. ssp. pekinensis (AA, 2n = 20) and Raphanus sativus L. var. rafiphera (RR, 2n = 18). Abnormalities in meiosis are main causes for infertility, especially in recent intergeneric allopolyploids. Several ×Brassicoraphanus lines showing varied fertility rates were produced previously, but no cytogenetic data specifying the reasons for infertility have been reported. In this study, we performed cytogenetic analyses in BB4, BB6, BB12, and BB50 lines to evaluate their chromosomal composition and behavior during meiosis. The four lines had relatively small chromosomes, ranging in length from 1.82 to 5.72 μm. BB6, BB12, and BB50 have euploid chromosome number of 2n = 38, whereas BB4 is an aneuploid with 2n − 1 = 37. Fluorescent in situ hybridization karyotype analysis by using 5S/45S rDNA revealed 5/7, 6/7, 5/5 and 5/5 pairs in BB4, BB6, BB12 and BB50, respectively. Genomic in situ hybridization analysis on cells in prophase I revealed varying frequencies of tetravalent pairing and sticky, ring, rod, and laggard chromosomes across the lines, which were more abundant in BB4 and BB6. Unlike BB4 and BB6, both BB12 and BB50 are known to have relatively higher seed fertility and uniform plant morphology. The varied degrees of chromosomal pairing stability during meiosis could explain the different fertility rates among the four ×Brassicoraphanus lines in this study. These data might facilitate breeding programs of ×Brassicoraphanus and further cytogenomic analyses.

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• Exploration of incompatible crosses in plants for novel and useful variations
  Visarada Kurella B.R.S., Jinu Jacob, Kanti Meena, Deepika Cheruku, Sujatha Mulpuri
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• Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites
  Nicole Bon Campomayor, Nomar Espinosa Waminal, Byung Yong Kang, Thi Hong Nguyen, Soo-Seong Lee, Jin Hoe Huh, Hyun Hee Kim
  Cells.2021; 10(9): 2358.     CrossRef

Repetitive DNA elements are ubiquitous in plant genomes. Although repeats provide relevant information for cytogenetic, evolutionary, and genomic studies, identifying and characterizing their sequence and chromosomal distribution are not always easily achieved through conventional methods. However, a high-throughput identification of genomic repeats can be obtained with short reads from next-generation sequencing data. Here, we identified the telomeric and two chromosome-specific repeats in Panax ginseng using low-coverage whole genome sequence data. The telomeric repeat sequence is same with the canonical angiosperm sequence, (TTTAGGG)_n, and localized mostly in every chromosome termini, except for an additional interstitial location in chromosome 10. A dinucleotide (GA) microsatellite, PgGA15, with total genome representation (GR) of more than 33 kb localized in the long arm of chromosome 20. An 11-bp minisatellite, Pgms1, with more than 58 kb of GR localized in the long arm of chromosome 1. This study provides chromosome-specific markers for cytogenetic studies in P. ginseng.

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• Beyond genome: Advanced omics progress of Panax ginseng
  Wenjing Yu, Siyuan Cai, Jiali Zhao, Shuhan Hu, Chen Zang, Jiang Xu, Lianghai Hu
  Plant Science.2024; 341: 112022.     CrossRef
• Identification and functional analysis of COLD-signaling-related genes in Panax ginseng
  Jeongeui Hong, Hojin Ryu
  Journal of Plant Biotechnology.2023;[Epub]     CrossRef
• Cell cycle synchronization in Panax ginseng roots for cytogenomics research
  Eliazar Alumbro Peniton, Nomar Espinosa Waminal, Tae-Jin Yang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2022; 63(1): 137.     CrossRef
• Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng
  Chang Pyo Hong, Jinsoo Kim, Jinsu Lee, Seung-il Yoo, Wonsil Bae, Kyoung Rok Geem, Jin Yu, Inbae Jang, Ick Hyun Jo, Hyunwoo Cho, Donghwan Shim, Hojin Ryu
  International Journal of Molecular Sciences.2021; 22(16): 8694.     CrossRef
• Functional characterization of gibberellin signaling-related genes in Panax ginseng
  Jinsoo Kim, Woo-Ri Shin, Yang-Hoon Kim, Donghwan Shim, Hojin Ryu
  Journal of Plant Biotechnology.2021; 48(3): 148.     CrossRef
• Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review
  Alexis J. Maravilla, Marcela Rosato, Josep A. Rosselló
  Plants.2021; 10(11): 2541.     CrossRef
• FISH Karyotype Comparison ofPlatycodon grandiflorus(Jacq.) A. DC. ‘Jangbaek’ and Its Colchicine-Induced Tetraploid ‘Etteumbaek
  Eliazar Alumbro Peniton Jr., Yurry Um, Hyun Hee Kim
  Plant Breeding and Biotechnology.2020; 8(4): 389.     CrossRef
• Five-color fluorescence in situ hybridization system for karyotyping of Panax ginseng
  Nomar Espinosa Waminal, Tae-Jin Yang, Jun-Gyo In, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2020; 61(5): 869.     CrossRef
• FISH Karyotype Comparison between Wild and CultivatedPerillaSpecies Using 5S and 45S rDNA Probes
  Eliazar Alumbro Peniton, Nomar Espinosa Waminal, Tae-Ho Kim, Hyun Hee Kim
  Plant Breeding and Biotechnology.2019; 7(3): 237.     CrossRef
• Rapid and Efficient FISH using Pre-Labeled Oligomer Probes
  Nomar Espinosa Waminal, Remnyl Joyce Pellerin, Nam-Soo Kim, Murukarthick Jayakodi, Jee Young Park, Tae-Jin Yang, Hyun Hee Kim
  Scientific Reports.2018;[Epub]     CrossRef
• Identification of ABSCISIC ACID (ABA) signaling related genes in Panax ginseng
  Jeongeui Hong, Hogyum Kim, Hojin Ryu
  Journal of Plant Biotechnology.2018; 45(4): 306.     CrossRef

The genus Senna in the family Fabaceae is distributed and cultivated around the world and has been used as sources of medicine and commercial goods. Molecular cytogenetic study based on FISH technique is useful for breeding and genomic research of the species. Triple-color FISH karyotype analyses were carried out to understand the genome structure of two Senna species, S. covesii (A. Gray) H. S. Irwin & Barneby and S. floribunda (Cav.) H. S. Irwin & Barneby using 5S rDNA, 45S rDNA, and telomeric repeat probes. Three and one pairs of 45S and 5S rDNA signals were detected, respectively, in S. covesii, whereas one pair each of 45S and 5S rDNA signals, were detected in S. floribunda. Telomeric signals appeared at all chromosome termini in both species. This result provides basic cytogenetic information which will be useful for future breeding and genomic research of Senna species.

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• Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna
  Thanh Dat Ta, Nomar Espinosa Waminal, Thi Hong Nguyen, Remnyl Joyce Pellerin, Hyun Hee Kim
  Genes & Genomics.2021; 43(3): 237.     CrossRef
• Comparative triple-color FISH mapping in eleven Senna species using rDNA and telomeric repeat probes
  Thi Hong Nguyen, Nomar Espinosa Waminal, Do Sin Lee, Remnyl Joyce Pellerin, Thanh Dat Ta, Nicole Bon Campomayor, Byung Yong Kang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2021; 62(6): 927.     CrossRef
• Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae
  Alexis J. Maravilla, Marcela Rosato, Inés Álvarez, Gonzalo Nieto Feliner, Josep A. Rosselló
  Plants.2021; 10(12): 2794.     CrossRef
• Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review
  Alexis J. Maravilla, Marcela Rosato, Josep A. Rosselló
  Plants.2021; 10(11): 2541.     CrossRef
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  Windy Mose, Theopilus Wilhelmus , Rita Lusian Kar
  Asian Journal of Plant Sciences.2020; 19(3): 313.     CrossRef
• Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat
  Hui Chao Zhou, Remnyl Joyce Pellerin, Nomar Espinosa Waminal, Tae-Jin Yang, Hyun Hee Kim
  Genes & Genomics.2019; 41(7): 839.     CrossRef

The genus Brassica is an important resource for major agricultural products such as oils, vegetable and fodder. The Brassiceae tribe-specific whole-genome triplication that occurred ~15.9 million years ago influenced the speciation and morphological diversification that has been exploited in agriculture, making Brassica an excellent model system for studying polyploidization-mediated evolution. Genome sequencing and comparative genome analysis have revealed conserved structures and uncovered the genome evolution of Brassica species. While chromosome shuffling and asymmetric subgenome gene retention are widely reported in Brassica species, limited information is available about the dynamics of repetitive elements (REs), which are central to epigenetic mechanisms and thus play a pivotal role in plant genome adaptation and evolution. The assembled reference genome sequences of B. rapa (AA) and B. oleracea (CC), and their derived allotetraploid, B. napus (AACC), cover 58%, 86%, and 75% of their respective estimated genome sizes. The remaining non-assembled genome portions vary between these three genome sequences, and the major components remain hidden in each genome. Here, we review the dynamics of the major Brassica repeats that have played roles in speciation of the AA, CC, and AACC genomes. We show that 10 major Brassica repeats appear to occupy more than 50% of each respective unassembled genome sequence, yet represent less than 1% of assembled reference genome sequences. We have estimated their genome proportions using whole-genome Illumina reads and cytogenetic analyses in an attempt to understand the role of these repeats in genome evolution.

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