Coix lacryma-jobi L. is a cereal crop belonging to the Poaceae family, valued for its nutritional, medicinal, and ornamental uses. Among its varieties, two prominent landraces, C. lacryma-jobi var. kiboa and var. tapol, are cultivated for their distinct grain morphologies and favorable agronomic traits. However, despite its economic importance, detailed cytogenetic and molecular phylogenetic studies remain limited. This study presents a cytogenetic and molecular phylogenetic analysis of C. lacryma-jobi L. var. kiboa and tapol. Partial cytogenomic characterization on the 45S and 5S rDNA loci as well as Arabidopsis- type telomeric repeats using pre-labeled oligomer probes for fluorescence in situ hybridization (PLOP-FISH) technique confirmed a diploid chromosome number of 2n = 20 in both varieties. The 45S and 5S rDNA loci were localized on the nucleolar organizer region (NOR) of the short arm of chromosome 1 and the long arm of chromosome 4, respectively, indicating conserved chromosomal arrangements. Additionally, Arabidopsis-type telomeric repeats were detected at the terminal regions of all chromosomes. Chromosome sizes ranged from 2.98 ± 0.07 to 3.74 ± 0.11 μm in var. kiboa and from 3.42 ± 0.08 to 4.12 ± 0.05 μm in var. tapol. Phylogenetic analyses based on the internal transcribed spacer (ITS1 and ITS4) genes revealed a close genetic relationship between the two varieties, supporting their shared evolutionary lineage. These findings enhanced our understanding of adlay genetic diversity and provide foundational insights for plant breeding improvement, conservation strategies, and future genomic research.

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
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  Journal of Ginseng Research.2026; 50(4): 101058.     CrossRef
• Cytogenomic evaluation of regenerated Aralia elata using PLOP-FISH and flow cytometry
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  Scientific Reports.2024;[Epub]     CrossRef
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  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

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
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  Journal of Plant Biotechnology.2023;[Epub]     CrossRef
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  Horticulture, Environment, and Biotechnology.2022; 63(1): 137.     CrossRef
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  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
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• 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
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• Cytogenetic Analysis of Seven Local Corn Cultivars from Kisar Island-southwest Maluku, Indonesia
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  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
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  Genes & Genomics.2019; 41(7): 839.     CrossRef