Morphological characterization under different ecological habitats and physical mapping of 5S and 45S rDNA in Lilium distichum with fluorescence in situ hybridization

Hwang, Yoon‐Jung; Song, Chang-Min; Younis, Adnan; Kim, Chang-Kil; Kang, Yoon-Im; Lim, Ki-Byung

doi:10.1186/s40693-015-0037-3

Cited by 6 publications

(2 citation statements)

References 32 publications

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“…The 45S rDNA repeats show complex distribution and organization patterns in plant genomes with wide variation between species ( Roa and Guerra, 2012 ). Previous studies have investigated this phenomenon by analyzing the localization patterns on chromosomes in several plant species such as Arabidopsis thaliana , Brassica rapa , Cucumis species, Lilium distichum , and Solanum chacoense ( Fukui et al., 1998 ; Hwang et al., 2015 ; Zhang et al., 2016 ). The mechanisms underlying rDNA distribution and homogenization are diverse and include transposition, unequal crossing-over, and gene conversion.…”

Section: Discussionmentioning

confidence: 99%

Chromosomal dynamics in Senna: comparative PLOP–FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations

Nguyen,

Kang,

Kim

2023

Front. Plant Sci.

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IntroductionTandem repeats (TRs) occur abundantly in plant genomes. They play essential roles that affect genome organization and evolution by inducing or generating chromosomal rearrangements such as duplications, deletions, inversions, and translocations. These impact gene expression and chromosome structure and even contribute to the emergence of new species.MethodWe investigated the effects of TRs on speciation in Senna genus by performing a comparative analysis using fluorescence in situ hybridization (FISH) with S. tora-specific TR probes. We examined the chromosomal distribution of these TRs and compared the genome sizes of seven Senna species (estimated using flow cytometry) to better understand their evolutionary relationships.ResultsTwo (StoTR03_159 and StoTR04_55) of the nine studied TRs were not detected in any of the seven Senna species, whereas the remaining seven were found in all or some species with patterns that were similar to or contrasted with those of S. tora. Of these studies species, only S. angulata showed significant genome rearrangements and dysploid karyotypes resembling those of S. tora. The genome sizes varied among these species and did not positively correlate with chromosome number. Notably, S. angulata had the fewest chromosomes (2n = 22) but a relatively large genome size.DiscussionThese findings reveal the dynamics of TRs and provide a cytogenetic depiction of chromosomal rearrangements during speciation in Senna. To further elucidate the dynamics of repeat sequences in Senna, future studies must include related species and extensive repeatomic studies, including those on transposable elements.

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Section: Discussionmentioning

confidence: 99%

Chromosomal dynamics in Senna: comparative PLOP–FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations

Nguyen,

Kang,

Kim

2023

Front. Plant Sci.

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“…In species with length of less than 3 µm and homomorphic chromosomes, such as Glycine max (Singh et al 2001) or species of the genera Coffea (Hamon et al 2009) and Eucalyptus (Ribeiro et al 2016), the localization of specific sequences by in situ techniques has also been applied to assist the accurate identification of homologous chromosomes. Ribosomal RNA genes (rD-NAs) have shown to be valuable markers in cytogenetic studies due to their repetitive nature and high conservation in base sequences (Hwang et al 2015, Scaldaferro et al 2015. In most cases, the mapping of rDNA sequences, 5S and 45S rDNA, comprises the starting point for the construction of physical maps in plant species (Kwon and Kim 2009, Hizume et al 2013, Scaldaferro et al 2015.…”

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Physical Mapping of 5S rDNA in <i>Eucalyptus dunnii</i> Maiden and <i>Zea mays</i> L. by PRINS

et al. 2019

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The in situ detection of specific DNA sequences by fluorescence in situ hybridization (FISH) is a widely used tool for physical mapping, which is important to understand genome structure and organization. For species with small chromosomes, detection of the position of marker sequences is useful to aid chromosome identification and classification. Primed in situ labeling (PRINS) comprises an alternative to FISH, but its specificity and sensitivity may be influenced by species-specific factors, as chromosome length and chromatin structure. To overcome these obstacles, we designed a reproducible PRINS protocol for physical mapping of 5S rDNA in Eucalyptus dunnii Maiden and Zea mays L. Slides containing mitotic metaphases were submitted to one cycle of PRINS using 5S rDNA primers. Clear signals for 5S rDNA were observed in metaphase chromosomes of both species. In E. dunnii, 5S rDNA was mapped on the pericentromeric region of the short arm of chromosome 5. For Z. mays, the signal was detected in the terminal region of the long arm of chromosome 2. Although chromosome structure may influence the PRINS resolution, a high signal/background ratio was obtained for both species. In Z. mays, clear 5S rDNA signals were obtained by PRINS and FISH. Nonetheless, the former was superior regarding the time required for signal detection. Therefore, PRINS has the potential to aid plant genome studies by allowing fast detection of repetitive sequences, even in species with small chromosomes. Moreover, this is the first report of specific sequence mapping in Eucalyptus by PRINS, contributing to physical mapping progress in this genus.

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FISH and GISH: molecular cytogenetic tools and their applications in ornamental plants

et al. 2015

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The innovations in chromosome engineering have improved the efficiency of interrogation breeding, and the identification and transfer of resistance genes from alien to native species. Recent advances in molecular biology and cytogenetics have brought revolutionary, conceptual developments in mitosis and meiosis research, chromosome structure and manipulation, gene expression and regulation, and gene silencing. Cytogenetic studies offer integrative tools for imaging, genetics, epigenetics, and cytological information that can be employed to enhance chromosome and molecular genomic research in plant taxa. In situ hybridization techniques, such as fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH), can identify chromosome morphologies and sequences, amount and distribution of various types of chromatin in chromosomes, and genome organization during the metaphase stage of meiosis. Over the past few decades, various new molecular cytogenetic applications have been developed. The FISH and GISH techniques present an authentic model for analyzing the individual chromosome, chromosomal segments, or the genomes of natural and artificial hybrid plants. These have become the most reliable techniques for studying allopolyploids, because most cultivated plants have been developed through hybridization or polyploidization. Moreover, introgression of the genes and chromatin from the wild types into cultivated species can also be analyzed. Since hybrid derivatives may have variable alien chromosome numbers or chromosome arms, the use of these approaches opens new avenues for accurately identifying genome differences.

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Morphological characterization under different ecological habitats and physical mapping of 5S and 45S rDNA in Lilium distichum with fluorescence in situ hybridization

Cited by 6 publications

References 32 publications

Chromosomal dynamics in Senna: comparative PLOP–FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations

Chromosomal dynamics in Senna: comparative PLOP–FISH analysis of tandem repeats and flow cytometric nuclear genome size estimations

Physical Mapping of 5S rDNA in <i>Eucalyptus dunnii</i> Maiden and <i>Zea mays</i> L. by PRINS

FISH and GISH: molecular cytogenetic tools and their applications in ornamental plants

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