International Journal of Molecular Sciences

Editorial

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6 pages, 206 KiB

Open AccessEditorial

Cytomolecular Organisation of the Nuclear Genome

by Robert Hasterok, Natalia Borowska-Zuchowska and Ewa Robaszkiewicz

Int. J. Mol. Sci. 2022, 23(21), 13028; https://doi.org/10.3390/ijms232113028 - 27 Oct 2022

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Abstract

Modern molecular cytogenetics allows many aspects of the nuclear genome structure, function, and evolution to be analysed within the topographic context of mitotic and meiotic chromosomes and interphase nuclei [...] Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

Research

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17 pages, 7576 KiB

Open AccessArticle

The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae)

by Gulru Yucel, Alexander Betekhtin, Evren Cabi, Metin Tuna, Robert Hasterok and Bozena Kolano

Int. J. Mol. Sci. 2022, 23(19), 11033; https://doi.org/10.3390/ijms231911033 - 20 Sep 2022

Cited by 6 | Viewed by 2164

Abstract

The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal [...] Read more.

The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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12 pages, 3779 KiB

Open AccessArticle

Unraveling the DNA Methylation in the rDNA Foci in Mutagen-Induced Brachypodium distachyon Micronuclei

by Adrianna W. Bara-Halama, Dominika Idziak-Helmcke and Jolanta Kwasniewska

Int. J. Mol. Sci. 2022, 23(12), 6797; https://doi.org/10.3390/ijms23126797 - 18 Jun 2022

Cited by 1 | Viewed by 1644

Abstract

Many years have passed since micronuclei were first observed then accepted as an indicator of the effect of mutagens. However, the possible mechanisms of their formation and elimination from the cell are still not fully understood. Various stresses, including mutagens, can alter gene [...] Read more.

Many years have passed since micronuclei were first observed then accepted as an indicator of the effect of mutagens. However, the possible mechanisms of their formation and elimination from the cell are still not fully understood. Various stresses, including mutagens, can alter gene expression through changes in DNA methylation in plants. In this study we demonstrate for the first time DNA methylation in the foci of 5S and 35S rDNA sequences in individual Brachypodium distachyon micronuclei that are induced by mutagenic treatment with maleic acid hydrazide (MH). The impact of MH on global epigenetic modifications in nuclei and micronuclei has been studied in plants before; however, no in situ analyses of DNA methylation in specific DNA sequence sites are known. To address this problem, we used sequential immunodetection of 5-methylcytosine and fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes on the non-dividing cells of B. distachyon. Such investigations into the presence or absence of DNA methylation within specific DNA sequences are extremely important in plant mutagenesis in the light of altering gene expression. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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14 pages, 2024 KiB

Open AccessArticle

Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

by Daniel Ramírez, María Esther Rodríguez, Ismael Cross, Alberto Arias-Pérez, Manuel Alejandro Merlo, Marco Anaya, Silvia Portela-Bens, Paulino Martínez, Francisca Robles, Carmelo Ruiz-Rejón and Laureana Rebordinos

Int. J. Mol. Sci. 2022, 23(10), 5353; https://doi.org/10.3390/ijms23105353 - 11 May 2022

Cited by 5 | Viewed by 1442

Abstract

The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to [...] Read more.

The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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26 pages, 21122 KiB

Open AccessArticle

Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato

by Magdalena Senderowicz, Teresa Nowak, Hanna Weiss-Schneeweiss, Laszlo Papp and Bozena Kolano

Int. J. Mol. Sci. 2022, 23(7), 3643; https://doi.org/10.3390/ijms23073643 - 26 Mar 2022

Cited by 7 | Viewed by 2211

Abstract

Although Crepis was the first model plant group in which chromosomal changes were considered to play an important role in speciation, their chromosome structure and evolution have been barely investigated using molecular cytogenetic methods. The aim of the study was to provide a [...] Read more.

Although Crepis was the first model plant group in which chromosomal changes were considered to play an important role in speciation, their chromosome structure and evolution have been barely investigated using molecular cytogenetic methods. The aim of the study was to provide a better understanding of the patterns and directions of Crepis chromosome evolution, using comparative analyses of rDNA loci number and localisation. The chromosome base number and chromosomal organisation of 5S and 35S rDNA loci were analysed in the phylogenetic background for 39 species of Crepis, which represent the evolutionary lineages of Crepis sensu stricto and Lagoseris, including Lapsana communis. The phylogenetic relationships among all the species were inferred from nrITS and newly obtained 5S rDNA NTS sequences. Despite high variations in rDNA loci chromosomal organisation, most species had a chromosome with both rDNA loci within the same (usually short) chromosomal arm. The comparative analyses revealed several independent rDNA loci number gains and loci repositioning that accompanied diversification and speciation in Crepis. Some of the changes in rDNA loci patterns were reconstructed for the same evolutionary lineages as descending dysploidy. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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10 pages, 2295 KiB

Open AccessArticle

The Sister Chromatid Division of the Heteromorphic Sex Chromosomes in Silene Species and Their Transmissibility towards the Mitosis

by Václav Bačovský, Tomáš Janíček and Roman Hobza

Int. J. Mol. Sci. 2022, 23(5), 2422; https://doi.org/10.3390/ijms23052422 - 22 Feb 2022

Cited by 1 | Viewed by 1619

Abstract

Young sex chromosomes possess unique and ongoing dynamics that allow us to understand processes that have an impact on their evolution and divergence. The genus Silene includes species with evolutionarily young sex chromosomes, and two species of section Melandrium, namely Silene latifolia [...] Read more.

Young sex chromosomes possess unique and ongoing dynamics that allow us to understand processes that have an impact on their evolution and divergence. The genus Silene includes species with evolutionarily young sex chromosomes, and two species of section Melandrium, namely Silene latifolia (24, XY) and Silene dioica (24, XY), are well-established models of sex chromosome evolution, Y chromosome degeneration, and sex determination. In both species, the X and Y chromosomes are strongly heteromorphic and differ in the genomic composition compared to the autosomes. It is generally accepted that for proper cell division, the longest chromosomal arm must not exceed half of the average length of the spindle axis at telophase. Yet, it is not clear what are the dynamics between males and females during mitosis and how the cell compensates for the presence of the large Y chromosome in one sex. Using hydroxyurea cell synchronization and 2D/3D microscopy, we determined the position of the sex chromosomes during the mitotic cell cycle and determined the upper limit for the expansion of sex chromosome non-recombining region. Using 3D specimen preparations, we found that the velocity of the large chromosomes is compensated by the distant positioning from the central interpolar axis, confirming previous mathematical modulations. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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13 pages, 1273 KiB

Open AccessArticle

Analyses of the Updated “Animal rDNA Loci Database” with an Emphasis on Its New Features

by Jana Sochorová, Francisco Gálvez, Roman Matyášek, Sònia Garcia and Aleš Kovařík

Int. J. Mol. Sci. 2021, 22(21), 11403; https://doi.org/10.3390/ijms222111403 - 22 Oct 2021

Cited by 9 | Viewed by 1963

Abstract

We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S [...] Read more.

We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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10 pages, 2157 KiB

Open AccessArticle

Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH

by Fan Yu, Jin Chai, Xueting Li, Zehuai Yu, Ruiting Yang, Xueer Ding, Qiusong Wang, Jiayun Wu, Xiping Yang and Zuhu Deng

Int. J. Mol. Sci. 2021, 22(16), 8539; https://doi.org/10.3390/ijms22168539 - 09 Aug 2021

Cited by 7 | Viewed by 2972

Abstract

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has [...] Read more.

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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16 pages, 4788 KiB

Open AccessArticle

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus

by Atiqa Sajid, El-Nasir Lalani, Bo Chen, Teruo Hashimoto, Darren K. Griffin, Archana Bhartiya, George Thompson, Ian K. Robinson and Mohammed Yusuf

Int. J. Mol. Sci. 2021, 22(11), 5987; https://doi.org/10.3390/ijms22115987 - 01 Jun 2021

Cited by 4 | Viewed by 4436

Abstract

Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) [...] Read more.

Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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18 pages, 17829 KiB

Open AccessArticle

A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps

by Natalya Kudryavtseva, Aleksey Ermolaev, Gennady Karlov, Ilya Kirov, Masayoshi Shigyo, Shusei Sato and Ludmila Khrustaleva

Int. J. Mol. Sci. 2021, 22(11), 5860; https://doi.org/10.3390/ijms22115860 - 30 May 2021

Cited by 4 | Viewed by 3364

Abstract

In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a [...] Read more.

In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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15 pages, 1854 KiB

Open AccessArticle

Epigenetic Distribution of Recombinant Plant Chromosome Fragments in a Human–Arabidopsis Hybrid Cell Line

by YengMun Liaw, Yikun Liu, CheeHow Teo, Petr Cápal, Naoki Wada, Kiichi Fukui, Jaroslav Doležel and Nobuko Ohmido

Int. J. Mol. Sci. 2021, 22(11), 5426; https://doi.org/10.3390/ijms22115426 - 21 May 2021

Cited by 1 | Viewed by 2642

Abstract

Methylation systems have been conserved during the divergence of plants and animals, although they are regulated by different pathways and enzymes. However, studies on the interactions of the epigenomes among evolutionarily distant organisms are lacking. To address this, we studied the epigenetic modification [...] Read more.

Methylation systems have been conserved during the divergence of plants and animals, although they are regulated by different pathways and enzymes. However, studies on the interactions of the epigenomes among evolutionarily distant organisms are lacking. To address this, we studied the epigenetic modification and gene expression of plant chromosome fragments (~30 Mb) in a human–Arabidopsis hybrid cell line. The whole-genome bisulfite sequencing results demonstrated that recombinant Arabidopsis DNA could retain its plant CG methylation levels even without functional plant methyltransferases, indicating that plant DNA methylation states can be maintained even in a different genomic background. The differential methylation analysis showed that the Arabidopsis DNA was undermethylated in the centromeric region and repetitive elements. Several Arabidopsis genes were still expressed, whereas the expression patterns were not related to the gene function. We concluded that the plant DNA did not maintain the original plant epigenomic landscapes and was under the control of the human genome. This study showed how two diverging genomes can coexist and provided insights into epigenetic modifications and their impact on the regulation of gene expressions between plant and animal genomes. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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12 pages, 1995 KiB

Open AccessArticle

DNA Organization along Pachytene Chromosome Axes and Its Relationship with Crossover Frequencies

by Lucía del Priore and María Inés Pigozzi

Int. J. Mol. Sci. 2021, 22(5), 2414; https://doi.org/10.3390/ijms22052414 - 27 Feb 2021

Cited by 3 | Viewed by 2500

Abstract

During meiosis, the number of crossovers vary in correlation to the length of prophase chromosome axes at the synaptonemal complex stage. It has been proposed that the regular spacing of the DNA loops, along with the close relationship of the recombination complexes and [...] Read more.

During meiosis, the number of crossovers vary in correlation to the length of prophase chromosome axes at the synaptonemal complex stage. It has been proposed that the regular spacing of the DNA loops, along with the close relationship of the recombination complexes and the meiotic axes are at the basis of this covariation. Here, we use a cytogenomic approach to investigate the relationship between the synaptonemal complex length and the DNA content in chicken oocytes during the pachytene stage of the first meiotic prophase. The synaptonemal complex to DNA ratios of specific chromosomes and chromosome segments were compared against the recombination rates obtained by MLH1 focus mapping. The present results show variations in the DNA packing ratios of macro- and microbivalents and also between regions within the same bivalent. Chromosome or chromosome regions with higher crossover rates form comparatively longer synaptonemal complexes than expected based on their DNA content. These observations are compatible with the formation of higher number of shorter DNA loops along meiotic axes in regions with higher recombination levels. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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17 pages, 1881 KiB

Open AccessArticle

Chromosome Painting in Cultivated Bananas and Their Wild Relatives (Musa spp.) Reveals Differences in Chromosome Structure

by Denisa Šimoníková, Alžběta Němečková, Jana Čížková, Allan Brown, Rony Swennen, Jaroslav Doležel and Eva Hřibová

Int. J. Mol. Sci. 2020, 21(21), 7915; https://doi.org/10.3390/ijms21217915 - 24 Oct 2020

Cited by 17 | Viewed by 3400

Abstract

Edible banana cultivars are diploid, triploid, or tetraploid hybrids, which originated by natural cross hybridization between subspecies of diploid Musa acuminata, or between M. acuminata and diploid Musa balbisiana. The participation of two other wild diploid species Musa schizocarpa and Musa [...] Read more.

Edible banana cultivars are diploid, triploid, or tetraploid hybrids, which originated by natural cross hybridization between subspecies of diploid Musa acuminata, or between M. acuminata and diploid Musa balbisiana. The participation of two other wild diploid species Musa schizocarpa and Musa textilis was also indicated by molecular studies. The fusion of gametes with structurally different chromosome sets may give rise to progenies with structural chromosome heterozygosity and reduced fertility due to aberrant chromosome pairing and unbalanced chromosome segregation. Only a few translocations have been classified on the genomic level so far, and a comprehensive molecular cytogenetic characterization of cultivars and species of the family Musaceae is still lacking. Fluorescence in situ hybridization (FISH) with chromosome-arm-specific oligo painting probes was used for comparative karyotype analysis in a set of wild Musa species and edible banana clones. The results revealed large differences in chromosome structure, discriminating individual accessions. These results permitted the identification of putative progenitors of cultivated clones and clarified the genomic constitution and evolution of aneuploid banana clones, which seem to be common among the polyploid banana accessions. New insights into the chromosome organization and structural chromosome changes will be a valuable asset in breeding programs, particularly in the selection of appropriate parents for cross hybridization. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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Review

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17 pages, 848 KiB

Open AccessReview

A Fish of Multiple Faces, Which Show Us Enigmatic and Incredible Phenomena in Nature: Biology and Cytogenetics of the Genus Carassius

by Martin Knytl, Adrian Forsythe and Lukáš Kalous

Int. J. Mol. Sci. 2022, 23(15), 8095; https://doi.org/10.3390/ijms23158095 - 22 Jul 2022

Cited by 13 | Viewed by 2499

Abstract

Sexual vs. asexual reproduction—unisexual vs. bisexual populations—diploid vs. polyploid biotypes—genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. This review places emphasis on two Carassius entities with completely different biological characteristics: one globally [...] Read more.

Sexual vs. asexual reproduction—unisexual vs. bisexual populations—diploid vs. polyploid biotypes—genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. This review places emphasis on two Carassius entities with completely different biological characteristics: one globally widespread and invasive Carassius gibelio, and the other C. carassius with a decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance the advantages of highly invasive and disadvantages of threatened species. For example, the benefits of a wide-ranged colonization can lead to the extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and the importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for the identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Furthermore, the review focuses on the consequences of the co-occurrence of native and non-native species and outlines future perspectives of Carassius research. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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17 pages, 2211 KiB

Open AccessReview

Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation

by Guanqing Liu and Tao Zhang

Int. J. Mol. Sci. 2021, 22(13), 7124; https://doi.org/10.3390/ijms22137124 - 01 Jul 2021

Cited by 12 | Viewed by 6936

Abstract

Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes [...] Read more.

Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing and large-scale synthesis, novel tools have been designed to increase the specificity of designed oligo probes and enable genome-scale oligo probe design, which has greatly improved the application of single copy oligo-FISH. Despite this, few studies have introduced the development of the oligo-FISH probe design tools and their application in FISH experiments systematically. Besides, a comprehensive comparison and evaluation is lacking for the available tools. In this review, we provide an overview of the oligo-FISH probe design process, summarize the development and application of the available tools, evaluate several state-of-art tools, and eventually provide guidance for single copy oligo-FISH probe design. Full article

(This article belongs to the Special Issue Cytomolecular Organisation of the Nuclear Genome)

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