Selected Papers from the Joint Meeting of the 23rd International Chromosome Conference (ICC) and the 24th International Colloquium in Animal Cytogenetics and Genomics (ICACG)

A special issue of DNA (ISSN 2673-8856).

Deadline for manuscript submissions: closed (15 January 2022) | Viewed by 28193

Special Issue Editor


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Guest Editor
School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
Interests: chromosomes; cytogenetics; aneuploidy; genome evolution; chromosome segregation; infertility; IVF
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Joint Meeting of the 23rd International Chromosome Conference (ICC) and the 24th International Colloquium in Animal Cytogenetics and Genomics (ICACG) will take place online from 13 to 17 July 2021 (https://www.griffin-lab.com/icc). ICC2021 and ICACG2021 will bring together researchers in cytogenetics, genetics, genomics, genome organization and related applied science in biomedical, plant and animal fields.

More specifically, the following areas will be covered:

  • Emerging technologies
  • Animal cytogenetics
  • Accessory chromosomes
  • Genome evolution
  • Chromosome dynamics in germ cells: structure, regulation and evolution
  • Complex, elusive, and functionally important elements of the genome
  • Mammalian reproduction and preimplantation testing
  • Genome instability
  • Genome function in the nucleus
  • Evolution, structure holo- and mono-centric chromosomes
  • ERVs

This Special Issue is being published in cooperation with ICC-ICACG. The papers that will be considered for publication are those that attract the most interest or that provide innovative contributions. It should be noted that submitted manuscripts should have at least 30% additional, new, and unpublished material compared to the ICC-ICACG published paper.

Prof. Dr. Darren Griffin
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. DNA is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cytogenetics
  • chromosome
  • genomics
  • FISH
  • chromosomics
  • cytogenomics
  • evolution
  • reproduction
  • cancer
  • holocentric
  • monocentric

Published Papers (8 papers)

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Editorial

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3 pages, 170 KiB  
Editorial
The Joint Meeting of the 23rd International Chromosome Conference (ICC) and the 24th International Colloquium in Animal Cytogenetics and Genomics (ICACG)
by Darren K. Griffin
DNA 2022, 2(3), 202-204; https://doi.org/10.3390/dna2030014 - 2 Sep 2022
Viewed by 1619
Abstract
As the coronavirus struck the globe, we were all affected, and cytogenetic conferences were no exception [...] Full article

Research

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13 pages, 3670 KiB  
Article
W Chromosome Evolution by Repeated Recycling in the Frog Glandirana rugosa
by Mitsuaki Ogata, Foyez Shams, Yuri Yoshimura, Tariq Ezaz and Ikuo Miura
DNA 2022, 2(3), 172-184; https://doi.org/10.3390/dna2030012 - 1 Aug 2022
Cited by 4 | Viewed by 3062
Abstract
The Y or W sex chromosome of a heteromorphic pair is usually heterochromatinised and degenerated. However, whether chromosome degeneration constantly proceeds toward an extreme end is not fully understood. Here, we present a case of intermittent evolution of W chromosomes caused by interpopulation [...] Read more.
The Y or W sex chromosome of a heteromorphic pair is usually heterochromatinised and degenerated. However, whether chromosome degeneration constantly proceeds toward an extreme end is not fully understood. Here, we present a case of intermittent evolution of W chromosomes caused by interpopulation hybridisation in the Japanese soil-frog, Glandirana rugosa. This species includes two heteromorphic sex chromosome systems, which are separated into geographic populations, namely the XY and ZW groups. In this study, to uncover the evolutionary mechanisms of the heterogeneous W chromosomes, we genetically investigated the geographic differentiation of the ZW populations along with the closely located XY populations. Analysis of mitochondrial cytochrome b sequences detected three distinct clades, named ZW1, ZW2, and ZW3. High throughput analyses of nuclear genomic DNA showed that autosomal alleles of XY populations were deeply introgressed into the ZW3 sub-group. Based on the genotypes of sex-linked single nucleotide polymorphisms, W-borne androgen receptor gene expression, and WW developmental mortality, we concluded that the X chromosomes were recycled to W chromosomes. Upon inclusion of two cases from another group, Neo-ZW, we observed that the X chromosomes were recycled independently at least four times to the new W chromosomes: a repetition of degeneration and resurrection. Full article
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18 pages, 4792 KiB  
Article
The Nature and Chromosomal Landscape of Endogenous Retroviruses (ERVs) Integrated in the Sheep Nuclear Genome
by Sarbast Ihsan Mustafa, Trude Schwarzacher and John S. Heslop-Harrison
DNA 2022, 2(1), 86-103; https://doi.org/10.3390/dna2010007 - 16 Mar 2022
Cited by 2 | Viewed by 2786
Abstract
Endogenous retroviruses (ERVs) represent genomic components of retroviral origin that are found integrated in the genomes of various species of vertebrates. These genomic elements have been widely characterized in model organisms and humans. However, composition and abundances of ERVs have not been categorized [...] Read more.
Endogenous retroviruses (ERVs) represent genomic components of retroviral origin that are found integrated in the genomes of various species of vertebrates. These genomic elements have been widely characterized in model organisms and humans. However, composition and abundances of ERVs have not been categorized fully in all domestic animals. The advent of next generation sequencing technologies, development of bioinformatics tools, availability of genomic databases, and molecular cytogenetic techniques have revolutionized the exploration of the genome structure. Here, we investigated the nature, abundance, organization and assembly of ERVs and complete genomes of Jaagsiekte sheep retrovirus (JSRV) from high-throughput sequencing (HTS) data from two Iraqi domestic sheep breeds. We used graph-based read clustering (RepeatExplorer), frequency analysis of short motifs (k-mers), alignment to reference genome assemblies and fluorescent in situ hybridization (FISH). Three classes of ERVs were identified with the total genomic proportions of 0.55% from all analyzed whole genome sequencing raw reads, while FISH to ovine metaphase chromosomes exhibited abundant centromeric to dispersed distribution of these ERVs. Furthermore, the complete genomes of JSRV of two Iraqi sheep breeds were assembled and phylogenetically clustered with the known enJSRV proviruses in sheep worldwide. Characterization of partial and complete sequences of mammalian ERVs is valuable in providing insights into the genome landscape, to help with future genome assemblies, and to identify potential sources of disease when ERVs become active. Full article
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7 pages, 1063 KiB  
Article
Karyotype Organization of the Endangered Species Yellow Cardinal (Gubernatrix cristata)
by Sandra Eloisa Bülau, Rafael Kretschmer, Ivanete de Oliveira Furo, Edivaldo Herculano Correa de Oliveira and Thales Renato Ochotorena de Freitas
DNA 2021, 1(2), 77-83; https://doi.org/10.3390/dna1020008 - 27 Oct 2021
Cited by 3 | Viewed by 3163
Abstract
Karyotypic analyses have several applications in studies of chromosome organization, evolution, and cytotaxonomy. They are also essential to genome assembly projects. Here, we present for the first time the karyotype description of the endangered species yellow cardinal, Gubernatrix cristata (Passeriformes, Thraupidae), using conventional [...] Read more.
Karyotypic analyses have several applications in studies of chromosome organization, evolution, and cytotaxonomy. They are also essential to genome assembly projects. Here, we present for the first time the karyotype description of the endangered species yellow cardinal, Gubernatrix cristata (Passeriformes, Thraupidae), using conventional staining with Giemsa and 18S rDNA probes. This species has 78 chromosomes, with 12 pairs of macrochromosomes and 27 microchromosome pairs. The 18S rDNA clusters were found in four microchromosomes. Our results revealed that G. cristata has a typical avian karyotype (approximately 80 chromosomes). However, G. cristata has an apomorphic state in relation to the 18S rDNA distribution since the ancestral condition corresponds to only two microchromosomes with these sequences. Probably, duplications and translocations were responsible for increasing the number of 18S rDNA clusters in G. cristata. The results were compared and discussed with respect to other Thraupidae and Passeriformes members. Considering the globally threatened status of G. cristata, we believe that its karyotype description could be a starting point for future cytogenetics and sequencing projects. Full article
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9 pages, 540 KiB  
Article
Incidence, Reproductive Outcome, and Economic Impact of Reciprocal Translocations in the Domestic Pig
by Nicole M. Lewis, Claudia C. Rathje, Carla Canedo-Ribeiro, Lisa M. Bosman, Lucas G. Kiazim, Rebecca L. Jennings, Rebecca E. O’Connor, Giuseppe Silvestri and Darren K. Griffin
DNA 2021, 1(2), 68-76; https://doi.org/10.3390/dna1020007 - 9 Oct 2021
Cited by 2 | Viewed by 3256
Abstract
Pigs (Sus scrofa) have vast economic importance, with pork accounting for over 30% of the global meat consumption. Chromosomal abnormalities, and in particular reciprocal translocations (RTs), are an important cause of hypoprolificacy (litter size reduction) in pigs. However, these do not [...] Read more.
Pigs (Sus scrofa) have vast economic importance, with pork accounting for over 30% of the global meat consumption. Chromosomal abnormalities, and in particular reciprocal translocations (RTs), are an important cause of hypoprolificacy (litter size reduction) in pigs. However, these do not necessarily present with a recognizable phenotype and may cause significant economic losses for breeders when undetected. Here, we present a reappraisal of the incidence of RTs across several European pig herds, using contemporary methodology, as well as an analysis modelling the economic impact of these abnormalities. Molecular cytogenetic investigation was completed by karyotyping and/or multiprobe FISH (fluorescence in situ hybridisation) between 2016–2021, testing 2673 animals. We identified 19 types of chromosome abnormalities, the prevalence of these errors in the database was 9.1%, and the estimated incidence of de novo errors was 0.90%. Financial modelling across different scenarios revealed the potential economic impact of an undetected RT, ranging from £69,802 for an individual affected terminal boar in a commercial farm selling weaned pigs, to £51,215,378 for a genetics company with an undetected RT in a dam line boar used in a nucleus farm. Moreover, the added benefits of screening by FISH instead of karyotyping were estimated, providing a strong case for proactive screening by this approach. Full article
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Review

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14 pages, 4283 KiB  
Review
3D Ultrastructural Imaging of Chromosomes Using Serial Block-Face Scanning Electron Microscopy (SBFSEM)
by Mohammed Yusuf, Atiqa Sajid, Ian K. Robinson and El-Nasir Lalani
DNA 2022, 2(1), 30-43; https://doi.org/10.3390/dna2010003 - 5 Feb 2022
Cited by 4 | Viewed by 3738
Abstract
To date, our understanding of how DNA is packaged in the cell nucleus, condensed from chromatin into chromosomes, and organized throughout the cell cycle remains sparse. Three dimensional (3D) ultrastructural imaging is an important tool for unravelling the organizational structure of chromosomes. For [...] Read more.
To date, our understanding of how DNA is packaged in the cell nucleus, condensed from chromatin into chromosomes, and organized throughout the cell cycle remains sparse. Three dimensional (3D) ultrastructural imaging is an important tool for unravelling the organizational structure of chromosomes. For large volume 3D imaging of biological samples, serial block-face scanning electron microscopy (SBFSEM) has been applied, whereby ultrastructural information is achieved by analyzing 3D reconstructions acquired from measured data sets. In this review, we summarize the contribution of SBFSEM for obtaining 3D images of chromosomes to investigate their ultrastructure and organization in the cell and its nucleus. Furthermore, this review highlights the potential of SBFSEM for advancing 3D chromosome research. Full article
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Other

8 pages, 1383 KiB  
Brief Report
Direct Chromosome Preparation Method in Avian Embryos for Cytogenetic Studies: Quick, Easy and Cheap
by Suziane Alves Barcellos, Marcelo Santos de Souza, Victoria Tura, Larissa Rodrigues Pereira, Rafael Kretschmer, Ricardo José Gunski and Analía Del Valle Garnero
DNA 2022, 2(1), 22-29; https://doi.org/10.3390/dna2010002 - 26 Jan 2022
Cited by 4 | Viewed by 5566
Abstract
Avian cell culture is widely applied for cytogenetic studies, the improvement of which increasingly allows for the production of high-quality chromosomes, essential to perform both classical and molecular cytogenetic studies. Among these approaches, there are two main types: fibroblast and bone marrow culture. [...] Read more.
Avian cell culture is widely applied for cytogenetic studies, the improvement of which increasingly allows for the production of high-quality chromosomes, essential to perform both classical and molecular cytogenetic studies. Among these approaches, there are two main types: fibroblast and bone marrow culture. Despite its high cost and complexity, fibroblast culture is considered the superior approach due to the quality of the metaphases produced. Short-term bone marrow cultivation provides more condensed chromosomes but nonetheless is quicker and easier. In the search for a quicker, cheaper way to prepare metaphases without losing quality, the present work developed a novel, widely applicable protocol for avian chromosome preparation. Twenty-one bird embryos from distinct families were sampled: Icteridae, Columbidae, Furnariidae, Estrildidae, Thraupidae, Troglodytidae and Ardeidae. The protocol was based on a combination of modified fibroblast culture and bone marrow cultivation, taking the advantages of both. The results show that all species consistently presented good mitotic indexes and high-quality chromosomes. Overall, the application of this protocol for bird cytogenetics can optimize the time, considering that most fibroblast cultures take at least 3 days and often much longer. However, our protocol can be performed in 3 h with a much-reduced cost of reagents and equipment. Full article
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7 pages, 1933 KiB  
Commentary
Classification Problems of Repetitive DNA Sequences
by Eva Šatović-Vukšić and Miroslav Plohl
DNA 2021, 1(2), 84-90; https://doi.org/10.3390/dna1020009 - 2 Nov 2021
Cited by 3 | Viewed by 3516
Abstract
Repetitive DNA sequences, satellite DNAs (satDNAs) and transposable elements (TEs) are essential components of the genome landscape, with many different roles in genome function and evolution. Despite significant advances in sequencing technologies and bioinformatics tools, detection and classification of repetitive sequences can still [...] Read more.
Repetitive DNA sequences, satellite DNAs (satDNAs) and transposable elements (TEs) are essential components of the genome landscape, with many different roles in genome function and evolution. Despite significant advances in sequencing technologies and bioinformatics tools, detection and classification of repetitive sequences can still be an obstacle to the analysis of genomic repeats. Here, we summarize how specificities in repetitive DNA organizational patterns can lead to an inability to classify (and study) a significant fraction of bivalve mollusk repetitive sequences. We suggest that the main reasons for this inability are: the predominant association of satDNA arrays with Helitron/Helentron TEs; the existence of many complex loci; and the unusual, highly scattered organization of short satDNA arrays or single monomers across the whole genome. The specificities of bivalve genomes confirm the need for introducing diverse organisms as models in order to understand all aspects of repetitive DNA biology. It is expected that further development of sequencing techniques and synergy among different bioinformatics tools and databases will enable quick and unambiguous characterization and classification of repetitive DNA sequences in assembled genomes. Full article
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