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Commemorating the Launch of the Section "Cytogenomics"

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Cytogenomics".

Deadline for manuscript submissions: 5 June 2024 | Viewed by 16254

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Prof. Dr. Darren Griffin

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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,

A new section of Genes (ISSN 2073-4425, IF 4.096), “Cytogenomics”, was launched in May 2021. This section aims to provide an international peer-reviewed medium for the dissemination and active discussion of the latest and most important advances in the field of genomics from a chromosomal perspective. We welcome the submission of high-quality research on various aspects of comparative genomics, nuclear organization, genome evolution and molecular cytogenetics.

We have also established a new Special Issue to commemorate the launch of the section “Cytogenomics”. The main focus of this Special Issue is review articles on “Chromosomics” where the status of chromosomal level genome assemblies and chromosome evolution is considered. High-quality research articles on any topic around this general area are welcomed.

It is our pleasure to invite you to submit your exceptional manuscripts for publication in this Special Issue.

Prof. Dr. Darren Griffin
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Genes is an international peer-reviewed open access monthly 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 2600 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

genome assembly
chromosome evolution
zoo-FISH
comparative genomics
chromosome painting

Published Papers (11 papers)

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Research

17 pages, 4455 KiB

Open AccessArticle

Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos

by Alona Yurchenko, Tomáš Pšenička, Pablo Mora, Juan Alberto Marchal Ortega, Antonio Sánchez Baca and Michail Rovatsos

Genes 2024, 15(4), 429; https://doi.org/10.3390/genes15040429 - 28 Mar 2024

Viewed by 649

Abstract

Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel’s leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther’s flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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13 pages, 2504 KiB

Open AccessArticle

Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors

by Vivek Gupta, Vishakha Vashisht, Ashutosh Vashisht, Ashis K. Mondal, Ahmet Alptekin, Harmanpreet Singh and Ravindra Kolhe

Genes 2024, 15(4), 396; https://doi.org/10.3390/genes15040396 - 23 Mar 2024

Viewed by 732

Abstract

Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina’s TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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19 pages, 10173 KiB

Open AccessArticle

Heterochromatin Is Not the Only Place for satDNAs: The High Diversity of satDNAs in the Euchromatin of the Beetle Chrysolina americana (Coleoptera, Chrysomelidae)

by José M. Rico-Porras, Pablo Mora, Teresa Palomeque, Eugenia E. Montiel, Diogo C. Cabral-de-Mello and Pedro Lorite

Genes 2024, 15(4), 395; https://doi.org/10.3390/genes15040395 - 22 Mar 2024

Viewed by 613

Abstract

The satellitome of the beetle Chrysolina americana Linneo, 1758 has been characterized through chromosomal analysis, genomic sequencing, and bioinformatics tools. C-banding reveals the presence of constitutive heterochromatin blocks enriched in A+T content, primarily located in pericentromeric regions. Furthermore, a comprehensive satellitome analysis unveils the extensive diversity of satellite DNA families within the genome of C. americana. Using fluorescence in situ hybridization techniques and the innovative CHRISMAPP approach, we precisely map the localization of satDNA families on assembled chromosomes, providing insights into their organization and distribution patterns. Among the 165 identified satDNA families, only three of them exhibit a remarkable amplification and accumulation, forming large blocks predominantly in pericentromeric regions. In contrast, the remaining, less abundant satDNA families are dispersed throughout euchromatic regions, challenging the traditional association of satDNA with heterochromatin. Overall, our findings underscore the complexity of repetitive DNA elements in the genome of C. americana and emphasize the need for further exploration to elucidate their functional significance and evolutionary implications. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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11 pages, 897 KiB

Open AccessArticle

Mapping of a Stripe Rust Resistance Gene Yr72 in the Common Wheat Landraces AUS27506 and AUS27894 from the Watkins Collection

by Mumta Chhetri, Hanif Miah, Debbie Wong, Matthew Hayden, Urmil Bansal and Harbans Bariana

Genes 2023, 14(11), 1993; https://doi.org/10.3390/genes14111993 - 25 Oct 2023

Viewed by 2018

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the major threats to global wheat production. The common wheat landraces AUS27506 and AUS27894 displayed stripe rust resistance against several commercially prevailing Pst pathotypes. These genotypes were crossed with a stripe-rust-susceptible landrace AUS27229 to understand the inheritance of resistance and to determine the genomic location(s) of underlying gene(s). F₃ generations of crosses AUS27506/AUS27229 and AUS27894/AUS27229 showed monogenic segregation for stripe rust resistance under greenhouse conditions. The absence of segregation for stripe rust response among the AUS27506/AUS27894-derived F₃ population suggested that both genotypes carry the same gene. The stripe rust resistance gene carried by AUS27506 and AUS27894 was tentatively named YrAW4. A bulked segregant analysis placed YrAW4 in the long arm of chromosome 2B. The AUS27506/AUS27229 F₃ population was enhanced to develop an F₆ recombinant inbred line (RIL) population for detailed mapping of chromosome 2BL. DArT-based SSR, STS and SNP markers were employed to enrich the 2BL map. DArT-based STS markers sun481 and SNP marker IWB12294 flanked YrAW4 proximally (1.8 cM) and distally (1.2 cM), respectively. Deletion mapping placed sun481 in the deletion bin 2BL-5. All stripe rust resistance genes, previously located on chromosome 2BL, neither express an infection type like YrAW4, nor are they mapped in the deletion bin 2BL-5. Hence, YrAW4 represented a new locus and was formally named Yr72. The usefulness of the markers IWB12294 and sun481 in marker-assisted selection was demonstrated by the amplification of alleles that are different to that linked with Yr72 in 19 common wheat and two durum wheat cultivars. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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14 pages, 4526 KiB

Open AccessArticle

Optical Genome Mapping: Integrating Structural Variations for Precise Homologous Recombination Deficiency Score Calculation

by Nikhil Shri Sahajpal, Ashis K. Mondal, Ashutosh Vashisht, Harmanpreet Singh, Andy Wing Chun Pang, Daniel Saul, Omar Nivin, Benjamin Hilton, Barbara R. DuPont, Vamsi Kota, Natasha M. Savage, Alex R. Hastie, Alka Chaubey and Ravindra Kolhe

Genes 2023, 14(9), 1683; https://doi.org/10.3390/genes14091683 - 25 Aug 2023

Viewed by 1513

Abstract

Homologous recombination deficiency (HRD) is characterized by the inability of a cell to repair the double-stranded breaks using the homologous recombination repair (HRR) pathway. The deficiency of the HRR pathway results in defective DNA repair, leading to genomic instability and tumorigenesis. The presence of HRD has been found to make tumors sensitive to ICL-inducing platinum-based therapies and poly(adenosine diphosphate [ADP]–ribose) polymerase (PARP) inhibitors (PARPi). However, there are no standardized methods to measure and report HRD phenotypes. Herein, we compare optical genome mapping (OGM), chromosomal microarray (CMA), and a 523-gene NGS panel for HRD score calculations. This retrospective study included the analysis of 196 samples, of which 10 were gliomas, 176 were hematological malignancy samples, and 10 were controls. The 10 gliomas were evaluated with both CMA and OGM, and 30 hematological malignancy samples were evaluated with both the NGS panel and OGM. To verify the scores in a larger cohort, 135 cases were evaluated with the NGS panel and 71 cases with OGM. The HRD scores were calculated using a combination of three HRD signatures that included loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale transitions (LST). In the ten glioma cases analyzed with OGM and CMA using the same DNA (to remove any tumor percentage bias), the HRD scores (mean ± SEM) were 13.2 (±4.2) with OGM compared to 3.7 (±1.4) with CMA. In the 30 hematological malignancy cases analyzed with OGM and the 523-gene NGS panel, the HRD scores were 7.6 (±2.2) with OGM compared to 2.6 (±0.8) with the 523-gene NGS panel. OGM detected 70.8% and 66.8% of additional variants that are considered HRD signatures in gliomas and hematological malignancies, respectively. The higher sensitivity of OGM to capture HRD signature variants might enable a more accurate and precise correlation with response to PARPi and platinum-based drugs. This study reveals HRD signatures that are cryptic to current standard of care (SOC) methods used for assessing the HRD phenotype and presents OGM as an attractive alternative with higher resolution and sensitivity to accurately assess the HRD phenotype. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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15 pages, 1701 KiB

Open AccessArticle

Integrating Genomic and Chromosomal Data: A Cytogenetic Study of Transancistrus santarosensis (Loricariidae: Hypostominae) with Characterization of a ZZ/ZW Sex Chromosome System

by Mauro Nirchio Tursellino, Marcelo de Bello Cioffi, Francisco de Menezes Cavalcante Sassi, Geize Aparecida Deon, Claudio Oliveira, Mariana Kuranaka, Jonathan Valdiviezo-Rivera, Víctor Hugo Gonzalez and Anna Rita Rossi

Genes 2023, 14(9), 1662; https://doi.org/10.3390/genes14091662 - 22 Aug 2023

Viewed by 1121

Abstract

The plecos (Loricariidae) fish represent a great model for cytogenetic investigations due to their variety of karyotypes, including diploid and polyploid genomes, and different types of sex chromosomes. In this study we investigate Transancistrus santarosensis a rare loricariid endemic to Ecuador, integrating cytogenetic methods with specimens’ molecular identification by mtDNA, to describe the the species karyotype. We aim to verify whether sex chromosomes are cytologically identifiable and if they are associated with the accumulation of repetitive sequences present in other species of the family. The analysis of the karyotype (2n = 54 chromosomes) excludes recent centric fusion and pericentromeric inversion and suggests the presence of a ZZ/ZW sex chromosome system at an early stage of differentiation: the W chromosome is degenerated but is not characterized by the presence of differential sex-specific repetitive DNAs. Data indicate that although T. santarosensis has retained the ancestral diploid number of Loricariidae, it accumulated heterochromatin and shows non-syntenic ribosomal genes localization, chromosomal traits considered apomorphic in the family. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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15 pages, 1846 KiB

Open AccessArticle

Optical Genome Mapping Reveals and Characterizes Recurrent Aberrations and New Fusion Genes in Adult ALL

by Lisa-Marie Vieler, Verena Nilius-Eliliwi, Roland Schroers, Deepak Ben Vangala, Huu Phuc Nguyen and Wanda Maria Gerding

Genes 2023, 14(3), 686; https://doi.org/10.3390/genes14030686 - 09 Mar 2023

Cited by 3 | Viewed by 2076

Abstract

(1) Background: In acute lymphoblastic leukemia (ALL) the genetic characterization remains challenging. Due to the genetic heterogeneity of mutations in adult patients, only a small proportion of aberrations can be analyzed with standard routine diagnostics. Optical genome mapping (OGM) has recently opened up new possibilities for the characterization of structural variants on a genome-wide level, thus enabling simultaneous analysis for a broad spectrum of genetic aberrations. (2) Methods: 11 adult ALL patients were examined using OGM. (3) Results: Genetic results obtained by karyotyping and FISH were confirmed by OGM for all patients. Karyotype was redefined, and additional genetic information was obtained in 82% (9/11) of samples by OGM, previously not diagnosed by standard of care. Besides gross-structural chromosome rearrangements, e.g., ring chromosome 9 and putative isodicentric chromosome 8q, deletions in CDKN2A/2B were detected in 7/11 patients, defining an approx. 20 kb minimum region of overlap, including an alternative exon 1 of the CDKN2A gene. The results further confirm recurrent ALL aberrations (e.g., PAX5, ETV6, VPREB1, IKZF1). (4) Conclusions: Genome-wide OGM analysis enables a broad genetic characterization in adult ALL patients in one single workup compared to standard clinical testing, facilitating a detailed genetic diagnosis, risk-stratification, and target-directed treatment strategies. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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11 pages, 2608 KiB

Open AccessArticle

Differential Repeat Accumulation in the Bimodal Karyotype of Agave L.

by Lamonier Chaves Ramos, Mariana Báez, Joerg Fuchs, Andreas Houben, Reginaldo Carvalho and Andrea Pedrosa-Harand

Genes 2023, 14(2), 491; https://doi.org/10.3390/genes14020491 - 15 Feb 2023

Viewed by 1806

Abstract

The genus Agave presents a bimodal karyotype with x = 30 (5L, large, +25S, small chromosomes). Bimodality within this genus is generally attributed to allopolyploidy in the ancestral form of Agavoideae. However, alternative mechanisms, such as the preferential accumulation of repetitive elements at the macrochromosomes, could also be important. Aiming to understand the role of repetitive DNA within the bimodal karyotype of Agave, genomic DNA from the commercial hybrid 11648 (2n = 2x = 60, 6.31 Gbp) was sequenced at low coverage, and the repetitive fraction was characterized. In silico analysis showed that ~67.6% of the genome is mainly composed of different LTR retrotransposon lineages and one satellite DNA family (AgSAT171). The satellite DNA localized at the centromeric regions of all chromosomes; however, stronger signals were observed for 20 of the macro- and microchromosomes. All transposable elements showed a dispersed distribution, but not uniform across the length of the chromosomes. Different distribution patterns were observed for different TE lineages, with larger accumulation at the macrochromosomes. The data indicate the differential accumulation of LTR retrotransposon lineages at the macrochromosomes, probably contributing to the bimodality. Nevertheless, the differential accumulation of the satDNA in one group of macro- and microchromosomes possibly reflects the hybrid origin of this Agave accession. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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10 pages, 1543 KiB

Open AccessArticle

Chromosomal Microarray Analysis Identifies a Novel SALL1 Deletion, Supporting the Association of Haploinsufficiency with a Mild Phenotype of Townes–Brocks Syndrome

by Anna Maria Innoceta, Giulia Olivucci, Giulia Parmeggiani, Emanuela Scarano, Antonella Pragliola and Claudio Graziano

Genes 2023, 14(2), 258; https://doi.org/10.3390/genes14020258 - 19 Jan 2023

Cited by 1 | Viewed by 1432

Abstract

SALL1 heterozygous pathogenic variants cause Townes–Brocks syndrome (TBS), a condition with variable clinical presentation. The main features are a stenotic or imperforate anus, dysplastic ears, and thumb malformations, and other common concerns are hearing impairments, foot malformations, and renal and heart defects. Most of the pathogenic SALL1 variants are nonsense and frameshift, likely escaping nonsense-mediated mRNA decay and causing disease via a dominant-negative mechanism. Haploinsufficiency may result in mild phenotypes, but only four families with distinct SALL1 deletions have been reported to date, with a few more being of larger size and also affecting neighboring genes. We report on a family with autosomal dominant hearing impairment and mild anal and skeletal anomalies, in whom a novel 350 kb SALL1 deletion, spanning exon 1 and the upstream region, was identified by array comparative genomic hybridization. We review the clinical findings of known individuals with SALL1 deletions and point out that the overall phenotype is milder, especially when compared with individuals who carry the recurrent p.Arg276Ter mutation, but with a possible higher risk of developmental delay. Chromosomal microarray analysis is still a valuable tool in the identification of atypical/mild TBS cases, which are likely underestimated. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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16 pages, 4217 KiB

Open AccessArticle

Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution

by Dominik Matoulek, Bruno Ježek, Marta Vohnoutová and Radka Symonová

Genes 2023, 14(2), 244; https://doi.org/10.3390/genes14020244 - 17 Jan 2023

Cited by 2 | Viewed by 1208

Abstract

Cytogenetic and compositional studies considered fish genomes rather poor in guanine-cytosine content (GC%) because of a putative “sharp increase in genic GC% during the evolution of higher vertebrates”. However, the available genomic data have not been exploited to confirm this viewpoint. In contrast, further misunderstandings in GC%, mostly of fish genomes, originated from a misapprehension of the current flood of data. Utilizing public databases, we calculated the GC% in animal genomes of three different, technically well-established fractions: DNA (entire genome), cDNA (complementary DNA), and cds (exons). Our results across chordates help set borders of GC% values that are still incorrect in literature and show: (i) fish in their immense diversity possess comparably GC-rich (or even GC-richer) genomes as higher vertebrates, and fish exons are GC-enriched among vertebrates; (ii) animal genomes generally show a GC-enrichment from the DNA, over cDNA, to the cds level (i.e., not only the higher vertebrates); (iii) fish and invertebrates show a broad(er) inter-quartile range in GC%, while avian and mammalian genomes are more constrained in their GC%. These results indicate no sharp increase in the GC% of genes during the transition to higher vertebrates, as stated and numerously repeated before. We present our results in 2D and 3D space to explore the compositional genome landscape and prepared an online platform to explore the AT/GC compositional genome evolution. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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12 pages, 1339 KiB

Open AccessArticle

12q21 Interstitial Deletions: Seven New Syndromic Cases Detected by Array-CGH and Review of the Literature

by Maria Paola Recalcati, Ilaria Catusi, Maria Garzo, Serena Redaelli, Marta Massimello, Silvia Beatrice Maitz, Mattia Gentile, Emanuela Ponzi, Paola Orsini, Anna Zilio, Annamaria Montaldi, Annapaola Calò, Anna Paola Capra, Silvana Briuglia, Maria Angela La Rosa, Lucia Grillo, Corrado Romano, Sebastiano Bianca, Michela Malacarne, Martina Busè, Maria Piccione and Lidia Larizza Show full author list Hide full author list

Genes 2022, 13(5), 780; https://doi.org/10.3390/genes13050780 - 27 Apr 2022

Viewed by 2057

Abstract

Interstitial deletions of the long arm of chromosome 12 are rare, with a dozen patients carrying a deletion in 12q21 being reported. Recently a critical region (CR) has been delimited and could be responsible for the more commonly described clinical features, such as developmental delay/intellectual disability, congenital genitourinary and brain malformations. Other, less frequent, clinical signs do not seem to be correlated to the proposed CR. We present seven new patients harboring non-recurrent deletions ranging from 1 to 18.5 Mb differentially scattered across 12q21. Alongside more common clinical signs, some patients have rarer features such as heart defects, hearing loss, hypotonia and dysmorphisms. The correlation of haploinsufficiency of genes outside the CR to specific signs contributes to our knowledge of the effect of the deletion of this gene-poor region of chromosome 12q. This work underlines the still important role of copy number variations in the diagnostic setting of syndromic patients and the positive reflection on management and family genetic counseling. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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