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22 pages, 3316 KiB

Open AccessArticle

Genome and Karyotype Reorganization after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum

by Kira S. Zadesenets, Ilyas Y. Jetybayev, Lukas Schärer and Nikolay B. Rubtsov

Int. J. Mol. Sci. 2020, 21(2), 680; https://doi.org/10.3390/ijms21020680 - 20 Jan 2020

Cited by 12 | Viewed by 5057

Abstract

The genus Macrostomum represents a diverse group of rhabditophoran flatworms with >200 species occurring around the world. Earlier we uncovered karyotype instability linked to hidden polyploidy in both M. lignano (2n = 8) and its sibling species M. janickei (2n = [...] Read more.

The genus Macrostomum represents a diverse group of rhabditophoran flatworms with >200 species occurring around the world. Earlier we uncovered karyotype instability linked to hidden polyploidy in both M. lignano (2n = 8) and its sibling species M. janickei (2n = 10), prompting interest in the karyotype organization of close relatives. In this study, we investigated chromosome organization in two recently described and closely related Macrostomum species, M. mirumnovem and M. cliftonensis, and explored karyotype instability in laboratory lines and cultures of M. lignano (DV1/10, 2n = 10) and M. janickei in more detail. We revealed that three of the four studied species are characterized by karyotype instability, while M. cliftonensis showed a stable 2n = 6 karyotype. Next, we performed comparative cytogenetics of these species using fluorescent in situ hybridization (FISH) with a set of DNA probes (including microdissected DNA probes generated from M. lignano chromosomes, rDNA, and telomeric DNA). To explore the chromosome organization of the unusual 2n = 9 karyotype discovered in M. mirumnovem, we then generated chromosome-specific DNA probes for all chromosomes of this species. Similar to M. lignano and M. janickei, our findings suggest that M. mirumnovem arose via whole genome duplication (WGD) followed by considerable chromosome reshuffling. We discuss possible evolutionary scenarios for the emergence and reorganization of the karyotypes of these Macrostomum species and consider their suitability as promising animal models for studying the mechanisms and regularities of karyotype and genome evolution after a recent WGD. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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11 pages, 1615 KiB

Open AccessArticle

Chip-Based Digital PCR Approach Provides A Sensitive and Cost-Effective Single-Day Screening Tool for Common Fetal Aneuploidies—A Proof of Concept Study

by Anna Nykel, Marcin Kaszkowiak, Wojciech Fendler and Agnieszka Gach

Int. J. Mol. Sci. 2019, 20(21), 5486; https://doi.org/10.3390/ijms20215486 - 4 Nov 2019

Cited by 8 | Viewed by 3853

Abstract

In the prenatal period, the copy number aberrations of chromosomes 13, 18, 21, X and Y account for over 80% of the clinically significant chromosome abnormalities. Classical cytogenetic analysis is the gold standard in invasive prenatal diagnostics but the long test waiting time [...] Read more.

In the prenatal period, the copy number aberrations of chromosomes 13, 18, 21, X and Y account for over 80% of the clinically significant chromosome abnormalities. Classical cytogenetic analysis is the gold standard in invasive prenatal diagnostics but the long test waiting time affects its clinical utility. Several molecular rapid tests have been developed and employed in clinical practice, however all have substantial drawbacks. The aim of the study was to design and evaluate an optimized tool for rapid molecular detection of fetal aneuploidies. We established a novel single-day method using a chip-based platform, the QuantStudio 3D Digital PCR system. In order to assess the clinical usefulness of our screening test, we analyzed 133 prenatal samples. The difference in distributions of euploid and aneuploid samples identified the ploidy of each of the target chromosomes with high precision. The distribution of the chromosome ratio for euploid and aneuploid samples showed a statistically significant result (p = 0.003 for trisomy 13, p = 0.001 for trisomies 18 and 21, Mann–Whitney U test). Our results suggest that this novel chip-based approach provides a tool for rapid, technically simple, cost-effective screening for common fetal aneuploidies. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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15 pages, 3287 KiB

Open AccessArticle

Presence of 15p Marker D15Z1 on the Short Arm of Acrocentric Chromosomes is Associated with Aneuploid Offspring in Mexican Couples

by Sandra Ramos, Rebeca Rodríguez, Oscar Castro, Patricia Grether, Bertha Molina and Sara Frias

Int. J. Mol. Sci. 2019, 20(21), 5251; https://doi.org/10.3390/ijms20215251 - 23 Oct 2019

Cited by 2 | Viewed by 3433

Abstract

Variation in the location of the 15p region D15Z1 is recognized as a polymorphism in several human populations. We used high-stringency Fluorescence In Situ Hybridization (FISH) to detect D15Z1 in a Mexican cohort. Here, we report the presence of extra D15Z1 sequences on [...] Read more.

Variation in the location of the 15p region D15Z1 is recognized as a polymorphism in several human populations. We used high-stringency Fluorescence In Situ Hybridization (FISH) to detect D15Z1 in a Mexican cohort. Here, we report the presence of extra D15Z1 sequences on the p-arm of acrocentric chromosomes other than 15 in two groups of Mexican couples, one with healthy offspring (n = 75) and the other with aneuploid offspring (n = 87), mainly trisomy 21. The additional D15Z1 polymorphism was significantly increased in individuals with aneuploid offspring (26.4%), in comparison to individuals with healthy offspring (14%). The most frequent acceptor chromosome of D15Z1 was chromosome 13p, followed by 14p, and finally, 21p. Our results show an overall frequency of 21.6% of this polymorphism in the Mexican population and suggest that its presence might be associated with the mis-segregation of other acrocentric chromosomes and aneuploid offspring. The high frequency of the polymorphism of the D15Z1 sequence on acrocentric chromosomes other than 15 suggests a sequence homogenization of the acrocentric p arms, related to the important function of the centromere and the nucleolar organization region, which flank satellite III DNA. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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14 pages, 5936 KiB

Open AccessArticle

Evolution of the Proto Sex-Chromosome in Solea senegalensis

by María Esther Rodríguez, Belén Molina, Manuel Alejandro Merlo, Alberto Arias-Pérez, Silvia Portela-Bens, Aglaya García-Angulo, Ismael Cross, Thomas Liehr and Laureana Rebordinos

Int. J. Mol. Sci. 2019, 20(20), 5111; https://doi.org/10.3390/ijms20205111 - 15 Oct 2019

Cited by 11 | Viewed by 4441

Abstract

Solea senegalensis is a flatfish belonging to the Soleidae family within the Pleuronectiformes order. It has a karyotype of 2n = 42 (FN = 60; 6M + 4 SM + 8 St + 24 T) and a XX/XY system. The first pair [...] Read more.

Solea senegalensis is a flatfish belonging to the Soleidae family within the Pleuronectiformes order. It has a karyotype of 2n = 42 (FN = 60; 6M + 4 SM + 8 St + 24 T) and a XX/XY system. The first pair of metacentric chromosomes has been proposed as a proto sex-chromosome originated by a Robertsonian fusion between acrocentric chromosomes. In order to elucidate a possible evolutionary origin of this chromosome 1, studies of genomic synteny were carried out with eight fish species. A total of 88 genes annotated within of 14 BACs located in the chromosome 1 of S. senegalensis were used to elaborate syntenic maps. Six BACs (BAC5K5, BAC52C17, BAC53B20, BAC84K7, BAC56H24, and BAC48P7) were distributed in, at least, 5 chromosomes in the species studied, and a group of four genes from BAC53B20 (grsf1, rufy3, slc4a4 and npffr2) and genes from BAC48K7 (dmrt2, dmrt3, dmrt1, c9orf117, kank1 and fbp1) formed a conserved cluster in all species. The analysis of repetitive sequences showed that the number of retroelements and simple repeat per BAC showed its highest value in the subcentromeric region where 53B20, 16E16 and 48K7 BACs were localized. This region contains all the dmrt genes, which are associated with sex determination in some species. In addition, the presence of a satellite “chromosome Y” (motif length: 860 bp) was detected in this region. These findings allowed to trace an evolutionary trend for the large metacentric chromosome of S. senegalensis, throughout different rearrangements, which could be at an initial phase of differentiation as sex chromosome. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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15 pages, 2337 KiB

Open AccessArticle

Adaptive Radiation from a Chromosomal Perspective: Evidence of Chromosome Set Stability in Cichlid Fishes (Cichlidae: Teleostei) from the Barombi Mbo Lake, Cameroon

by Zuzana Majtánová, Adrian Indermaur, Arnold Roger Bitja Nyom, Petr Ráb and Zuzana Musilova

Int. J. Mol. Sci. 2019, 20(20), 4994; https://doi.org/10.3390/ijms20204994 - 9 Oct 2019

Cited by 4 | Viewed by 4235

Abstract

Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely [...] Read more.

Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely Konia eisentrauti, Konia dikume, Myaka myaka, Pungu maclareni, Sarotherodon steinbachi, Sarotherodon lohbergeri, Sarotherodon linnellii, Sarotherodon caroli, Stomatepia mariae, Stomatepia pindu, and Stomatepia mongo. These species supposedly evolved via sympatric ecological speciation from a common ancestor, which colonized the lake no earlier than one million years ago. Here we present the first comparative cytogenetic analysis of cichlid species from Barombi Mbo Lake using both conventional (Giemsa staining, C-banding, and CMA₃/DAPI staining) and molecular (fluorescence in situ hybridization with telomeric, 5S, and 28S rDNA probes) methods. We observed stability on both macro and micro-chromosomal levels. The diploid chromosome number was 2n = 44, and the karyotype was invariably composed of three pairs of meta/submetacentric and 19 pairs of subtelo/acrocentric chromosomes in all analysed species, with the same numbers of rDNA clusters and distribution of heterochromatin. The results suggest the evolutionary stability of chromosomal set; therefore, the large-scale chromosomal rearrangements seem to be unlikely associated with the sympatric speciation in Barombi Mbo. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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12 pages, 2689 KiB

Open AccessArticle

Possible Phenotypic Consequences of Structural Differences in Idic(15) in a Small Cohort of Patients

by Márta Czakó, Ágnes Till, András Szabó, Réka Ripszám, Béla Melegh and Kinga Hadzsiev

Int. J. Mol. Sci. 2019, 20(19), 4935; https://doi.org/10.3390/ijms20194935 - 5 Oct 2019

Cited by 1 | Viewed by 3490

Abstract

Among human supernumerary marker chromosomes, the occurrence of isodicentric form of 15 origin is relatively well known due to its high frequency, both in terms of gene content and associated clinical symptoms. The associated epilepsy and autism are typically more severe than in [...] Read more.

Among human supernumerary marker chromosomes, the occurrence of isodicentric form of 15 origin is relatively well known due to its high frequency, both in terms of gene content and associated clinical symptoms. The associated epilepsy and autism are typically more severe than in cases with interstitial 15q duplication, despite copy number gain of approximately the same genomic region. Other mechanisms besides segmental aneuploidy and epigenetic changes may also cause this difference. Among the factors influencing the expression of members of the GABA_A gene cluster, the imprinting effect and copy number differences has been debated. Limited numbers of studies investigate factors influencing the interaction of GABA_A cluster homologues. Five isodicentric (15) patients are reported with heterogeneous symptoms, and structural differences of their isodicentric chromosomes based on array comparative genomic hybridization results. Relations between the structure and the heterogeneous clinical picture are discussed, raising the possibility that the structure of the isodicentric (15), which has an asymmetric breakpoint and consequently a lower copy number segment, would be the basis of the imbalance of the GABA_A homologues. Studies of trans interaction and regulation of GABA_A cluster homologues are needed to resolve this issue, considering copy number differences within the isodicentric chromosome 15. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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13 pages, 5612 KiB

Open AccessArticle

Chromosome Translocations as a Driver of Diversification in Mole Voles Ellobius (Rodentia, Mammalia)

by Svetlana A. Romanenko, Elena A. Lyapunova, Abdusattor S. Saidov, Patricia C.M. O’Brien, Natalia A. Serdyukova, Malcolm A. Ferguson-Smith, Alexander S. Graphodatsky and Irina Bakloushinskaya

Int. J. Mol. Sci. 2019, 20(18), 4466; https://doi.org/10.3390/ijms20184466 - 10 Sep 2019

Cited by 19 | Viewed by 2777

Abstract

The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying [...] Read more.

The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying the G-band structure of chromosomes in numerous individuals revealed subsequent homologous, step-by-step, Robertsonian translocations, which changed diploid numbers from 54 to 30. Here we used a molecular cytogenetic strategy which demonstrates that chromosomal translocations are not always homologous; consequently, karyotypes with the same diploid number can carry different combinations of metacentrics. We further showed that at least three chromosomal forms with 2n = 34 and distinct metacentrics inhabit the Pamir-Alay mountains. Each of these forms independently hybridized with E. tancrei, 2n = 54, forming separate hybrid zones. The chromosomal variations correlate slightly with geographic barriers. Additionally, we confirmed that the emergence of partial or monobrachial homology appeared to be a strong barrier for hybridization in nature, in contradistinction to experiments which we reported earlier. We discuss the possibility of whole arm reciprocal translocations for mole voles. Our findings suggest that chromosomal translocations lead to diversification and speciation. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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19 pages, 2979 KiB

Open AccessArticle

Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics

by Marcelo de Bello Cioffi, Petr Ráb, Tariq Ezaz, Luiz Antonio Carlos Bertollo, Sebastien Lavoué, Ezequiel Aguiar de Oliveira, Alexandr Sember, Wagner Franco Molina, Fernando Henrique Santos de Souza, Zuzana Majtánová, Thomas Liehr, Ahmed Basheer Hamid Al-Rikabi, Cassia Fernanda Yano, Patrik Viana, Eliana Feldberg, Peter Unmack, Terumi Hatanaka, Alongklod Tanomtong and Manolo Fernandez Perez

Int. J. Mol. Sci. 2019, 20(17), 4296; https://doi.org/10.3390/ijms20174296 - 2 Sep 2019

Cited by 17 | Viewed by 7049

Abstract

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of [...] Read more.

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA₃/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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14 pages, 8661 KiB

Open AccessArticle

Karyotypes and Sex Chromosomes in Two Australian Native Freshwater Fishes, Golden Perch (Macquaria ambigua) and Murray Cod (Maccullochella peelii) (Percichthyidae)

by Foyez Shams, Fiona Dyer, Ross Thompson, Richard P. Duncan, Jason D. Thiem, Zuzana Majtánová and Tariq Ezaz

Int. J. Mol. Sci. 2019, 20(17), 4244; https://doi.org/10.3390/ijms20174244 - 30 Aug 2019

Cited by 7 | Viewed by 6897

Abstract

Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational [...] Read more.

Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational and commercial value. The arid landscape over much of these fishes’ range, coupled with the boom and bust hydrology of their habitat, means that these species have potential to provide useful evolutionary insights, such as karyotypes and sex chromosome evolution in vertebrates. Here we applied standard and molecular cytogenetic techniques to characterise karyotypes for golden perch and Murray cod. Both species have a diploid chromosome number 2n = 48 and a male heterogametic sex chromosome system (XX/XY). While the karyotype of golden perch is composed exclusively of acrocentric chromosomes, the karyotype of Murray cod consists of two submetacentric and 46 subtelocentric/acrocentric chromosomes. We have identified variable accumulation of repetitive sequences (AAT)₁₀ and (CGG)₁₀ along with diverse methylation patterns, especially on the sex chromosomes in both species. Our study provides a baseline for future cytogenetic analyses of other Australian freshwater fishes, especially species from the family Percichthyidae, to better understand their genome and sex chromosome evolution. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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15 pages, 5275 KiB

Open AccessArticle

Extensive Chromosomal Reorganization in Apistogramma Fishes (Cichlidae, Cichlinae) Fits the Complex Evolutionary Diversification of the Genus

by Gideão Wagner Werneck Félix da Costa, Marcelo de Bello Cioffi, Thomas Liehr, Eliana Feldberg, Luiz Antonio Carlos Bertollo and Wagner Franco Molina

Int. J. Mol. Sci. 2019, 20(17), 4077; https://doi.org/10.3390/ijms20174077 - 21 Aug 2019

Cited by 5 | Viewed by 3700

Abstract

Neotropical cichlid fishes are one of the most diversified and evolutionarily successful species assemblages. Extremely similar forms and intraspecific polychromatism present challenges for the taxonomy of some of these groups. Several species complexes have a largely unknown origin and unresolved evolutionary processes. Dwarf [...] Read more.

Neotropical cichlid fishes are one of the most diversified and evolutionarily successful species assemblages. Extremely similar forms and intraspecific polychromatism present challenges for the taxonomy of some of these groups. Several species complexes have a largely unknown origin and unresolved evolutionary processes. Dwarf cichlids of the genus Apistogramma, comprising more than a hundred species, exhibit intricate taxonomic and biogeographic patterns, with both allopatric and sympatric distributions. However, karyotype evolution and the role of chromosomal changes in Apistogramma are still unknown. In the present study, nine South American Apistogramma species were analyzed using conventional cytogenetic methods and the mapping of repetitive DNA sequences [18S rDNA, 5S rDNA, and (TTAGGG)n] by fluorescence in situ hybridization (FISH). Our results showed that Apistogramma has unique cytogenetic characteristics in relation to closely related groups, such as a reduced 2n and a large number of bi-armed chromosomes. Interspecific patterns revealed a scenario of remarkable karyotypic changes, including a reduction of 2n, the occurrence of B-chromosomes and evolutionary dynamic of rDNA tandem repeats. In addition to the well-known pre-zygotic reproductive isolation, the karyotype reorganization in the genus suggests that chromosomal changes could act as postzygotic barriers in areas where Apistogramma congeners overlap. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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16 pages, 2866 KiB

Open AccessArticle

Deciphering the Origin and Evolution of the X₁X₂Y System in Two Closely-Related Oplegnathus Species (Oplegnathidae and Centrarchiformes)

by Dongdong Xu, Alexandr Sember, Qihui Zhu, Ezequiel Aguiar de Oliveira, Thomas Liehr, Ahmed B. H. Al-Rikabi, Zhizhong Xiao, Hongbin Song and Marcelo de Bello Cioffi

Int. J. Mol. Sci. 2019, 20(14), 3571; https://doi.org/10.3390/ijms20143571 - 22 Jul 2019

Cited by 18 | Viewed by 3900

Abstract

Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X₁X₂Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of [...] Read more.

Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X₁X₂Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of these sex chromosomes, with the aim to elucidate whether they had a single or convergent origin. To achieve this, conventional and molecular cytogenetic protocols, involving the mapping of repetitive DNA markers, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) were applied. Both species presented similar 2n, karyotype structure and hybridization patterns of repetitive DNA classes. 5S rDNA loci, besides being placed on the autosomal pair 22, resided in the terminal region of the long arms of both X₁ chromosomes in females, and on the X₁ and Y chromosomes in males. Furthermore, WCP experiments with a probe derived from the Y chromosome of O. fasciatus (OFAS-Y) entirely painted the X₁ and X₂ chromosomes in females and the X₁, X₂, and Y chromosomes in males of both species. CGH failed to reveal any sign of sequence differentiation on the Y chromosome in both species, thereby suggesting the shared early stage of neo-Y chromosome differentiation. Altogether, the present findings confirmed the origin of the X₁X₂Y sex chromosomes via Y-autosome centric fusion and strongly suggested their common origin. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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18 pages, 4768 KiB

Open AccessArticle

Genomic Organization of Repetitive DNA Elements and Extensive Karyotype Diversity of Silurid Catfishes (Teleostei: Siluriformes): A Comparative Cytogenetic Approach

by Sukhonthip Ditcharoen, Luiz Antonio Carlos Bertollo, Petr Ráb, Eva Hnátková, Wagner Franco Molina, Thomas Liehr, Alongklod Tanomtong, Costas Triantaphyllidis, Catherine Ozouf-Costaz, Sampan Tongnunui, Puan Pengseng, Weerayuth Supiwong, Rouben Aroutiounian and Marcelo de Bello Cioffi

Int. J. Mol. Sci. 2019, 20(14), 3545; https://doi.org/10.3390/ijms20143545 - 19 Jul 2019

Cited by 12 | Viewed by 4051

Abstract

The catfish family Siluridae contains 107 described species distributed in Asia, but with some distributed in Europe. In this study, karyotypes and other chromosomal characteristics of 15 species from eight genera were examined using conventional and molecular cytogenetic protocols. Our results showed the [...] Read more.

The catfish family Siluridae contains 107 described species distributed in Asia, but with some distributed in Europe. In this study, karyotypes and other chromosomal characteristics of 15 species from eight genera were examined using conventional and molecular cytogenetic protocols. Our results showed the diploid number (2n) to be highly divergent among species, ranging from 2n = 40 to 92, with the modal frequency comprising 56 to 64 chromosomes. Accordingly, the ratio of uni- and bi-armed chromosomes is also highly variable, thus suggesting extensive chromosomal rearrangements. Only one chromosome pair bearing major rDNA sites occurs in most species, except for Wallago micropogon, Ompok siluroides, and Kryptoterus giminus with two; and Silurichthys phaiosoma with five such pairs. In contrast, chromosomes bearing 5S rDNA sites range from one to as high as nine pairs among the species. Comparative genomic hybridization (CGH) experiments evidenced large genomic divergence, even between congeneric species. As a whole, we conclude that karyotype features and chromosomal diversity of the silurid catfishes are unusually extensive, but parallel some other catfish lineages and primary freshwater fish groups, thus making silurids an important model for investigating the evolutionary dynamics of fish chromosomes. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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17 pages, 3429 KiB

Open AccessArticle

Chromosomal Evolution and Evolutionary Relationships of Lebiasina Species (Characiformes, Lebiasinidae)

by Francisco de Menezes Cavalcante Sassi, Ezequiel Aguiar de Oliveira, Luiz Antonio Carlos Bertollo, Mauro Nirchio, Terumi Hatanaka, Manoela Maria Ferreira Marinho, Orlando Moreira-Filho, Rouben Aroutiounian, Thomas Liehr, Ahmed B. H. Al-Rikabi and Marcelo de Bello Cioffi

Int. J. Mol. Sci. 2019, 20(12), 2944; https://doi.org/10.3390/ijms20122944 - 16 Jun 2019

Cited by 29 | Viewed by 4209

Abstract

We present the first cytogenetic data for Lebiasina bimaculata and L. melanoguttata with the aim of (1) investigating evolutionary events within Lebiasina and their relationships with other Lebiasinidae genera and (2) checking the evolutionary relationships between Lebiasinidae and Ctenoluciidae. Both species have a [...] Read more.

We present the first cytogenetic data for Lebiasina bimaculata and L. melanoguttata with the aim of (1) investigating evolutionary events within Lebiasina and their relationships with other Lebiasinidae genera and (2) checking the evolutionary relationships between Lebiasinidae and Ctenoluciidae. Both species have a diploid number 2n = 36 with similar karyotypes and microsatellite distribution patterns but present contrasting C-positive heterochromatin and CMA₃⁺ banding patterns. The remarkable interstitial series of C-positive heterochromatin occurring in L. melanoguttata is absent in L. bimaculata. Accordingly, L. bimaculata shows the ribosomal DNA sites as the only GC-rich (CMA₃⁺) regions, while L. melanoguttata shows evidence of a clear intercalated CMA₃⁺ banding pattern. In addition, the multiple 5S and 18S rDNA sites in L. melanogutatta contrast with single sites present in L. bimaculata. Comparative genomic hybridization (CGH) experiments also revealed a high level of genomic differentiation between both species. A polymorphic state of a conspicuous C-positive, CMA₃⁺, and (CGG)n band was found only to occur in L. bimaculata females, and its possible relationship with a nascent sex chromosome system is discussed. Whole chromosome painting (WCP) and CGH experiments indicate that the Lebiasina species examined and Boulengerella maculata share similar chromosomal sequences, thus supporting the relatedness between them and the evolutionary relationships between the Lebiasinidae and Ctenoluciidae families. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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20 pages, 2285 KiB

Open AccessArticle

Detection and Correlation of Single and Concomitant TP53, PTEN, and CDKN2A Alterations in Gliomas

by Igor Andrade Pessôa, Carolina Koury Amorim, Wallax Augusto Silva Ferreira, Fernanda Sagica, José Reginaldo Brito, Moneeb Othman, Britta Meyer, Thomas Liehr and Edivaldo Herculano C. de Oliveira

Int. J. Mol. Sci. 2019, 20(11), 2658; https://doi.org/10.3390/ijms20112658 - 30 May 2019

Cited by 20 | Viewed by 3395

Abstract

Gliomas are the most frequent primary tumors of central nervous system and represent a heterogeneous group of tumors that originates from the glial cells. TP53, PTEN, and CDKN2A are important tumor suppressor genes that encode proteins involved in sustaining cellular homeostasis [...] Read more.

Gliomas are the most frequent primary tumors of central nervous system and represent a heterogeneous group of tumors that originates from the glial cells. TP53, PTEN, and CDKN2A are important tumor suppressor genes that encode proteins involved in sustaining cellular homeostasis by different signaling pathways. Though genetic alterations in these genes play a significant role in tumorigenesis, few studies are available regarding the incidence and relation of concomitant TP53, PTEN, and CDKN2A alterations in gliomas. The purpose of this study was to evaluate the occurrence of mutation and deletion in these genes, through single-strand conformational polymorphism, array-comparative genomic hybridization, and fluorescence in situ hybridization techniques, in 69 gliomas samples. Molecular results demonstrated a significant higher prevalence of TP53, PTEN, and CDKN2A alterations in astrocytoma than other tumor subtypes, and heterozygous deletion was the most frequent event. In addition, a significant association was observed between TP53 and CDKN2A alterations (p = 0.0424), which tend to coexist in low grade astrocytomas (5/46 cases (10.9%)), suggesting that they are early events in development of these tumors, and PTEN and CDKN2A deletions (p = 0.0022), which occurred concomitantly in 9/50 (18%) patients, with CDKN2A changes preceding PTEN deletions, present preferably in high-grade gliomas. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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Review

Jump to: Research

19 pages, 272 KiB

Open AccessReview

DNA Copy Number Variations as Markers of Mutagenic Impact

by Galina Hovhannisyan, Tigran Harutyunyan, Rouben Aroutiounian and Thomas Liehr

Int. J. Mol. Sci. 2019, 20(19), 4723; https://doi.org/10.3390/ijms20194723 - 24 Sep 2019

Cited by 23 | Viewed by 4573

Abstract

DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution [...] Read more.

DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution of environmental factors, such as mutagens, in the origin of CNVs, is poorly understood. In this review, we summarize current knowledge about mutagen-induced CNVs in human, animal and plant cells. Differences in CNV frequencies induced by radiation and chemical mutagens, distribution of CNVs in the genome, as well as adaptive effects in plants, are discussed. Currently available information concerning impact of mutagens in induction of CNVs in germ cells is presented. Moreover, the potential of CNVs as a new endpoint in mutagenicity test-systems is discussed. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

13 pages, 1347 KiB

Open AccessReview

Cytogenetics and Cytogenomics Evaluation in Cancer

by Ilda Patrícia Ribeiro, Joana Barbosa Melo and Isabel Marques Carreira

Int. J. Mol. Sci. 2019, 20(19), 4711; https://doi.org/10.3390/ijms20194711 - 23 Sep 2019

Cited by 21 | Viewed by 9187

Abstract

The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer [...] Read more.

The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer candidate biomarkers associated with diagnosis, prognosis, and therapeutics. The advent of array comparative genomic hybridization and next-generation sequencing technologies has significantly improved the knowledge about cancer biology, underlining driver genes to guide targeted therapy development, drug-resistance prediction, and pharmacogenetics. However, few of these candidate biomarkers have made the transition to the clinic with a clear benefit for the patients. Technological progress helped to demonstrate that cellular heterogeneity plays a significant role in tumor progression and resistance/sensitivity to cancer therapies, representing the major challenge of precision cancer therapy. A paradigm shift has been introduced in cancer genomics with the recent advent of single-cell sequencing, since it presents a lot of applications with a clear benefit to oncological patients, namely, detection of intra-tumoral heterogeneity, mapping clonal evolution, monitoring the development of therapy resistance, and detection of rare tumor cell populations. It seems now evident that no single biomarker could provide the whole information necessary to early detect and predict the behavior and prognosis of tumors. The promise of precision medicine is based on the molecular profiling of tumors being vital the continuous progress of high-throughput technologies and the multidisciplinary efforts to catalogue chromosomal rearrangements and genomic alterations of human cancers and to do a good interpretation of the relation genotype—phenotype. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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22 pages, 1326 KiB

Open AccessReview

The Pleiotropic Role of Retinoic Acid/Retinoic Acid Receptors Signaling: From Vitamin A Metabolism to Gene Rearrangements in Acute Promyelocytic Leukemia

by Maria Rosa Conserva, Luisa Anelli, Antonella Zagaria, Giorgina Specchia and Francesco Albano

Int. J. Mol. Sci. 2019, 20(12), 2921; https://doi.org/10.3390/ijms20122921 - 14 Jun 2019

Cited by 22 | Viewed by 11920

Abstract

The family of retinoic acid receptors (RARs: RARα, -β, and -γ) has remarkable pleiotropy characteristics, since the retinoic acid/RARs pathway is involved in numerous biological processes not only during embryonic development, but also in the postnatal phase and during adulthood. In this review, [...] Read more.

The family of retinoic acid receptors (RARs: RARα, -β, and -γ) has remarkable pleiotropy characteristics, since the retinoic acid/RARs pathway is involved in numerous biological processes not only during embryonic development, but also in the postnatal phase and during adulthood. In this review, we trace the roles of RA/RARs signaling in the immune system (where this pathway has both an immunosuppressive role or is involved in the inflammatory response), in hematopoiesis (enhancing hematopoietic stem cell self-renewal, progenitor cells differentiation or maintaining the bone marrow microenvironment homeostasis), and in bone remodeling (where this pathway seems to have controversial effects on bone formation or osteoclast activation). Moreover, in this review is shown the involvement of RAR genes in multiple chromosomal rearrangements generating different fusion genes in hematological neoplasms, with a particular focus on acute promyelocytic leukemia and its variant subtypes. The effect of different RARs fusion proteins on leukemic transformation, on patients’ outcome, and on therapy response is also discussed. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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12 pages, 372 KiB

Open AccessReview

From Human Cytogenetics to Human Chromosomics

by Thomas Liehr

Int. J. Mol. Sci. 2019, 20(4), 826; https://doi.org/10.3390/ijms20040826 - 14 Feb 2019

Cited by 15 | Viewed by 6438

Abstract

Background: The concept of “chromosomics” was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a “chromosomic view” of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is [...] Read more.

Background: The concept of “chromosomics” was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a “chromosomic view” of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945–20 July 2008). Recent findings: Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches. Conclusion: Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary. Full article

(This article belongs to the Special Issue Chromosome and Karyotype Variation)

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