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14 pages, 3136 KiB

Open AccessArticle

Maps of Constitutive-Heterochromatin Distribution for Four Martes Species (Mustelidae, Carnivora, Mammalia) Show the Formative Role of Macrosatellite Repeats in Interspecific Variation of Chromosome Structure

by Violetta R. Beklemisheva, Natalya A. Lemskaya, Dmitry Yu. Prokopov, Polina L. Perelman, Svetlana A. Romanenko, Anastasia A. Proskuryakova, Natalya A. Serdyukova, Yaroslav A. Utkin, Wenhui Nie, Malcolm A. Ferguson-Smith, Fentang Yang and Alexander S. Graphodatsky

Genes 2023, 14(2), 489; https://doi.org/10.3390/genes14020489 - 14 Feb 2023

Viewed by 1366

Abstract

Constitutive-heterochromatin placement in the genome affects chromosome structure by occupying centromeric areas and forming large blocks. To investigate the basis for heterochromatin variation in the genome, we chose a group of species with a conserved euchromatin part: the genus Martes [stone marten ( [...] Read more.

Constitutive-heterochromatin placement in the genome affects chromosome structure by occupying centromeric areas and forming large blocks. To investigate the basis for heterochromatin variation in the genome, we chose a group of species with a conserved euchromatin part: the genus Martes [stone marten (M. foina, 2n = 38), sable (M. zibellina, 2n = 38), pine marten (M. martes, 2n = 38), and yellow-throated marten (M. flavigula, 2n = 40)]. We mined the stone marten genome for the most abundant tandem repeats and selected the top 11 macrosatellite repetitive sequences. Fluorescent in situ hybridization revealed distributions of the tandemly repeated sequences (macrosatellites, telomeric repeats, and ribosomal DNA). We next characterized the AT/GC content of constitutive heterochromatin by CDAG (Chromomycin A3-DAPI-after G-banding). The euchromatin conservatism was shown by comparative chromosome painting with stone marten probes in newly built maps of the sable and pine marten. Thus, for the four Martes species, we mapped three different types of tandemly repeated sequences critical for chromosome structure. Most macrosatellites are shared by the four species with individual patterns of amplification. Some macrosatellites are specific to a species, autosomes, or the X chromosome. The variation of core macrosatellites and their prevalence in a genome are responsible for the species-specific variation of the heterochromatic blocks. Full article

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

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13 pages, 5716 KiB

Open AccessArticle

Whole-Genome Analysis Reveals the Dynamic Evolution of Holocentric Chromosomes in Satyrine Butterflies

by Elena A. Pazhenkova and Vladimir A. Lukhtanov

Genes 2023, 14(2), 437; https://doi.org/10.3390/genes14020437 - 08 Feb 2023

Cited by 2 | Viewed by 2081

Abstract

Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are [...] Read more.

Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are poorly understood. Here, we analyzed chromosome-scale genome assemblies to identify structural rearrangements between karyotypes of satyrine butterfly species. For the species pair Erebia ligea–Maniola jurtina, sharing the ancestral diploid karyotype 2n = 56 + ZW, we demonstrate a high level of chromosomal macrosynteny and nine inversions separating these species. We show that the formation of a karyotype with a low number of chromosomes (2n = 36 + ZW) in Erebia aethiops was based on ten fusions, including one autosome–sex chromosome fusion, resulting in a neo-Z chromosome. We also detected inversions on the Z sex chromosome that were differentially fixed between the species. We conclude that chromosomal evolution is dynamic in the satyrines, even in the lineage that preserves the ancestral chromosome number. We hypothesize that the exceptional role of Z chromosomes in speciation may be further enhanced by inversions and sex chromosome–autosome fusions. We argue that not only fusions/fissions but also inversions are drivers of the holocentromere-mediated mode of chromosomal speciation. Full article

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

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13 pages, 2118 KiB

Open AccessArticle

Occurrence of Sex Chromosomes in Fish of the Genus Ancistrus with a New Description of Multiple Sex Chromosomes in the Ecuadorian Endemic Ancistrus clementinae (Loricariidae)

by Mauro Nirchio, Claudio Oliveira, Marcelo de Bello Cioffi, Francisco de Menezes Cavalcante Sassi, Jonathan Valdiviezo, Fabilene Gomes Paim, Leticia Batista Soares and Anna Rita Rossi

Genes 2023, 14(2), 306; https://doi.org/10.3390/genes14020306 - 24 Jan 2023

Cited by 5 | Viewed by 1695

Abstract

Ancistrus Kner, 1854, is the most diverse genus among the Ancistrini (Loricariidae) with 70 valid species showing a wide geographic distribution and great taxonomic and systematic complexity. To date, about 40 Ancistrus taxa have been karyotyped, all from Brazil and Argentina, but the [...] Read more.

Ancistrus Kner, 1854, is the most diverse genus among the Ancistrini (Loricariidae) with 70 valid species showing a wide geographic distribution and great taxonomic and systematic complexity. To date, about 40 Ancistrus taxa have been karyotyped, all from Brazil and Argentina, but the statistic is uncertain because 30 of these reports deal with samples that have not yet been identified at the species level. This study provides the first cytogenetic description of the bristlenose catfish, Ancistrus clementinae Rendahl, 1937, a species endemic to Ecuador, aiming to verify whether a sex chromosome system is identifiable in the species and, if so, which, and if its differentiation is associated with the presence of repetitive sequences reported for other species of the family. We associated the karyotype analysis with the COI molecular identification of the specimens. Karyotype analysis suggested the presence of a ♂ZZ/♀ZW₁W₂ sex chromosome system, never detected before in Ancistrus, with both W₁W₂ chromosomes enriched with heterochromatic blocks and 18S rDNA, in addition to GC-rich repeats (W₂). No differences were observed between males and females in the distribution of 5S rDNA or telomeric repeats. Cytogenetic data here obtained confirm the huge karyotype diversity of Ancistrus, both in chromosome number and sex-determination systems. Full article

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

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17 pages, 3668 KiB

Open AccessArticle

Parallel Evolution of Sex-Linked Genes across XX/XY and ZZ/ZW Sex Chromosome Systems in the Frog Glandirana rugosa

by Shuuji Mawaribuchi, Michihiko Ito, Mitsuaki Ogata, Yuri Yoshimura and Ikuo Miura

Genes 2023, 14(2), 257; https://doi.org/10.3390/genes14020257 - 18 Jan 2023

Cited by 1 | Viewed by 6173

Abstract

Genetic sex-determination features male (XX/XY) or female heterogamety (ZZ/ZW). To identify similarities and differences in the molecular evolution of sex-linked genes between these systems, we directly compared the sex chromosome systems existing in the frog Glandirana rugosa. The heteromorphic X/Y and Z/W [...] Read more.

Genetic sex-determination features male (XX/XY) or female heterogamety (ZZ/ZW). To identify similarities and differences in the molecular evolution of sex-linked genes between these systems, we directly compared the sex chromosome systems existing in the frog Glandirana rugosa. The heteromorphic X/Y and Z/W sex chromosomes were derived from chromosomes 7 (2n = 26). RNA-Seq, de novo assembly, and BLASTP analyses identified 766 sex-linked genes. These genes were classified into three different clusters (XW/YZ, XY/ZW, and XZ/YW) based on sequence identities between the chromosomes, probably reflecting each step of the sex chromosome evolutionary history. The nucleotide substitution per site was significantly higher in the Y- and Z-genes than in the X- and W- genes, indicating male-driven mutation. The ratio of nonsynonymous to synonymous nucleotide substitution rates was higher in the X- and W-genes than in the Y- and Z-genes, with a female bias. Allelic expression in gonad, brain, and muscle was significantly higher in the Y- and W-genes than in the X- and Z-genes, favoring heterogametic sex. The same set of sex-linked genes showed parallel evolution across the two distinct systems. In contrast, the unique genomic region of the sex chromosomes demonstrated a difference between the two systems, with even and extremely high expression ratios of W/Z and Y/X, respectively. Full article

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

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9 pages, 649 KiB

Open AccessArticle

ZZ/ZW Sex Chromosomes in the Madagascar Girdled Lizard, Zonosaurus madagascariensis (Squamata: Gerrhosauridae)

by Alexander Kostmann, Lukáš Kratochvíl and Michail Rovatsos

Genes 2023, 14(1), 99; https://doi.org/10.3390/genes14010099 - 29 Dec 2022

Viewed by 1961

Abstract

Scincoidea, the reptilian clade that includes girdled lizards, night lizards, plated lizards and skinks, are considered as a lineage with diversity in sex-determining systems. Recently, the hypothesis on the variability in sex determination in skinks and even more the absence of sex chromosomes [...] Read more.

Scincoidea, the reptilian clade that includes girdled lizards, night lizards, plated lizards and skinks, are considered as a lineage with diversity in sex-determining systems. Recently, the hypothesis on the variability in sex determination in skinks and even more the absence of sex chromosomes in some of them has been rivalling. Homologous, evolutionary stable XX/XY sex chromosomes were documented to be widespread across skinks. However, sex determination in the other scincoidean families is highly understudied. ZZ/ZW sex chromosomes have been identified only in night lizards and a single species of plated lizards. It seems that although there are different sex chromosome systems among scincoidean lineages, they share one common trait: they are mostly poorly differentiated and often undetectable by cytogenetic methods. Here, we report one of the exceptions, demonstrating for the first time ZZ/ZW sex chromosomes in the plated lizard Zonosaurus madagascariensis. Its sex chromosomes are morphologically similar, but the W is clearly detectable by comparative genomic hybridization (CGH), suggesting that the Z and W chromosomes highly differ in sequence content. Our findings confirm the presence of female heterogamety in plated lizards and provides novel insights to expand our understanding of sex chromosome evolution in scincoidean lizards. Full article

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

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13 pages, 1914 KiB

Open AccessArticle

The Satellite DNA Catalogues of Two Serrasalmidae (Teleostei, Characiformes): Conservation of General satDNA Features over 30 Million Years

by Caio Augusto Gomes Goes, Natalia dos Santos, Pedro Henrique de Mira Rodrigues, José Henrique Forte Stornioli, Amanda Bueno da Silva, Rodrigo Zeni dos Santos, Jhon Alex Dziechciarz Vidal, Duílio Mazzoni Zerbinato de Andrade Silva, Roberto Ferreira Artoni, Fausto Foresti, Diogo Teruo Hashimoto, Fábio Porto-Foresti and Ricardo Utsunomia

Genes 2023, 14(1), 91; https://doi.org/10.3390/genes14010091 - 28 Dec 2022

Cited by 4 | Viewed by 1565

Abstract

Satellite DNAs (satDNAs) are tandemly repeated sequences that are usually located on the heterochromatin, and the entire collection of satDNAs within a genome is called satellitome. Primarily, these sequences are not under selective pressure and evolve by concerted evolution, resulting in elevated rates [...] Read more.

Satellite DNAs (satDNAs) are tandemly repeated sequences that are usually located on the heterochromatin, and the entire collection of satDNAs within a genome is called satellitome. Primarily, these sequences are not under selective pressure and evolve by concerted evolution, resulting in elevated rates of divergence between the satDNA profiles of reproductive isolated species/populations. Here, we characterized two additional satellitomes of Characiformes fish (Colossoma macropomum and Piaractus mesopotamicus) that diverged approximately 30 million years ago, while still retaining conserved karyotype features. The results we obtained indicated that several satDNAs (50% of satellite sequences in P. mesopotamicus and 43% in C. macropomum) show levels of conservation between the analyzed species, in the nucleotide and chromosomal levels. We propose that long-life cycles and few genomic changes could slow down rates of satDNA differentiation. Full article

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

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12 pages, 2120 KiB

Open AccessArticle

Five Species of Taxus Karyotype Based on Oligo-FISH for 5S rDNA and (AG₃T₃)₃

by Zhoujian He, Xiaomei Luo, Yuting Lei and Wei Zhang

Genes 2022, 13(12), 2209; https://doi.org/10.3390/genes13122209 - 25 Nov 2022

Viewed by 1222

Abstract

As a relict plant, Taxus is used in a variety of medicinal ingredients, for instance to treat a variety of cancers. Taxus plants are difficult to distinguish from one another due to their similar morphology; indeed, some species of Taxus cytogenetic data still [...] Read more.

As a relict plant, Taxus is used in a variety of medicinal ingredients, for instance to treat a variety of cancers. Taxus plants are difficult to distinguish from one another due to their similar morphology; indeed, some species of Taxus cytogenetic data still are unclear. Oligo-FISH can rapidly and efficiently provide insight into the genetic composition and karyotype. This is important for understanding the organization and evolution of chromosomes in Taxus species. We analysed five Taxus species using two oligonucleotide probes. (AG₃T₃)₃ signals were distributed at the chromosome ends and the centromere of five species of Taxus. The 5S rDNA signal was displayed on two chromosomes of five species of Taxus. In addition to Taxus wallichiana var. mairei, 5S rDNA signals were found proximal in the remaining four species, which signals a difference in its location. The karyotype formula of Taxus wallichiana was 2n = 2x = 24m, its karyotype asymmetry index was 55.56%, and its arm ratio was 3.0087. Taxus × media’s karyotype formula was 2n = 2x = 24m, its karyotype asymmetry index was 55.09%, and its arm ratio was 3.4198. The karyotype formula of Taxus yunnanensis was 2n = 2x = 24m, its karyotype asymmetry index was 55.56%, and its arm ratio was 2.6402. The karyotype formula of Taxus cuspidate was 2n = 2x = 24m, its karyotype asymmetry index was 54.67%, its arm ratio was 3.0135, and two chromosomes exhibited the 5S rDNA signal. The karyotype formula of T. wallichiana var. mairei was 2n= 2x = 22m + 2sm, its karyotype asymmetry index was 54.33%, and its arm ratio was 2.8716. Our results provide the karyotype analysis and physical genetic map of five species of Taxus, which contributes to providing molecular cytogenetics data for Taxus. Full article

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

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12 pages, 22020 KiB

Open AccessArticle

Nonhomologous Chromosome Interactions in Prophase I: Dynamics of Bizarre Meiotic Contacts in the Alay Mole Vole Ellobius alaicus (Mammalia, Rodentia)

by Sergey Matveevsky, Irina Bakloushinskaya, Valentina Tambovtseva, Maret Atsaeva, Tatiana Grishaeva, Aleksey Bogdanov and Oxana Kolomiets

Genes 2022, 13(12), 2196; https://doi.org/10.3390/genes13122196 - 23 Nov 2022

Cited by 3 | Viewed by 1336

Abstract

Nonhomologous chromosome interactions take place in both somatic and meiotic cells. Prior to this study, we had discovered special contacts through the SYCP3 (synaptonemal complex protein 3) filament between the short arms of nonhomologous acrocentrics at the pachytene stage in the Alay mole [...] Read more.

Nonhomologous chromosome interactions take place in both somatic and meiotic cells. Prior to this study, we had discovered special contacts through the SYCP3 (synaptonemal complex protein 3) filament between the short arms of nonhomologous acrocentrics at the pachytene stage in the Alay mole vole, and these contacts demonstrate several patterns from proximity to the complete fusion stage. Here, we investigated the nonhomologous chromosome contacts in meiotic prophase I. It turned out that such contacts do not introduce changes into the classic distribution of DNA double-strand breaks. It is noteworthy that not all meiotic contacts were localized in the H3k9me3-positive heterochromatic environment. Both in the mid zygotene and in the early–mid diplotene, three types of contacts (proximity, touching, and anchoring/tethering) were observed, whereas fusion seems to be characteristic only for pachytene. The number of contacts in the mid pachytene is significantly higher than that in the zygotene, and the distance between centromeres in nonhomologous contacts is also the smallest in mid pachytene for all types of contacts. Thus, this work provides a new insight into the behavior of meiotic contacts during prophase I and points to avenues of further research. Full article

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

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13 pages, 2304 KiB

Open AccessArticle

Cytogenetic Investigation of Infertile Patients in Hungary: A 10-Year Retrospective Study

by Szilvia Andó, Katalin Koczok, Beáta Bessenyei, István Balogh and Anikó Ujfalusi

Genes 2022, 13(11), 2086; https://doi.org/10.3390/genes13112086 - 10 Nov 2022

Cited by 3 | Viewed by 2048

Abstract

Chromosome abnormalities play a crucial role in reproductive failure. The presence of numerical or structural aberrations may induce recurrent pregnancy loss or primary infertility. The main purpose of our study was to determine the types and frequency of chromosomal aberrations in infertile patients [...] Read more.

Chromosome abnormalities play a crucial role in reproductive failure. The presence of numerical or structural aberrations may induce recurrent pregnancy loss or primary infertility. The main purpose of our study was to determine the types and frequency of chromosomal aberrations in infertile patients and to compare the frequency of structural aberrations to a control group. Karyotyping was performed in 1489 men and 780 women diagnosed with reproductive failure between 2010 and 2020. The control group included 869 male and 1160 female patients having cytogenetic evaluations for reasons other than infertility. Sex chromosomal aberrations were detected in 33/1489 (2.22%) infertile men and 3/780 (0.38%) infertile women. Structural abnormalities (e.g., translocation, inversion) were observed in 89/1489 (5.98%) infertile men and 58/780 (7.44%) infertile women. The control population showed structural chromosomal abnormalities in 27/869 (3.11%) men and 39/1160 (3.36%) women. There were significant differences in the prevalence of single-cell translocations between infertile individuals (males: 3.5%; females: 3.46%) and control patients (males: 0.46%; females: 0.7%). In summary, this is the first report of cytogenetic alterations in infertile patients in Hungary. The types of chromosomal abnormalities were comparable to previously published data. The prevalence of less-studied single-cell translocations was significantly higher in infertile patients than in the control population, supporting an earlier suggestion that these aberrations may be causally related to infertility. Full article

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

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14 pages, 1581 KiB

Open AccessArticle

Mapping Retrotransposon LINE-1 Sequences into Two Cebidae Species and Homo sapiens Genomes and a Short Review on Primates

by Vanessa Milioto, Polina L. Perelman, Laura La Paglia, Larisa Biltueva, Melody Roelke and Francesca Dumas

Genes 2022, 13(10), 1742; https://doi.org/10.3390/genes13101742 - 27 Sep 2022

Cited by 4 | Viewed by 1375

Abstract

This work focuses on the distribution of LINE-1 (a Long Interspersed Nuclear Element) in primates and its role during evolution and as a constituent of the architecture of primate genomes. To pinpoint the LINE-1 repeat distribution and its role among primates, LINE-1 probes [...] Read more.

This work focuses on the distribution of LINE-1 (a Long Interspersed Nuclear Element) in primates and its role during evolution and as a constituent of the architecture of primate genomes. To pinpoint the LINE-1 repeat distribution and its role among primates, LINE-1 probes were mapped onto chromosomes of Homo sapiens (Hominidae, Catarrhini), Sapajus apella, and Cebus capucinus (Cebidae, Platyrrhini) using fluorescence in situ hybridisation (FISH). The choice of platyrrhine species are due to the fact they are taxa characterised by a high level of rearrangements; for this reason, they could be a useful model for the study of LINE-1 and chromosome evolution. LINE-1 accumulation was found in the two Cebidae at the centromere of almost all acrocentric chromosomes 16–22 and on some bi-armed chromosomes. LINE-1 pattern was similar in the two species but only for chromosomes 6, 8, 10, and 18, due to intrachromosomal rearrangements in agreement with what was previously hypothesised as through g banding. LINE-1 interstitial accumulation was found in humans on the 1, 8, 9, 13–15, and X chromosomes; on chromosomes 8, 9, and 13–15, the signal was also at the centromeric position. This is in agreement with recent and complete molecular sequence analysis of human chromosomes 8 and some acrocentric ones. Thus, the hypothesis regarding a link between LINE-1 and centromeres as well as a link with rearrangements are discussed. Indeed, data analysis leads us to support a link between LINE-1 and inter- and intrachromosomal rearrangements, as well as a link between LINE-1 and structural functions at centromeres in primates. Full article

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

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15 pages, 39180 KiB

Open AccessArticle

Cytogenetic Analysis in the Toad Species Bufo spinosus, Bufotes viridis and Epidalea calamita (Anura, Bufonidae) from the Mediterranean Area

by Katerina Guzmán-Markevich, Álvaro S. Roco, Adrián Ruiz-García and Mónica Bullejos

Genes 2022, 13(8), 1475; https://doi.org/10.3390/genes13081475 - 18 Aug 2022

Cited by 3 | Viewed by 1631

Abstract

Taxonomy in Bufonidae witnessed notable transformations. Bufotes viridis and Epidalea calamita, previously included in genus Bufo, were relocated in other genera, while the genus Bufo was restricted to members of the earlier Bufo bufo group. On the other hand, Bufo bufo [...] Read more.

Taxonomy in Bufonidae witnessed notable transformations. Bufotes viridis and Epidalea calamita, previously included in genus Bufo, were relocated in other genera, while the genus Bufo was restricted to members of the earlier Bufo bufo group. On the other hand, Bufo bufo sensu lato now includes four species: Bufo bufo, Bufo spinosus, Bufo verrucosissimus and Bufo eichwaldi. In this study, we examined three species of three Bufonidae genera (B. spinosus, B. viridis and E. calamita) by conventional (C-banding and Ag-NOR staining) and molecular (in situ hybridization with probes for telomeric repeats and rDNA loci, and genomic in situ hybridization (GISH)) cytogenetic methods. C-banding patterns are reported for the first time for B. spinosus and E. calamita populations from Iberian Peninsula and for B. viridis from Greece, and reveal several differences with the reported C-banded karyotypes described for other European populations of these species. Silver staining shows size heteromorphisms of the signals at the Nucleolar Organizing Region (NOR). By contrast, FISH with ribosomal probes only reveal size heteromorphism of rDNA sequences in E. calamita, suggesting that the differences observed after silver staining in B. spinosus and B. viridis should be attributed to differences in chromosomal condensation and/or gene activity rather than to differences in the copy number for ribosomal genes. Regarding telomeric repeats, E. calamita is the only species with interstitial telomeric sequences (ITS) located on centromeric regions, probably originated by accumulation of telomeric sequences in the centromeric heterochromatin. Finally, we analyzed the composition and distribution of repetitive sequences by genome in situ hybridization. These experiments reveal the accumulation of repetitive sequences in centromeric regions of the three species, although these sequences are not conserved when species from different genera are compared. Full article

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

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15 pages, 7528 KiB

Open AccessArticle

Karyotypes of Manatees: New Insights into Hybrid Formation (Trichechus inunguis × Trichechus m. manatus) in the Amazon Estuary

by Renata C. R. Noronha, Bruno R. R. Almeida, Monique C. S. Chagas, Flávia S. Tavares, Adauto L. Cardoso, Carlos E. M. C. Bastos, Natalia K. N. Silva, Alex G. C. M. Klautau, Fábia O. Luna, Fernanda L. N. Attademo, Danielle S. Lima, Luiz A. Sabioni, Maria I. C. Sampaio, Jairo Moura Oliveira, Luís Adriano Santos do Nascimento, Cesar Martins, Marcelo R. Vicari, Cleusa Y. Nagamachi and Julio C. Pieczarka

Genes 2022, 13(7), 1263; https://doi.org/10.3390/genes13071263 - 16 Jul 2022

Cited by 7 | Viewed by 2145

Abstract

Great efforts have been made to preserve manatees. Recently, a hybrid zone was described between Trichechus inunguis (TIN) and the Trichechus manatus manatus (TMM) in the Amazon estuary. Cytogenetic data on these sirenians are limited, despite being fundamental to understanding the hybridization/introgression dynamics [...] Read more.

Great efforts have been made to preserve manatees. Recently, a hybrid zone was described between Trichechus inunguis (TIN) and the Trichechus manatus manatus (TMM) in the Amazon estuary. Cytogenetic data on these sirenians are limited, despite being fundamental to understanding the hybridization/introgression dynamics and genomic organization in Trichechus. We analyzed the karyotype of TMM, TIN, and two hybrid specimens (“Poque” and “Vitor”) by classical and molecular cytogenetics. G-band analysis revealed that TMM (2n = 48) and TIN (2n = 56) diverge by at least six Robertsonian translocations and a pericentric inversion. Hybrids had 2n = 50, however, with Autosomal Fundamental Number (FNA) = 88 in “Poque” and FNA = 74 in “Vitor”, and chromosomal distinct pairs in heterozygous; additionally, “Vitor” exhibited heteromorphisms and chromosomes whose pairs could not be determined. The U2 snDNA and Histone H3 multi genes are distributed in small clusters along TIN and TMM chromosomes and have transposable Keno and Helitron elements (TEs) in their sequences. The different karyotypes observed among manatee hybrids may indicate that they represent different generations formed by crossing between fertile hybrids and TIN. On the other hand, it is also possible that all hybrids recorded represent F1 and the observed karyotype differences must result from mechanisms of elimination. Full article

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

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24 pages, 5029 KiB

Open AccessArticle

FISH Mapping of Telomeric and Non-Telomeric (AG₃T₃)₃ Reveal the Chromosome Numbers and Chromosome Rearrangements of 41 Woody Plants

by Xiaomei Luo, Zhoujian He, Juncheng Liu, Hongyi Wu and Xiao Gong

Genes 2022, 13(7), 1239; https://doi.org/10.3390/genes13071239 - 14 Jul 2022

Cited by 2 | Viewed by 1672

Abstract

Data for the chromosomal FISH mapping localization of (AG₃T₃)₃ are compiled for 37 species belonging 27 families; for 24 species and 14 families, this is the first such report. The chromosome number and length ranged from 14–136 and [...] Read more.

Data for the chromosomal FISH mapping localization of (AG₃T₃)₃ are compiled for 37 species belonging 27 families; for 24 species and 14 families, this is the first such report. The chromosome number and length ranged from 14–136 and 0.56–14.48 μm, respectively. A total of 23 woody plants presented chromosome length less than 3 μm, thus belonging to the small chromosome group. Telomeric signals were observed at each chromosome terminus in 38 plants (90.5%) and were absent at several chromosome termini in only four woody plants (9.5%). Non-telomeric signals were observed in the chromosomes of 23 plants (54.8%); in particular, abundant non-telomeric (AG₃T₃)₃ was obviously observed in Chimonanthus campanulatus. Telomeric signals outside of the chromosome were observed in 11 woody plants (26.2%). Overall, ten (AG₃T₃)₃ signal pattern types were determined, indicating the complex genome architecture of the 37 considered species. The variation in signal pattern was likely due to chromosome deletion, duplication, inversion, and translocation. In addition, large primary constriction was observed in some species, probably due to or leading to chromosome breakage and the formation of new chromosomes. The presented results will guide further research focused on determining the chromosome number and disclosing chromosome rearrangements of woody plants. Full article

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

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13 pages, 14857 KiB

Open AccessArticle

Cytogenetic Analysis of the Members of the Snake Genera Cylindrophis, Eryx, Python, and Tropidophis

by Tomáš Charvát, Barbora Augstenová, Daniel Frynta, Lukáš Kratochvíl and Michail Rovatsos

Genes 2022, 13(7), 1185; https://doi.org/10.3390/genes13071185 - 01 Jul 2022

Cited by 2 | Viewed by 1865

Abstract

The recent discovery of two independently evolved XX/XY sex determination systems in the snake genera Python and Boa sparked a new drive to study the evolution of sex chromosomes in poorly studied lineages of snakes, where female heterogamety was previously assumed. Therefore, we [...] Read more.

The recent discovery of two independently evolved XX/XY sex determination systems in the snake genera Python and Boa sparked a new drive to study the evolution of sex chromosomes in poorly studied lineages of snakes, where female heterogamety was previously assumed. Therefore, we examined seven species from the genera Eryx, Cylindrophis, Python, and Tropidophis by conventional and molecular cytogenetic methods. Despite the fact that these species have similar karyotypes in terms of chromosome number and morphology, we detected variability in the distribution of heterochromatin, telomeric repeats, and rDNA loci. Heterochromatic blocks were mainly detected in the centromeric regions in all species, although accumulations were detected in pericentromeric and telomeric regions in a few macrochromosomes in several of the studied species. All species show the expected topology of telomeric repeats at the edge of all chromosomes, with the exception of Eryx muelleri, where additional accumulations were detected in the centromeres of three pairs of macrochromosomes. The rDNA loci accumulate in one pair of microchromosomes in all Eryx species and in Cylindrophis ruffus, in one macrochromosome pair in Tropidophis melanurus and in two pairs of microchromosomes in Python regius. Sex-specific differences were not detected, suggesting that these species likely have homomorphic, poorly differentiated sex chromosomes. Full article

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

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16 pages, 5999 KiB

Open AccessArticle

Near-Hexaploid and Near-Tetraploid Aneuploid Progenies Derived from Backcrossing Tetraploid Parents Hibiscus syriacus × (H. syriacus × H. paramutabilis)

by Hsuan Chen and Ryan N. Contreras

Genes 2022, 13(6), 1022; https://doi.org/10.3390/genes13061022 - 06 Jun 2022

Cited by 2 | Viewed by 2254

Abstract

Hibiscus syriacus, azalea, is an important woody ornamental shrub planted throughout many temperate and subtropical regions of the world. However, flower size is smaller in this species than some of its relatives. To increase flower size, interspecific hybridization has been used, and [...] Read more.

Hibiscus syriacus, azalea, is an important woody ornamental shrub planted throughout many temperate and subtropical regions of the world. However, flower size is smaller in this species than some of its relatives. To increase flower size, interspecific hybridization has been used, and such hybrid cultivars are usually characterized by larger flowers, increased vigor, diverse leaf shapes, and reduced fertility. Our earlier studies have shown that these hybrid cultivars could backcross with H. syriacus when used as male parents. To understand the breeding potential of these hybrid cultivars, two popular tetraploid hybrid cultivars, ‘Lohengrin’ and ‘Resi’, were used as pollen parents to backcross several tetraploid H. syriacus cultivars. As a result, 28.76% and 64.4% of ‘Lohengrin’ and ‘Resi’ progenies exhibited larger flowers than both of their parents. Interestingly, 14 of 18 progenies of ‘Resi’ were putative hexaploids, whereas 19 tested ‘Lohengrin’ progenies were tetraploid. Because putative hexaploid progenies were only observed among progenies of ‘Resi’, this hybrid cultivar appears to produce unreduced gametes. In addition, among the 14 putative hexaploids derived from ‘Resi’, 11 had larger flowers than both of their parents and their tetraploid siblings (p < 0.05). The 45S rDNA and 5S rDNA locus segregation among those BC₁F₁ progenies was tested by fluorescent in situ hybridization (FISH), and the wide range of 45S rDNA signal numbers among siblings indicated that these aneuploids resulted from unequal segregation or chromosome rearrangement. Chromosome counting confirmed aneuploidy among BC₁F₁ progenies. Ploidy diversity and aneuploidy have been known to contribute to various elements of morphological diversity, such as larger flower size and reduced fertility, which are important in ornamental plant breeding. The present study demonstrated the breeding potential of interspecific Hibiscus cultivars for increasing ploidy level and flower size. Full article

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

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18 pages, 2918 KiB

Open AccessArticle

Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Prunus Subgenus Cerasus and Its Relatives

by Lei Wang, Yan Wang, Jing Zhang, Yan Feng, Qing Chen, Zhen-Shan Liu, Cong-Li Liu, Wen He, Hao Wang, Shao-Feng Yang, Yong Zhang, Ya Luo, Hao-Ru Tang and Xiao-Rong Wang

Genes 2022, 13(4), 641; https://doi.org/10.3390/genes13040641 - 02 Apr 2022

Cited by 9 | Viewed by 2512

Abstract

The subgenus Cerasus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the [...] Read more.

The subgenus Cerasus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the variation in their genomes remains poorly understood. This work conducted a comprehensive repetitive sequence identification across the draft genomes of eight taxa of the genus Prunus, including four of the Prunus subgenus Cerasus (Prunus pseudocerasus, P. avium, P. yedoensis and P. × yedoensis) as well as congeneric species (Prunus salicina, P. armeniaca, P. dulcis and P. persica). Annotation results showed high proportions of transposable elements in their genomes, ranging from 52.28% (P. armeniaca) to 61.86% (P. pseudocerasus). The most notable differences in the contents of long terminal repeat retrotransposons (LTR-RTs) and tandem repeats (TRs) were confirmed with de novo identification based on the structure of each genome, which significantly contributed to their genome size variation, especially in P. avium and P.salicina. Sequence comparisons showed many similar LTR-RTs closely related to their phylogenetic relationships, and a highly similar monomer unit of the TR sequence was conserved among species. Additionally, the predicted centromere-associated sequence was located in centromeric regions with FISH in the 12 taxa of Prunus. It presented significantly different signal intensities, even within the diverse interindividual phenotypes for Prunus tomentosa. This study provides insight into the LTR-RT and TR variation within Prunus and increases our knowledge about its role in genome evolution. Full article

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

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14 pages, 3279 KiB

Open AccessArticle

Aphids and Ants, Mutualistic Species, Share a Mariner Element with an Unusual Location on Aphid Chromosomes

by Jesús Vela, Eugenia E. Montiel, Pablo Mora, Pedro Lorite and Teresa Palomeque

Genes 2021, 12(12), 1966; https://doi.org/10.3390/genes12121966 - 09 Dec 2021

Cited by 7 | Viewed by 2843

Abstract

Aphids (Hemiptera, Aphididae) are small phytophagous insects. The aim of this study was to determine if the mariner elements found in the ant genomes are also present in Aphis fabae and Aphis hederae genomes and the possible existence of horizontal transfer events. Aphids [...] Read more.

Aphids (Hemiptera, Aphididae) are small phytophagous insects. The aim of this study was to determine if the mariner elements found in the ant genomes are also present in Aphis fabae and Aphis hederae genomes and the possible existence of horizontal transfer events. Aphids maintain a relationship of mutualism with the ants. The close contact between these insects could favour horizontal transfer events of transposable elements. Myrmar mariner element isolated from Myrmica ruginodis and Tapinoma ibericum ants have also been found in the two Aphis species: A. fabae and A. hederae (Afabmar-Mr and Ahedmar-Mr elements). Besides, Afabmar-Mr could be an active transposon. Myrmar-like elements are also present in other insect species as well as in one Crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the existence of horizontal transfer. Most aphids have 2n = 8 with a XX-X0 sex determination system. Their complicated life cycle is mostly parthenogenetic with sexual individuals only in autumn. The production of X0 males, originated by XX females which produce only spermatozoa with one X chromosome, must necessarily occur through specialized cytogenetic and molecular mechanisms which are not entirely known. In both aphid species, the mariner elements are located on all chromosomes, including the X chromosomes. However, on the two X chromosomes, no positive signals are detected in their small DAPI-negative telomere regions. The rDNA sites are located, as in the majority of Aphids species, on one of the telomere regions of each X chromosome. The hybridization patterns obtained by double FISH demonstrate that Afabmar-Mr and Ahedmar-Mr elements do not hybridize at the rDNA sites of their host species. Possible causes for the absence of these transposons in the rDNA genes are discussed, probably related with the X chromosome biology. Full article

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

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12 pages, 1346 KiB

Open AccessArticle

Molecular Cytogenetic and Y Copy Number Analysis of a Reciprocal ECAY-ECA13 Translocation in a Stallion with Complete Meiotic Arrest

by Caitlin Castaneda, Agustin J. Ruiz, Ahmed Tibary and Terje Raudsepp

Genes 2021, 12(12), 1892; https://doi.org/10.3390/genes12121892 - 26 Nov 2021

Cited by 1 | Viewed by 1599

Abstract

We present a detailed molecular cytogenetic analysis of a reciprocal translocation between horse (ECA) chromosomes Y and 13 in a Friesian stallion with complete meiotic arrest and azoospermia. We use dual-color fluorescence in situ hybridization with select ECAY and ECA13 markers and show [...] Read more.

We present a detailed molecular cytogenetic analysis of a reciprocal translocation between horse (ECA) chromosomes Y and 13 in a Friesian stallion with complete meiotic arrest and azoospermia. We use dual-color fluorescence in situ hybridization with select ECAY and ECA13 markers and show that the translocation breakpoint in ECAY is in the multicopy region and in ECA13, at the centromere. One resulting derivative chromosome, Y;13p, comprises of ECAY heterochromatin (ETSTY7 array), a small single copy and partial Y multicopy region, and ECA13p. Another derivative chromosome 13q;Y comprises of ECA13q and most of the single copy ECAY, the pseudoautosomal region and a small part of the Y multicopy region. A copy number (CN) analysis of select ECAY multicopy genes shows that the Friesian stallion has significantly (p < 0.05) reduced CNs of TSPY, ETSTY1, and ETSTY5, suggesting that the translocation may not be completely balanced, and genetic material is lost. We discuss likely meiotic behavior of abnormal chromosomes and theorize about the possible effect of the aberration on Y regulation and the progression of meiosis. The study adds a unique case to equine clinical cytogenetics and contributes to understanding the role of the Y chromosome in male meiosis. Full article

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

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Review

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12 pages, 989 KiB

Open AccessReview

Comparative Karyotype Analysis of Parasitoid Hymenoptera (Insecta): Major Approaches, Techniques, and Results

by Vladimir E. Gokhman

Genes 2022, 13(5), 751; https://doi.org/10.3390/genes13050751 - 25 Apr 2022

Cited by 4 | Viewed by 3846

Abstract

A comprehensive review of main approaches, techniques and results of the chromosome study of parasitic wasps is given. In this group, the haploid chromosome number ranges from n = 3 to 23. Distribution of parasitic wasp species by the chromosome number is bimodal, [...] Read more.

A comprehensive review of main approaches, techniques and results of the chromosome study of parasitic wasps is given. In this group, the haploid chromosome number ranges from n = 3 to 23. Distribution of parasitic wasp species by the chromosome number is bimodal, with two obvious modes at n = 6 and 11. Karyotype analysis based on routinely stained preparations of mitotic chromosomes can be used to identify members of taxonomically complicated parasitoid taxa and to distinguish between them. Morphometric study effectively reveals subtle differences between similar chromosome sets of parasitic wasps. If combined with meiotic analysis and/or cytometric data, information on mitotic karyotypes can highlight pathways of the genome evolution in certain parasitoid taxa. C- and AgNOR-banding as well as staining with base-specific fluorochromes detected important interspecific differences within several groups of parasitic wasps. Fluorescence in situ hybridization (FISH) is successfully used for physical mapping of various DNA sequences on parasitoid chromosomes. These techniques demonstrate that heterochromatic segments are usually restricted to pericentromeric regions of chromosomes of parasitic wasps. Haploid karyotypes carrying one or two nucleolus organizing regions (NORs) are the most frequent among parasitoid Hymenoptera. In combination with chromosome microdissection, FISH could become a powerful tool exploring the genome evolution of parasitic wasps. Perspectives of the comparative cytogenetic study of parasitoid Hymenoptera are outlined. Full article

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

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