Fish Cytogenetics: Present and Future

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 January 2021) | Viewed by 95583

Special Issue Editor


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Guest Editor
Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, via Borelli 50, 00161 Roma, Italy
Interests: fish; phylogenetics; conservation biology; population genetics; cytogenetics; evolutionary biology

Special Issue Information

Dear Colleagues,

Fishes represent about half of vertebrate species and are characterized by high diversity, that is revealed by the variety of the habitats they occupy. The genome of fishes is however poorly studied compared to other vertebrates, or at least not proportionally to the species richness of this group. In the last decade new sibling (or cryptic) species were disclosed thanks to cytogentic analysis, and karyotypes of rare species, from remote geographic areas, were described. In addition the use of molecular cytogenetic through chromosome painting, complete genome hybridization and in situ hibridization with repeated gene families opened new scenarios in Teleost cytogenetics. New original data have allowed the comparison of genomes and karyotypes and thus the reconstruction of the evolutionary paths of karyotypes and phylogenetic relationships within fish families. In addition, the advance of next generation sequences has led to an initial scaffold of the genome, with specific sequences anchored to specific chromosomes, in some economically important species.

This issue will provide a collection of review articles and new original researches in cytogenetics of teleost species that cover different geographic area and habitat and will give a picture of what is going on in this promising field.

Dr. Anna Rita Rossi
Guest Editor

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Keywords

  • Repetitive sequence
  • Heterochromatin distribution
  • Ribosomal genes
  • Telomeres
  • Genome evolution
  • CGH
  • FISH
  • Sex chromosomes
  • B chromosome

Published Papers (12 papers)

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Editorial

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5 pages, 203 KiB  
Editorial
Fish Cytogenetics: Present and Future
by Anna Rita Rossi
Genes 2021, 12(7), 983; https://doi.org/10.3390/genes12070983 - 28 Jun 2021
Cited by 4 | Viewed by 1883
Abstract
Fish is the most species-rich class of vertebrates, including a number of species that correspond to about half of the total vertebrates [...] Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)

Research

Jump to: Editorial

16 pages, 1301 KiB  
Article
Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution
by Veronika Borůvková, W. Mike Howell, Dominik Matoulek and Radka Symonová
Genes 2021, 12(2), 312; https://doi.org/10.3390/genes12020312 - 22 Feb 2021
Cited by 8 | Viewed by 2821
Abstract
Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the [...] Read more.
Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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15 pages, 4578 KiB  
Article
GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional Cytogenomics
by Dominik Matoulek, Veronika Borůvková, Konrad Ocalewicz and Radka Symonová
Genes 2021, 12(1), 50; https://doi.org/10.3390/genes12010050 - 31 Dec 2020
Cited by 10 | Viewed by 3070
Abstract
The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does [...] Read more.
The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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12 pages, 1762 KiB  
Article
A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858)
by Manuel A. Merlo, Silvia Portela-Bens, María E. Rodríguez, Aglaya García-Angulo, Ismael Cross, Alberto Arias-Pérez, Emilio García and Laureana Rebordinos
Genes 2021, 12(1), 49; https://doi.org/10.3390/genes12010049 - 31 Dec 2020
Cited by 5 | Viewed by 3245
Abstract
Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in [...] Read more.
Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species’ chromosome dynamics and evolution. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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13 pages, 1949 KiB  
Article
Latitudinal Cline in Chromosome Numbers of Ice Cod A. glacialis (Gadidae) from Northeast Greenland
by Laura Ghigliotti, Jørgen S. Christiansen, Erica Carlig, Davide Di Blasi and Eva Pisano
Genes 2020, 11(12), 1515; https://doi.org/10.3390/genes11121515 - 18 Dec 2020
Cited by 5 | Viewed by 2209
Abstract
The ice cod Arctogadus glacialis (Peters, 1872) is one of the few fish species endemic to the Arctic. With a circumpolar distribution, the species is confined to the fjords and shelves of the Arctic seas. Biological information on A. glacialis is scarce, with [...] Read more.
The ice cod Arctogadus glacialis (Peters, 1872) is one of the few fish species endemic to the Arctic. With a circumpolar distribution, the species is confined to the fjords and shelves of the Arctic seas. Biological information on A. glacialis is scarce, with genomic information restricted to microsatellites. Within the frame of the TUNU-Programme: Arctic Ocean Fishes—Diversity, Adaptation and Conservation, we studied A. glacialis at the chromosomal level to explore fish diversity and evolutionary aspects. The analysis of over 50 individuals from the Northeast Greenland fjords between latitudes 71°09′ N and 76°42′ N revealed a remarkable intraspecific diversity epitomized by chromosome numbers spanning from 28 to 33, the occurrence of putative B chromosomes, and diversified patterns of distribution of heterochromatin and rDNAs. The number of B chromosomes followed a latitudinal gradient from 0–2 in the north to 2–5 in the south. Considering the benthic and rather stationary life history of this species, the observed chromosomal differences might have arisen independently, possibly driven and/or fostered by the dynamics of repetitive sequences, and are being fixed in relatively isolated fjord populations. The resulting latitudinal cline we observe today might have repercussions on the fate of local populations facing the ongoing climate-driven environmental changes. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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19 pages, 2260 KiB  
Article
Present and Future Salmonid Cytogenetics
by Muhammet Gaffaroglu, Zuzana Majtánová, Radka Symonová, Šárka Pelikánová, Sevgi Unal, Zdeněk Lajbner and Petr Ráb
Genes 2020, 11(12), 1462; https://doi.org/10.3390/genes11121462 - 6 Dec 2020
Cited by 12 | Viewed by 2942
Abstract
Salmonids are extremely important economically and scientifically; therefore, dynamic developments in their research have occurred and will continue occurring in the future. At the same time, their complex phylogeny and taxonomy are challenging for traditional approaches in research. Here, we first provide discoveries [...] Read more.
Salmonids are extremely important economically and scientifically; therefore, dynamic developments in their research have occurred and will continue occurring in the future. At the same time, their complex phylogeny and taxonomy are challenging for traditional approaches in research. Here, we first provide discoveries regarding the hitherto completely unknown cytogenetic characteristics of the Anatolian endemic flathead trout, Salmo platycephalus, and summarize the presently known, albeit highly complicated, situation in the genus Salmo. Secondly, by outlining future directions of salmonid cytogenomics, we have produced a prototypical virtual karyotype of Salmo trutta, the closest relative of S. platycephalus. This production is now possible thanks to the high-quality genome assembled to the chromosome level in S. trutta via soft-masking, including a direct labelling of repetitive sequences along the chromosome sequence. Repetitive sequences were crucial for traditional fish cytogenetics and hence should also be utilized in fish cytogenomics. As such virtual karyotypes become increasingly available in the very near future, it is necessary to integrate both present and future approaches to maximize their respective benefits. Finally, we show how the presumably repetitive sequences in salmonids can change the understanding of the overall relationship between genome size and G+C content, creating another outstanding question in salmonid cytogenomics waiting to be resolved. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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12 pages, 1991 KiB  
Article
Chromosome Mapping of 5S Ribosomal Genes in Indo-Pacific and Atlantic Muraenidae: Comparative Analysis by Dual Colour Fluorescence In Situ Hybridisation
by Elisabetta Coluccia, Federica Deidda, Cinzia Lobina, Riccardo Melis, Cristina Porcu, Blondine Agus and Susanna Salvadori
Genes 2020, 11(11), 1319; https://doi.org/10.3390/genes11111319 - 6 Nov 2020
Cited by 2 | Viewed by 2117
Abstract
The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending [...] Read more.
The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending the karyology of this fish group, the chromosomal mapping of the 5S ribosomal gene family was performed on seven species belonging to the genera Muraena and Gymnothorax from both the Atlantic and Pacific oceans. Fluorescence in situ hybridisation (FISH) experiments were realized using species-specific 5S rDNA probes; in addition, two-colour FISH was performed to investigate the possible association with the 45S ribosomal gene family. Multiple 5S rDNA clusters, located either in species-specific or in possibly homoeologous chromosomes, were found. Either a syntenic or different chromosomal location of the two ribosomal genes was detected. Our results revealed variability in the number and location of 5S rDNA clusters and confirmed a substantial conservation of the number and location of the 45S rDNA. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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13 pages, 3214 KiB  
Article
B Chromosomes and Cytogenetic Characteristics of the Common Nase Chondrostoma nasus (Linnaeus, 1758)
by Alicja Boroń, Anna Grabowska, Aneta Spóz and Anna Przybył
Genes 2020, 11(11), 1317; https://doi.org/10.3390/genes11111317 - 6 Nov 2020
Cited by 3 | Viewed by 2280
Abstract
Supernumerary B chromosomes (Bs) are very promising structures, among others, in that they are an additional genomic compartment for evolution. In this study, we tested the presence and frequency of B chromosomes and performed the first cytogenetic examination of the common nase ( [...] Read more.
Supernumerary B chromosomes (Bs) are very promising structures, among others, in that they are an additional genomic compartment for evolution. In this study, we tested the presence and frequency of B chromosomes and performed the first cytogenetic examination of the common nase (Chondrostoma nasus). We investigated the individuals from two populations in the Vistula River basin, in Poland, according to the chromosomal distribution of the C-bands and silver nucleolar organizer regions (Ag-NORs), using sequential staining with AgNO3 and chromomycin A3 (CMA3). Furthermore, we analyzed the chromosomal localization of two rDNA families (45S and 5S rDNA) using fluorescence in situ hybridization (FISH) with rDNA probes. Chondrostoma nasus individuals showed a standard (A) chromosome set consisting of 2n = 50: 12 metacentric, 32 submetacentric, and 6 acrocentric chromosomes (NF = 94). Fourteen out of the 20 analyzed individuals showed 1–2 mitotically unstable submetacentric B chromosomes of different sizes. Six of them, in 14.1% of the analyzed metaphase plates, had a single, medium-sized submetacentric B (Bsm) chromosome (2n = 51) with a heterochromatic block located in its pericentromeric region. The other seven individuals possessed a Bsm (2n = 51) in 19.4% of the analyzed metaphase plates, and a second Bsm chromosome (2n = 52), the smallest in the set, in 15.5% of metaphase plates, whereas one female was characterized by both Bsm chromosomes (2n = 52) in 14.3% of the analyzed metaphase plates. AgNORs, GC-rich DNA sites, and 28S rDNA hybridization sites were observed in the short arms of two submetacentric chromosome pairs of A set. The constitutive heterochromatin was visible as C bands in the centromeric regions of almost all Chondrostoma nasus chromosomes and in the pericentromeric region of several chromosome pairs. Two 5S rDNA hybridization sites in the pericentromeric position of the largest acrocentric chromosome pair were observed, whereas two other such sites in co-localization on a smaller pair of NOR chromosomes indicate a species-specific character. The results herein broaden our knowledge in the field of B chromosome distribution and molecular cytogenetics of Chondrostoma nasus: a freshwater species from the Leuciscidae family. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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15 pages, 3807 KiB  
Article
Multiple Sex Chromosomes and Evolutionary Relationships in Amazonian Catfishes: The Outstanding Model of the Genus Harttia (Siluriformes: Loricariidae)
by Francisco de M. C. Sassi, Geize A. Deon, Orlando Moreira-Filho, Marcelo R. Vicari, Luiz A. C. Bertollo, Thomas Liehr, Ezequiel Aguiar de Oliveira and Marcelo B. Cioffi
Genes 2020, 11(10), 1179; https://doi.org/10.3390/genes11101179 - 10 Oct 2020
Cited by 19 | Viewed by 3100
Abstract
The armored Harttia catfishes present great species diversity and remarkable cytogenetic variation, including different sex chromosome systems. Here we analyzed three new species, H. duriventris, H. villasboas and H. rondoni, using both conventional and molecular cytogenetic techniques (Giemsa-staining and C-banding), including [...] Read more.
The armored Harttia catfishes present great species diversity and remarkable cytogenetic variation, including different sex chromosome systems. Here we analyzed three new species, H. duriventris, H. villasboas and H. rondoni, using both conventional and molecular cytogenetic techniques (Giemsa-staining and C-banding), including the mapping of repetitive DNAs using fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) experiments. Both H. duriventris and H. villasboas have 2n = ♀56/♂55 chromosomes, and an X1X1X2X2 /X1X2Y sex chromosome system, while a proto or neo-XY system is proposed for H. rondoni (2n = 54♀♂). Single motifs of 5S and 18S rDNA occur in all three species, with the latter being also mapped in the sex chromosomes. The results confirm the general evolutionary trend that has been noticed for the genus: an extensive variation on their chromosome number, single sites of rDNA sequences and the occurrence of multiple sex chromosomes. Comparative genomic analyses with another congeneric species, H. punctata, reveal that the X1X2Y sex chromosomes of these species share the genomic contents, indicating a probable common origin. The remarkable karyotypic variation, including sex chromosomes systems, makes Harttia a suitable model for evolutionary studies focusing on karyotype differentiation and sex chromosome evolution among lower vertebrates. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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12 pages, 2501 KiB  
Article
Telomere Dynamics in the Diploid and Triploid Rainbow Trout (Oncorhynchus mykiss) Assessed by Q-FISH Analysis
by Ligia Panasiak, Stefan Dobosz and Konrad Ocalewicz
Genes 2020, 11(7), 786; https://doi.org/10.3390/genes11070786 - 13 Jul 2020
Cited by 13 | Viewed by 3143
Abstract
Changes of telomere length with age were assessed in diploid and triploid rainbow trout (Oncorhynchus mykiss) females in the cross-sectional study using Q-FISH technique. Triploid trout as sterile do not invest an energy in gametogenesis and continue to grow, whereas fertile diploid [...] Read more.
Changes of telomere length with age were assessed in diploid and triploid rainbow trout (Oncorhynchus mykiss) females in the cross-sectional study using Q-FISH technique. Triploid trout as sterile do not invest an energy in gametogenesis and continue to grow, whereas fertile diploid individuals suffer from declines in growth and survival during sexual maturation. However, triploid and diploid specimens exhibited similar patterns of telomere dynamics. Telomere length in the embryos, larvae and one-year-old juveniles did not change significantly. In the second year after hatching, subadults exhibited substantially shortened telomeres, while significant increase of the telomere length was reported in the three-year-old adults. On the other hand, correlation between telomere length and body size was observed in the triploid, but not in the diploid rainbow trout. Telomere shortening observed in two-year-old subadults may have been associated with the premature period of the fast growth in rainbow trout. Similar pattern of the telomere dynamics reported in the fertile diploids and sterile triploids indicated processes related to reproduction did not affect telomere dynamics in this species. Unexpected increase of the telomere length reported during the third year of life confirmed that in rainbow trout telomeric DNA shortens and lengthens, depending on the developmental stage. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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17 pages, 2875 KiB  
Article
Hybridization of Russian Sturgeon (Acipenser gueldenstaedtii, Brandt and Ratzeberg, 1833) and American Paddlefish (Polyodon spathula, Walbaum 1792) and Evaluation of Their Progeny
by Jenő Káldy, Attila Mozsár, Gyöngyvér Fazekas, Móni Farkas, Dorottya Lilla Fazekas, Georgina Lea Fazekas, Katalin Goda, Zsuzsanna Gyöngy, Balázs Kovács, Kenneth Semmens, Miklós Bercsényi, Mariann Molnár and Eszter Patakiné Várkonyi
Genes 2020, 11(7), 753; https://doi.org/10.3390/genes11070753 - 6 Jul 2020
Cited by 24 | Viewed by 61897
Abstract
Two species from the families Acipenseridae and Polyodontidae, Russian sturgeon (Acipenser gueldenstaedtii, Brandt and Ratzeberg, 1833; functional tetraploid) and American paddlefish (Polyodon spathula, Walbaum 1792, functional diploid) were hybridized. The hybridization was repeated using eggs from three sturgeon and [...] Read more.
Two species from the families Acipenseridae and Polyodontidae, Russian sturgeon (Acipenser gueldenstaedtii, Brandt and Ratzeberg, 1833; functional tetraploid) and American paddlefish (Polyodon spathula, Walbaum 1792, functional diploid) were hybridized. The hybridization was repeated using eggs from three sturgeon and sperm from four paddlefish individuals. Survival in all hybrid family groups ranged from 62% to 74% 30 days after hatching. This was the first successful hybridization between these two species and between members of the family Acipenseridae and Polyodontidae. Flow cytometry and chromosome analysis revealed two ploidy levels in hybrids. The chromosome numbers of the hybrids ranged between 156–184 and 300–310, in “functional” triploids and “functional” pentaploids, respectively. The hybrid origin and the ploidy levels were also confirmed by microsatellite analyses. In hybrids, the size and the number of dorsal and ventral scutes correlated with the ploidy levels as well as with the calculated ratio of the maternal and paternal chromosome sets. An extra haploid cell lineage was found in three hybrid individuals irrespective of the ploidy level, suggesting polyspermy. Although the growth performance showed high variance in hybrids (mean: 1.2 kg, SD: 0.55), many individuals reached a size of approximately 1 kg by the age of one year under intensive rearing conditions. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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12 pages, 1336 KiB  
Article
Sex Chromosomes and Internal Telomeric Sequences in Dormitator latifrons (Richardson 1844) (Eleotridae: Eleotrinae): An Insight into Their Origin in the Genus
by Fabilene Gomes Paim, Mauro Nirchio, Claudio Oliveira and Anna Rita Rossi
Genes 2020, 11(6), 659; https://doi.org/10.3390/genes11060659 - 17 Jun 2020
Cited by 5 | Viewed by 5158
Abstract
The freshwater fish species Dormitator latifrons, commonly named the Pacific fat sleeper, is an important food resource in CentralSouth America, yet almost no genetic information on it is available. A cytogenetic analysis of this species was undertaken by standard and molecular techniques [...] Read more.
The freshwater fish species Dormitator latifrons, commonly named the Pacific fat sleeper, is an important food resource in CentralSouth America, yet almost no genetic information on it is available. A cytogenetic analysis of this species was undertaken by standard and molecular techniques (chromosomal mapping of 18S rDNA, 5S rDNA, and telomeric repeats), aiming to describe the karyotype features, verify the presence of sex chromosomes described in congeneric species, and make inferences on chromosome evolution in the genus. The karyotype (2n = 46) is mainly composed of metacentric and submetacentic chromosomes, with nucleolar organizer regions (NORs) localized on the short arms of submetacentric pair 10. The presence of XX/XY sex chromosomes was observed, with the X chromosome carrying the 5S rDNA sequences. These heterochromosomes likely appeared before 1 million years ago, since they are shared with another derived Dormitator species (Dormitator maculatus) distributed in the Western Atlantic. Telomeric repeats hybridize to the terminal portions of almost all chromosomes; additional interstitial sites are present in the centromeric region, suggesting pericentromeric inversions as the main rearrangement mechanisms that has driven karyotypic evolution in the genus. The data provided here contribute to improving the cytogenetics knowledge of D. latifrons, offering basic information that could be useful in aquaculture farming of this neotropical fish. Full article
(This article belongs to the Special Issue Fish Cytogenetics: Present and Future)
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