Comparative cytogenetic analyses in Ancistrus species (Siluriformes: Loricariidae)

ABSTRACT Ancistrus is a specious genus of armored catfishes that has been extensively used for cytogenetic studies in the last 17 years. A comparison of the extensive karyotypic plasticity within this genus is presented with new cytogenetic analysis for Ancistrus cf. multispinis and Ancistrus aguaboensis. This study aims to improve our understanding of chromosomal evolution associated with changes in the diploid number (2n) and the dispersion of ribosomal DNAs (rDNAs) within Ancistrus. Ancistrus cf. multispinis and A. aguaboensis exhibit 2n of 52 and 50 chromosomes, respectively. Given that A. cf. multispinis shares a 2n = 52 also found in Pterygoplichthyini, the sister group for Ancistrini, a Robertsonian (Rb) fusion event is proposed for the 2n reduction in A. aguaboensis. 5S rDNAs pseudogenes sites have already been associated with Rb fusion in Ancistrus and our analysis suggests that the 2n reduction in A. aguaboensis was triggered by double strand breaks (DSBs) and chromosomal rearrangements at 5S rDNA sites. The presence of evolutionary breakpoint regions (EBRs) into rDNA cluster is proposed to explain part of the Rb fusion in Ancistrus. Cytogenetic data presented extends the diversity already documented in Ancistrus to further understand the role of chromosomal rearrangements in the diversification of Ancistrini.

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Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution in Cucumis

Genome ◽

10.1139/gen-2015-0207 ◽

2016 ◽

Vol 59 (7) ◽

pp. 449-457 ◽

Cited By ~ 15

Author(s):

Zhen-Tao Zhang ◽

Shu-Qiong Yang ◽

Zi-Ang Li ◽

Yun-Xia Zhang ◽

Yun-Zhu Wang ◽

...

Keyword(s):

Chromosomal Localization ◽

5S Rdna ◽

Chromosome Analysis ◽

45S Rdna ◽

Evolutionary Patterns ◽

Site Number ◽

Rdna Sites ◽

Wild Accessions ◽

Ribosomal Dnas

Ribosomal DNAs are useful cytogenetic markers for chromosome analysis. Studies investigating site numbers and distributions of rDNAs have provided important information for elucidating genome organization and chromosomal relationships of many species by fluorescence in situ hybridization. But relevant studies are scarce for species of the genus Cucumis, especially in wild species. In the present study, FISH was conducted to investigate the organization of 45S and 5S rDNA among 20 Cucumis accessions, including cultivars and wild accessions. Our results showed that the number of 45S rDNA sites varied from one to five pairs in different accessions, and most of these sites are located at the terminal regions of chromosomes. Interestingly, up to five pairs of 45S rDNA sites were observed in C. sativus var. sativus, the species which has the lowest chromosome number, i.e., 2n = 14. Only one pair of 5S rDNA sites was detected in all accessions, except for C. heptadactylus, C. sp, and C. spp that had two pairs of 5S rDNA sites. The distributions of 5S rDNA sites showed more variation than 45S rDNA sites. The phylogenetic analysis in this study showed that 45S and 5S rDNA have contrasting evolutionary patterns. We find that 5S rDNA has a polyploidization-related tendency towards the terminal location from an interstitial location but maintains a conserved site number, whereas the 45S rDNA showed a trend of increasing site number but a relatively conserved location.

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Cytogenetic analysis of the 18S, 5S rDNA and B chromosome of Iheringichthys labrosus (Lütken, 1874) (Siluriformes, Pimelodidae)

Brazilian Journal of Biology ◽

10.1590/s1519-69842010000300021 ◽

2010 ◽

Vol 70 (3) ◽

pp. 631-636 ◽

Cited By ~ 10

Author(s):

RA. Carvalho ◽

A. Laudicina ◽

L. Giuliano-Caetano ◽

IC. Martins-Santos ◽

AL. Dias

Keyword(s):

Chromosome Pair ◽

Base Composition ◽

5S Rdna ◽

B Chromosome ◽

Positive Staining ◽

Strong Fluorescence ◽

Terminal Position ◽

Cytogenetic Analyses ◽

Iheringichthys Labrosus ◽

Ribosomal Dnas

Cytogenetic analyses of the location of 18S and 5S ribosomal DNAs, and the base composition of B chromosomes of Iheringichthys labrosus from Tibagi River, Paraná, Brazil, are provided. AgNORs were observed in the terminal position on the long arm of a subtelocentric chromosome pair. CMA3-positive staining was observed in some chromosomes, which besides being associated with NORs, were all DAPI-negative. Chromosome B showed a strong fluorescence with CMA3. The concomitant use of 18S and 5S rDNA probes using the FISH technique revealed 18S ribosomal cistrons in a pair of subtelocentric chromosomes, on the long arm in the terminal position, coinciding with the AgNOR. The 5S sites were found in another subtelocentric pair, on the long arm in the interstitial region, near the centromere. The findings of the present study suggest that, although there are some more conserved cytogenetic characteristics, populations of I. labrosus may show their own characteristics.

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Genome-Wide Amplifications Caused by Chromosomal Rearrangements Play a Major Role in the Adaptive Evolution of Natural Yeast

Genetics ◽

10.1093/genetics/165.4.1745 ◽

2003 ◽

Vol 165 (4) ◽

pp. 1745-1759 ◽

Cited By ~ 1

Author(s):

Juan J Infante ◽

Kenneth M Dombek ◽

Laureana Rebordinos ◽

Jesús M Cantoral ◽

Elton T Young

Keyword(s):

Adaptive Evolution ◽

Chromosomal Rearrangements ◽

Sexual Isolation ◽

Chromosomal Evolution ◽

Double Strand Breaks ◽

Chromosomal Dna ◽

Strand Breaks ◽

Yeast Strains ◽

Gross Chromosomal Rearrangements ◽

Flor Yeast

Abstract The relative importance of gross chromosomal rearrangements to adaptive evolution has not been precisely defined. The Saccharomyces cerevisiae flor yeast strains offer significant advantages for the study of molecular evolution since they have recently evolved to a high degree of specialization in a very restrictive environment. Using DNA microarray technology, we have compared the genomes of two prominent variants of S. cerevisiae flor yeast strains. The strains differ from one another in the DNA copy number of 116 genomic regions that comprise 38% of the genome. In most cases, these regions are amplicons flanked by repeated sequences or other recombination hotspots previously described as regions where double-strand breaks occur. The presence of genes that confer specific characteristics to the flor yeast within the amplicons supports the role of chromosomal rearrangements as a major mechanism of adaptive evolution in S. cerevisiae. We propose that nonallelic interactions are enhanced by ethanol- and acetaldehyde-induced double-strand breaks in the chromosomal DNA, which are repaired by pathways that yield gross chromosomal rearrangements. This mechanism of chromosomal evolution could also account for the sexual isolation shown among the flor yeast.

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

International Journal of Molecular Sciences ◽

10.3390/ijms20143545 ◽

2019 ◽

Vol 20 (14) ◽

pp. 3545

Author(s):

Sukhonthip Ditcharoen ◽

Luiz Antonio Carlos Bertollo ◽

Petr Ráb ◽

Eva Hnátková ◽

Wagner Franco Molina ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Chromosomal Rearrangements ◽

5S Rdna ◽

Comparative Genomic ◽

Molecular Cytogenetic ◽

Rdna Sites ◽

Genomic Divergence ◽

Fish Chromosomes ◽

Dna Elements ◽

Repetitive Dna Elements

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.

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Chromosomal Mapping of Repeat DNA in Bergiaria westermanni (Pimelodidae, Siluriformes): Localization of 45S rDNA in B Chromosomes

Cytogenetic and Genome Research ◽

10.1159/000487652 ◽

2018 ◽

Vol 154 (2) ◽

pp. 99-106 ◽

Cited By ~ 5

Author(s):

Geovana C. Malimpensa ◽

Josiane B. Traldi ◽

Danyelle Toyama ◽

Flávio Henrique-Silva ◽

Marcelo R. Vicari ◽

...

Keyword(s):

Chromosomal Rearrangements ◽

Indirect Evidence ◽

5S Rdna ◽

B Chromosomes ◽

Chromosomal Mapping ◽

Interindividual Variation ◽

Rrna Genes ◽

45S Rdna ◽

Rdna Sites ◽

Repeat Dna

The occurrence of repetitive DNA in autosomes and B chromosomes of Bergiaria westermanni was examined using conventional and molecular cytogenetic techniques. This species exhibited 2n = 56 chromosomes, with intra- and interindividual variation in the number of heterochromatic B chromosomes (from 0 to 4). The 5S rDNA was localized in pairs 1 and 5, and histone probes (H1, H3, and H4) and U2 small nuclear RNA were syntenic with 5S rDNA in pair 5. Histone sequences were also located in chromosome pair 14. The (GATA)n sequence was dispersed throughout the autosomes and B chromosomes, with clusters (microsatellite accumulation) in some chromosome regions. The telomeric probe revealed no signs of chromosomal rearrangements in the genome of B. westermanni. The 45S rDNA sites were detected in the terminal region of pair 27; these sites corresponded to a GC-rich heterochromatin block. In addition, 3 of the 4 B chromosomes also contained 45S rDNA copies. Silver nitrate staining in interphase nuclei provided indirect evidence of the expression of these rRNA genes in B chromosomes, indicating the probable origin of these elements. This report shows plasticity in the chromosomal localization of repeat DNA in B. westermanni and features a discussion of genomic diversification.

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Cytogenetic characterization, rDNA mapping and quantification of the nuclear DNA content in Seriolella violacea Guichenot, 1848 (Perciformes, Centrolophidae)

Comparative Cytogenetics ◽

10.3897/compcytogen.v14i3.53087 ◽

2020 ◽

Vol 14 (3) ◽

pp. 319-328

Author(s):

Cristian Araya-Jaime ◽

Claudio Palma-Rojas ◽

Elisabeth Von Brand ◽

Alfonso Silva

Keyword(s):

Dna Content ◽

Nuclear Dna ◽

Molecular Cytogenetics ◽

Fish Fauna ◽

Nuclear Dna Content ◽

5S Rdna ◽

Chromosomal Evolution ◽

Rdna Sequences ◽

Rdna Sites ◽

Karyotype Structure

Seriolella violacea Guichenot, 1848 is an important component of the fish fauna of the Chilean coast and is of great economic interest. Cytogenetic information for the family Centrolophidae is lacking and the genomic size of five of the twenty-eight species described for this family are is barely known. This study aimed to describe for the first time the karyotype structure via classical and molecular cytogenetics analysis with the goal of identifying the constitutive heterochromatin distribution, chromosome organization of rDNA sequences and quantification of nuclear DNA content. The karyotype of S. violacea is composed of 48 chromosomes, with the presence of conspicuous blocks of heterochromatin on chromosomal pairs one and two. FISH assay with a 5S rDNA probe, revealed the presence of fluorescent markings on the heterochromatic block of pair one. The 18S rDNA sites are located exclusively on pair two, characterizing this pair as the carrier of the NOR. Finally, the genomic size of S. violacea was estimated at 0.59 pg of DNA as C-value. This work represents the first effort to document the karyotype structure and physical organization of the rDNA sequences in the Seriolella genome, contributing with new information to improve our understanding of chromosomal evolution and genomic organization in marine perciforms.

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New Comparative Cytogenetic Data on Three Genera of Armored Catfishes of Ancistrini (Loricariidae: Hypostominae)

Cytogenetic and Genome Research ◽

10.1159/000504723 ◽

2019 ◽

Vol 159 (4) ◽

pp. 208-214

Author(s):

Sandra Mariotto ◽

Liano Centofante ◽

Paulo C. Venere ◽

Daniela C. Ferreira ◽

Roberto F. Artoni

Keyword(s):

Dna Barcoding ◽

Diploid Number ◽

Chromosomal Rearrangements ◽

5S Rdna ◽

Coi Gene ◽

Published Data ◽

Distance Analysis ◽

C Banding ◽

Mtdna Coi ◽

Rdna Sites

The karyotypes and other chromosomal markers of 4 catfish species, namely Lasiancistrus schomburgkii, Lasiancistrus sp., Araichthysloro, and Megalancistrus sp., members of a taxonomically complex and speciose tribe of catfishes Ancistrini, Hypostominae, were examined using conventional (Giemsa staining, Ag-NOR, and C-banding) and molecular cytogenetic protocols (FISH) and DNA barcoding. In L. schomburgkii, Lasiancistrus sp., and A.loro a diploid number 2n = 54 was observed, with karyotypes composed of 28m + 16sm + 10st, 36m + 12sm + 6st chromosomes, while Megalancistrus sp. had 2n = 52, with the karyotype composed of 28m + 16sm + 8st chromosomes. The Ag-NOR phenotypes were simple in all 4 species, which was confirmed by FISH with an 18S rDNA probe. However, the positive 5S rDNA sites varied among species: 2 chromosome pairs in L. schomburgkii, Lasiancistrus sp., and A. loro, and only 1 pair in Megalancistrus sp. The blocks of constitutive heterochromatin were poorly visible in the pericentromeric and telomeric regions of most chromosomes of the examined species by C-banding. The genetic distance analysis, based on mtDNA COI gene sequences (DNA barcoding), confirmed the species as 4 taxonomic units. Ours and other published data indicate that karyotype differentiation among Ancistrini is complex and divergent and indicates the occurrence of common chromosomal rearrangements, such as pericentric inversions conserving the diploid number, and other rearrangements that are more frequent in some genera, such as centric fusions in Ancistrus.

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Comparative cytogenetics of Serrasalmidae (Teleostei: Characiformes): The relationship between chromosomal evolution and molecular phylogenies

PLoS ONE ◽

10.1371/journal.pone.0258003 ◽

2021 ◽

Vol 16 (10) ◽

pp. e0258003

Author(s):

Ramon Marin Favarato ◽

Leila Braga Ribeiro ◽

Alber Campos ◽

Jorge Ivan Rebelo Porto ◽

Celeste Mutuko Nakayama ◽

...

Keyword(s):

Chromosome Number ◽

Chromosomal Rearrangements ◽

5S Rdna ◽

Chromosomal Evolution ◽

Comparative Cytogenetics ◽

Molecular Cytogenetic ◽

The Family ◽

Identification Of Species ◽

Molecular Cytogenetic Techniques ◽

The Relationship

Serrasalmidae has high morphological and chromosomal diversity. Based on molecular hypotheses, the family is currently divided into two subfamilies, Colossomatinae and Serrasalminae, with Serrasalminae composed of two tribes: Myleini (comprising most of pacus species) and Serrasalmini (represented by Metynnis, Catoprion, and remaining piranha’s genera). This study aimed to analyze species of the tribes Myleini (Myloplus asterias, M. lobatus, M. rubripinnis, M. schomburgki, and Tometes camunani) and Serrasalmini (Metynnis cuiaba, M. hypsauchen, and M. longipinnis) using classical and molecular cytogenetic techniques in order to understand the chromosomal evolution of the family. The four species of the genus Myloplus and T. camunani presented 2n = 58 chromosomes, while the species of Metynnis presented 2n = 62 chromosomes. The distribution of heterochromatin occurred predominantly in pericentromeric regions in all species. Tometes camunani and Myloplus spp. presented only one site with 5S rDNA. Multiple markers of 18S rDNA were observed in T. camunani, M. asterias, M. lobatus, M. rubripinnis, and M. schomburgkii. For Metynnis, however, synteny of the 18S and 5S rDNA was observed in the three species, in addition to an additional 5S marker in M. longipinnis. These data, when superimposed on the phylogeny of the family, suggest a tendency to increase the diploid chromosome number from 54 to 62 chromosomes, which occurred in a nonlinear manner and is the result of several chromosomal rearrangements. In addition, the different karyotype formulas and locations of ribosomal sequences can be used as cytotaxonomic markers and assist in the identification of species.

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Molecular Cytogenetic Analysis of Cucumis Wild Species Distributed in Southern Africa: Physical Mapping of 5S and 45S rDNA with DAPI

Cytogenetic and Genome Research ◽

10.1159/000433572 ◽

2015 ◽

Vol 146 (1) ◽

pp. 80-87 ◽

Cited By ~ 6

Author(s):

Kouhei Yagi ◽

Magdalena Pawełkowicz ◽

Paweł Osipowski ◽

Ewa Siedlecka ◽

Zbigniew Przybecki ◽

...

Keyword(s):

Cytogenetic Analysis ◽

Chromosomal Rearrangements ◽

Evolutionary Relationship ◽

Chromosomal Evolution ◽

Rdna Site ◽

45S Rdna ◽

Polyploid Evolution ◽

Molecular Cytogenetic ◽

Rdna Sites ◽

Cucumis Species

Wild Cucumis species have been divided into Australian/Asian and African groups using morphological and phylogenetic characteristics, and new species have been described recently. No molecular cytogenetic information is available for most of these species. The crossability between 5 southern African Cucumis species (C. africanus, C. anguria, C. myriocarpus, C. zeyheri, and C. heptadactylus) has been reported; however, the evolutionary relationship among them is still unclear. Here, a molecular cytogenetic analysis using FISH with 5S and 45S ribosomal DNA (rDNA) was used to investigate these Cucumis species based on sets of rDNA-bearing chromosomes (rch) types I, II and III. The molecular cytogenetic and phylogenetic results suggested that at least 2 steps of chromosomal rearrangements may have occurred during the evolution of tetraploid C. heptadactylus. In step 1, an additional 45S rDNA site was observed in the chromosome (type III). In particular, C. myriocarpus had a variety of rch sets. Our results suggest that chromosomal rearrangements may have occurred in the 45S rDNA sites. We propose that polyploid evolution occurred in step 2. This study provides insights into the chromosomal characteristics of African Cucumis species and contributes to the understanding of chromosomal evolution in this genus.

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Effects of the diploidisation process upon the 5S and 35S rDNA sequences in the allopolyploid species of the Dilatata group of Paspalum (Poaceae, Paniceae)

Australian Journal of Botany ◽

10.1071/bt18236 ◽

2019 ◽

Vol 67 (7) ◽

pp. 521

Author(s):

Magdalena Vaio ◽

Cristina Mazzella ◽

Marcelo Guerra ◽

Pablo Speranza

Keyword(s):

Evolutionary Dynamics ◽

In Situ Hybridisation ◽

5S Rdna ◽

Its Region ◽

Variable Number ◽

Rrna Genes ◽

Fluorescence In Situ Hybridisation ◽

Rdna Sites ◽

35S Rdna ◽

Genome Restructuring

The Dilatata group of Paspalum includes species and biotypes native to temperate South America. Among them, five sexual allotetraploids (x = 10) share the same IIJJ genome formula: P. urvillei Steud, P. dasypleurum Kunze ex Desv., P. dilatatum subsp. flavescens Roseng., B.R. Arrill. & Izag., and two biotypes P. dilatatum Vacaria and P. dilatatum Virasoro. Previous studies suggested P. intermedium Munro ex Morong & Britton and P. juergensii Hack. or related species as their putative progenitors and donors of the I and J genome, respectively, and pointed to a narrow genetic base for their maternal origin. It has not yet been established whether the various members of the Dilatata group are the result of a single or of multiple allopolyploid formations. Here, we aimed to study the evolutionary dynamics of rRNA genes after allopolyploidisation in the Dilatata group of Paspalum and shed some light into the genome restructuring of the tetraploid taxa with the same genome formula. We used double target fluorescence in situ hybridisation of 35S and 5S rDNA probes and sequenced the nrDNA internal transcribed spacer (ITS) region. A variable number of loci at the chromosome ends were observed for the 35S rDNA, from 2 to 6, suggesting gain and loss of sites. For the 5S rDNA, only one centromeric pair of signals was observed, indicating a remarkable loss after polyploidisation. All ITS sequences generated were near identical to the one found for P. intermedium. Although sequences showed a directional homogeneisation towards the putative paternal progenitor in all tetraploid species, the observed differences in the number and loss of rDNA sites suggest independent ongoing diploidisation processes in all taxa and genome restructuring following polyploidy.

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