scholarly journals Chromosomal Spreading of Microsatellites and (TTAGGG)n Sequences in the Characidium zebra and C. gomesi Genomes (Characiformes: Crenuchidae)

2016 ◽  
Vol 149 (3) ◽  
pp. 182-190 ◽  
Author(s):  
Marcela B. Pucci ◽  
Patricia Barbosa ◽  
Viviane Nogaroto ◽  
Mara C. Almeida ◽  
Roberto F. Artoni ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Additional Data ◽  
Sex Chromosome ◽  
Binding Motif ◽  
W Chromosome ◽  
Repeat Sequences ◽  
Heteromorphic Sex Chromosomes

Sex chromosome evolution involves the accumulation of repeat sequences such as multigenic families, noncoding repetitive DNA (satellite, minisatellite, and microsatellite), and mobile elements such as transposons and retrotransposons. Most species of Characidium exhibit heteromorphic ZZ/ZW sex chromosomes; the W is characterized by an intense accumulation of repetitive DNA including dispersed satellite DNA sequences and transposable elements. The aim of this study was to analyze the distribution pattern of 18 different tandem repeats, including (GATA)n and (TTAGGG)n, in the genomes of C. zebra and C. gomesi, especially in the C. gomesi W chromosome. In the C. gomesi W chromosome, weak signals were seen for (CAA)10, (CAC)10, (CAT)10, (CGG)10, (GAC)10, and (CA)15 probes. (GA)15 and (TA)15 hybridized to the autosomes but not to the W chromosome. The (GATA)n probe hybridized to the short arms of the W chromosome as well as the (CG)15 probe. The (GATA)n repeat is known to be a protein-binding motif. GATA-binding proteins are necessary for the decondensation of heterochromatic regions that hold coding genes, especially in some heteromorphic sex chromosomes that may keep genes related to oocyte development. The (TAA)10 repeat is accumulated in the entire W chromosome, and this microsatellite accumulation is probably involved in the sex chromosome differentiation process and crossover suppression in C. gomesi. These additional data on the W chromosome DNA composition help to explain the evolution of sex chromosomes in Characidium.

Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing

2020 ◽  
Vol 160 (3) ◽  
pp. 141-147 ◽  
Author(s):  
Marcelo J. da Silva ◽  
Raquel Fogarin Destro ◽  
Thiago Gazoni ◽  
Hideki Narimatsu ◽  
Paulo S. Pereira dos Santos ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Centromere Function ◽  
Sex Chromosome System ◽  
First Time ◽  
Eukaryotic Genomes

Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.

scholarly journals Repetitive Sequence and Sex Chromosome Evolution in Vertebrates

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Tariq Ezaz ◽  
Janine E. Deakin
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Repetitive Sequence ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Sex Chromosome Evolution ◽  
Genomic Changes ◽  
Heteromorphic Sex Chromosomes ◽  
Simple Repetitive Sequences

Sex chromosomes are the most dynamic entity in any genome having unique morphology, gene content, and evolution. They have evolved multiple times and independently throughout vertebrate evolution. One of the major genomic changes that pertain to sex chromosomes involves the amplification of common repeats. It is hypothesized that such amplification of repeats facilitates the suppression of recombination, leading to the evolution of heteromorphic sex chromosomes through genetic degradation of Y or W chromosomes. Although contrasting evidence is available, it is clear that amplification of simple repetitive sequences played a major role in the evolution of Y and W chromosomes in vertebrates. In this review, we present a brief overview of the repetitive DNA classes that accumulated during sex chromosome evolution, mainly focusing on vertebrates, and discuss their possible role and potential function in this process.

scholarly journals Chromosomal Mapping of Repetitive DNAs in Characidium (Teleostei, Characiformes): Genomic Organization and Diversification of ZW Sex Chromosomes

2015 ◽  
Vol 146 (2) ◽  
pp. 136-143 ◽  
Author(s):  
Priscilla C. Scacchetti ◽  
Ricardo Utsunomia ◽  
José C. Pansonato-Alves ◽  
Marcelo R. Vicari ◽  
Roberto F. Artoni ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
5S Rdna ◽  
Chromosome Mapping ◽  
Chromosomal Mapping ◽  
Specific Probe ◽  
W Chromosome ◽  
Sex Chromosome System

The speciose neotropical genus Characidium has proven to be a good model for cytogenetic exploration. Representatives of this genus often have a conserved diploid chromosome number; some species exhibit a highly differentiated ZZ/ZW sex chromosome system, while others do not show any sex-related chromosome heteromorphism. In this study, chromosome painting using a W-specific probe and comparative chromosome mapping of repetitive sequences, including ribosomal clusters and 4 microsatellite motifs - (CA)15, (GA)15, (CG)15, and (TTA)10 -, were performed in 6 Characidium species, 5 of which possessed a heteromorphic ZW sex chromosome system. The W-specific probe showed hybridization signals on the W chromosome of all analyzed species, indicating homology among the W chromosomes. Remarkably, a single major rDNA-bearing chromosome pair was found in all species. The 18S rDNA localized to the sex chromosomes in C. lanei, C. timbuiense and C. pterostictum, while the major rDNA localized to one autosome pair in C. vidali and C. gomesi. In contrast, the number of 5S rDNA-bearing chromosomes varied. Notably, minor ribosomal clusters were identified in the W chromosome of C. vidali. Microsatellites were widely distributed across almost all chromosomes of the karyotypes, with a greater accumulation in the subtelomeric regions. However, clear differences in the abundance of each motif were detected in each species. In addition, the Z and W chromosomes showed the differential accumulation of distinct motifs. Our results revealed variability in the distribution of repetitive DNA sequences and their possible association with sex chromosome diversification in Characidium species.

scholarly journals Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Shed Light on Their Roles in Sex Chromosome Evolution

2021 ◽  
Vol 11 ◽  
Author(s):  
Ning Li ◽  
Xiaoyue Li ◽  
Jian Zhou ◽  
Li’ang Yu ◽  
Shufen Li ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Chromosome 1 ◽  
Sex Chromosome Evolution ◽  
Satellite Dnas ◽  
Heteromorphic Sex Chromosomes

Sex chromosome evolution has mostly been studied in species with heteromorphic sex chromosomes. The Spinacia genus serves as an ideal model for investigating evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution while their forces have not been fully explored in Spinacia species. Here, we identified major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative sugar beet to elucidate the evolutionary processes of sex chromosome evolution using next-generation sequencing (NGS) data. Comparative analysis revealed that the repeat elements of Spinacia species are considerably higher than of sugar beet, especially the Ty3/Gypsy and Ty1/Copia retrotransposons. The long terminal repeat retroelements (LTR) Angela, Athila, and Ogre may be accounted for the higher proportion of repeats in the spinach genome. Comparison of the repeats proportion between female and male genomes of three Spinacia species indicated the different representation in Spinacia tetrandra samples but not in the S. oleracea or S. turkestanica samples. From these results, we speculated that emergence of repetitive DNA sequences may correlate the formation of sex chromosome and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes as heteromorphic sex chromosomes exclusively existed in Spinacia tetrandra. Three novel sugar beet-specific satellites were identified and confirmed by fluorescence in situ hybridization (FISH); six out of eight new spinach-specific satellites were mapped to the short arm of sex chromosomes. A total of 141 copies of SolSat01-171-s were found in the sex determination region (SDR). Thus, the accumulation of satellite DNA on the short arm of chromosome 1 may be involved in the sex chromosome evolution in Spinacia species. Our study provides a fundamental resource for understanding repeat sequences in Spinacia species and their roles in sex chromosome evolution.

Cloning and characterization of dispersed repetitive DNA derived from microdissected sex chromosomes of Rumex acetosa

Genome ◽  
2006 ◽  
Vol 49 (2) ◽  
pp. 114-121 ◽  
Author(s):  
Beatrice Mariotti ◽  
Rafael Navajas-Pérez ◽  
Rafael Lozano ◽  
John S Parker ◽  
Roberto de la Herrán ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
Rumex Acetosa ◽  
Dioecious Species ◽  
Rumex Crispus ◽  
Origin And Evolution ◽  
Y Chromosomes ◽  
Plant Sex Chromosomes

Rumex acetosa is characterized by a multiple chromosome system (2n = 12 + XX for females, and 2n = 12 + XY1Y2 for males), in which sex is determined by the ratio between the number of X chromosomes and autosome sets. For a better understanding of the molecular structure and evolution of plant sex chromosomes, we have generated a sex chromosome specific library of R. acetosa by microdissection. The screening of this library has allowed us to identify 5 repetitive DNA families that have been characterized in detail. One of these families, DOP-20, has shown no homology with other sequences in databases. Nevertheless, the putative proteins encoded by the other 4 families, DOP-8, DOP-47, DOP-60, and DOP-61, show homology with proteins from different plant retroelements, including poly proteins from Ty3-gypsy- and Ty1-copia-like long terminal repeat (LTR) retroelements, and reverse transcriptase from non-LTR retro elements. Results indicate that sequences from these 5 families are dispersed throughout the genome of both males and females, but no appreciable accumulation or differentiation of these types of sequences have been found in the Y chromosomes. These repetitive DNA sequences are more conserved in the genome of other dioecious species such as Rumex papillaris, Rumex intermedius, Rumex thyrsoides, Rumex hastatulus, and Rumex suffruticosus, than in the polygamous, gynodioecious, or hermaphrodite species Rumex induratus, Rumex lunaria, Rumex con glom er atus, Rumex crispus, and Rumex bucephalo phorus, which supports a single origin of dioecious species in this genus. The implication of these transposable elements in the origin and evolution of the heteromorphic sex chromosomes of R. acetosa is discussed.Key words: Rumex acetosa, sex chromosomes, microdissection, evolution, retroelements.

scholarly journals The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 483
Author(s):  
Wen-Juan Ma ◽  
Paris Veltsos
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Comparative Genomic ◽  
Ancestral State ◽  
Heteromorphic Sex Chromosomes ◽  
Genomic Studies ◽  
Evolutionary Trajectories ◽  
Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativum L.)

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 716-728 ◽  
Author(s):  
Pavel Neumann ◽  
Marcela Nouzová ◽  
Jirí Macas
Keyword(s):  
Pisum Sativum ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Genomic Library ◽  
Chromosome Morphology ◽  
Plant Genome ◽  
Genomic Repeats ◽  
Dispersed Repeats

A set of pea DNA sequences representing the most abundant genomic repeats was obtained by combining several approaches. Dispersed repeats were isolated by screening a short-insert genomic library using genomic DNA as a probe. Thirty-two clones ranging from 149 to 2961 bp in size and from 1000 to 39 000/1C in their copy number were sequenced and further characterized. Fourteen clones were identified as retrotransposon-like sequences, based on their homologies to known elements. Fluorescence in situ hybridization using clones of reverse transcriptase and integrase coding sequences as probes revealed that corresponding retroelements were scattered along all pea chromosomes. Two novel families of tandem repeats, named PisTR-A and PisTR-B, were isolated by screening a genomic DNA library with Cot-1 DNA and by employing genomic self-priming PCR, respectively. PisTR-A repeats are 211–212 bp long, their abundance is 2 × 104 copies/1C, and they are partially clustered in a secondary constriction of one chromosome pair with the rest of their copies dispersed on all chromosomes. PisTR-B sequences are of similar abundance (104 copies/1C) but differ from the "A" family in their monomer length (50 bp), high A/T content, and chromosomal localization in a limited number of discrete bands. These bands are located mainly in (sub)telomeric and pericentromeric regions, and their patterns, together with chromosome morphology, allow discrimination of all chromosome types within the pea karyotype. Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia.Key words: repetitive DNA, plant genome, retroelements, satellite DNA, Pisum sativum.

Heteromorphic Sex Chromosomes and Their DNA Content in Fish: An Insight through Satellite DNA Accumulation in Megaleporinus elongatus

2020 ◽  
Vol 160 (1) ◽  
pp. 38-46 ◽  
Author(s):  
Carolina Crepaldi ◽  
Patricia P. Parise-Maltempi
Keyword(s):  
Sex Chromosomes ◽  
Dna Content ◽  
Satellite Dna ◽  
Sex Chromosome ◽  
Neotropical Fish ◽  
High Throughput Analysis ◽  
Multiple Sex Chromosomes ◽  
Heteromorphic Sex Chromosomes ◽  
Sex Chromosome System ◽  
Graph Based Clustering

The repetitive DNA content of fish sex chromosomes provides valuable insights into specificities and patterns of their genetic sex determination systems. In this study, we revealed the genomic satellite DNA (satDNA) content of Megaleporinuselongatus, a Neotropical fish species with Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosomes, through high-throughput analysis and graph-based clustering, isolating 68 satDNA families. By physically mapping these sequences in female metaphases, we discovered 15 of the most abundant satDNAs clustered in its chromosomes, 9 of which were found exclusively in the highly heterochromatic W1. This heteromorphic sex chromosome showed the highest amount of satDNA accumulations in this species. The second most abundant family, MelSat02-26, shared FISH signals with the NOR-bearing pair in similar patterns and is linked to the multiple sex chromosome system. Our results demonstrate the diverse satDNA content in M. elongatus, especially in its heteromorphic sex chromosome. Additionally, we highlighted the different accumulation patterns and distribution of these sequences across species by physically mapping these satDNAs in other Anostomidae, Megaleporinusmacrocephalus and Leporinusfriderici (a species without differentiated sex chromosomes).

Codling moth cytogenetics: karyotype, chromosomal location of rDNA, and molecular differentiation of sex chromosomes

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1083-1092 ◽  
Author(s):  
Iva Fuková ◽  
Petr Nguyen ◽  
František Marec
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Codling Moth ◽  
Dna Probe ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
W Chromosome ◽  
Genomic Hybridization ◽  
Molecular Differentiation ◽  
Sex Chromatin

We performed a detailed karyotype analysis in the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), the key pest of pome fruit in the temperate regions of the world. The codling moth karyotype consisted of 2n = 56 chromosomes of a holokinetic type. The chromosomes were classified into 5 groups according to their sizes: extra large (3 pairs), large (3 pairs), medium (15 pairs), small (5 pairs), and dot-like (2 pairs). In pachytene nuclei of both sexes, a curious NOR (nucleolar organizer region) bivalent was observed. It carried 2 nucleoli, each associated with one end of the bivalent. FISH with an 18S ribosomal DNA probe confirmed the presence of 2 clusters of rRNA genes at the opposite ends of the bivalent. In accordance with this finding, 2 homologous NOR chromosomes were identified in mitotic metaphase, each showing hybridization signals at both ends. In highly polyploid somatic nuclei, females showed a large heterochromatin body, the so-called sex chromatin or W chromatin. The heterochromatin body was absent in male nuclei, indicating a WZ/ZZ (female/male) sex chromosome system. In keeping with the sex chromatin status, pachytene oocytes showed a sex chromosome bivalent (WZ) that was easily discernible by its heterochromatic W thread. To study molecular differentiation of the sex chromosomes, we employed genomic in situ hybridization (GISH) and comparative genomic hybridization (CGH). GISH detected the W chromosome by strong binding of the Cy3-labelled, female-derived DNA probe. With CGH, both the Cy3-labelled female-derived probe and Fluor-X labelled male-derived probe evenly bound to the W chromosome. This suggested that the W chromosome is predominantly composed of repetitive DNA sequences occurring scattered in other chromosomes but accumulated in the W chromosome. The demonstrated ways of W chromosome identification will facilitate the development of genetic sexing strains desirable for pest control using the sterile insect technique.Key words: CGH, codling moth, FISH, GISH, genomic hybridization, heterochromatin, holokinetic chromosomes, karyotype, NOR, rDNA, SIT, sex chromosomes.

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