Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus)

2017 ◽  
Vol 152 (3) ◽  
pp. 148-157 ◽  
Author(s):  
Larisa S. Biltueva ◽  
Dimitry Y. Prokopov ◽  
Alexey I. Makunin ◽  
Alexey S. Komissarov ◽  
Anna V. Kudryavtseva ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Repetitive Sequences ◽  
Satellite Dnas ◽  
Repetitive Dnas ◽  
Acipenser Ruthenus ◽  
Isolation And Characterization ◽  
And Cluster Analysis ◽  
Cryptic Sex ◽  
Sterlet Acipenser Ruthenus

Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order.

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.

Isolation and characterization of a satellite DNA family in the Saccharum complex

Genome ◽  
1998 ◽  
Vol 41 (6) ◽  
pp. 854-864 ◽  
Author(s):  
Karine Alix ◽  
Franc-Christophe Baurens ◽  
Florence Paulet ◽  
Jean-Christophe Glaszmann ◽  
Angélique D'Hont
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Satellite Dna ◽  
Repetitive Sequences ◽  
Repeat Sequence ◽  
Miscanthus Sinensis ◽  
Saccharum Complex ◽  
Satellite Dnas ◽  
Isolation And Characterization

EaCIR1, a 371-bp Erianthus-specific satellite DNA sequence, was cloned from TaqI restricted genomic DNA after agarose-gel electrophoresis. This sequence has 77% homology with a 365-bp satellite of Helictotrichon convolutum and 72% homology with a 353-bp tandem repeat sequence from Oryza sativa. PCR primers defined in the conserved regions of these repetitive sequences were used to isolate other satellite DNAs in different representatives of the Saccharum complex: SoCIR1 in Saccharum officinarum, SrCIR1 in Saccharum robustum, SsCIR1 and SsCIR2 in Saccharum spontaneum, and MsCIR1 in Miscanthus sinensis. EaCIR1 and SoCIR1 were localized to subtelomeric regions of the chromosomes by fluorescence in situ hybridization. Southern hybridization experiments, using two representatives of this repeat sequence family as probes, illustrated contrasting species-specificity and demonstrated the existence of similar repetitive elements in sorghum and maize.Key words: satellite DNA, sugarcane, Saccharum complex, Gramineae, fluorescence in situ hybridization, FISH.

scholarly journals Rex Retroelements and Teleost Genomes: An Overview

2018 ◽  
Vol 19 (11) ◽  
pp. 3653 ◽  
Author(s):  
Federica Carducci ◽  
Marco Barucca ◽  
Adriana Canapa ◽  
Maria Biscotti
Keyword(s):  
Transposable Elements ◽  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Genomic Organization ◽  
Karyotype Evolution ◽  
High Variability ◽  
Satellite Dnas ◽  
Supernumerary Chromosomes ◽  
Species Evolution ◽  
Evolutionary Mode

Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts.

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.

scholarly journals Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

2020 ◽  
Author(s):  
Mariela Sader ◽  
Magdalena Vaio ◽  
Luiz Augusto Cauz-Santos ◽  
Marcelo Carnier Dornelas ◽  
Maria Lucia Carneiro Vieira ◽  
...  
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Size Variation ◽  
Repetitive Dna Sequences ◽  
Ltr Retrotransposons ◽  
Genome Size Variation ◽  
Satellite Dnas

ABSTRACTRepetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs.MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

scholarly journals Novel repetitive sequences decipher the evolution and phylogeny in Carthamus L

2019 ◽  
Author(s):  
Shweta Mehrotra ◽  
Vinod Goyal
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Carthamus Tinctorius ◽  
Phylogeny Reconstruction ◽  
Reconstruction Method ◽  
Crop Species ◽  
Isolation And Characterization ◽  
Eukaryotic Genomes

Abstract Repetitive sequences are ubiquitous features of eukaryotic genomes, which contribute up to 70-80% of the nuclear genomic DNA. They are known to impact genome evolution and organization and play important role in genome remodelling. The widespread distribution and sufficient conservation of repeats reinforce the value of repetitive DNA sequences as markers of evolutionary processes. The repetitive DNA-based phylogeny reconstruction method is consistent in resolving expected phylogenetic and evolutionary relationships. In the present study, we address the isolation and characterization of four novel repetitive sequences (pCtHaeIII-I, pCtHaeIII-II, pCtHaeIII-III and pCtTaqI-I) from Carthamus tinctorius. Detailed phylogenetic analysis of 18 taxa belonging to 7 species of Carthamus has also been done with pCtHaeIII-I, and pCtHaeIII-II which clearly indicated concerted evolution while delineating phylogenetic relationships among the 18 taxa studied. The above understanding can assist in the marker assisted genetic improvement/ enhancement programmes in this crop species.

scholarly journals Small, Repetitive DNAs Contribute Significantly to the Expanded Mitochondrial Genome of Cucumber

Genetics ◽  
2001 ◽  
Vol 159 (1) ◽  
pp. 317-328
Author(s):  
Jason W Lilly ◽  
Michael J Havey
Keyword(s):  
Mitochondrial Genome ◽  
Repetitive Dna ◽  
Repetitive Sequences ◽  
Dot Blot ◽  
Replication Slippage ◽  
Repetitive Dnas ◽  
Dna Motifs ◽  
Coding Regions ◽  
Strong Hybridization ◽  
Mitochondrial Sequences

Abstract Closely related cucurbit species possess eightfold differences in the sizes of their mitochondrial genomes. We cloned mitochondrial DNA (mtDNA) fragments showing strong hybridization signals to cucumber mtDNA and little or no signal to watermelon mtDNA. The cucumber mtDNA clones carried short (30–53 bp), repetitive DNA motifs that were often degenerate, overlapping, and showed no homology to any sequences currently in the databases. On the basis of dot-blot hybridizations, seven repetitive DNA motifs accounted for >13% (194 kb) of the cucumber mitochondrial genome, equaling >50% of the size of the Arabidopsis mitochondrial genome. Sequence analysis of 136 kb of cucumber mtDNA revealed only 11.2% with significant homology to previously characterized mitochondrial sequences, 2.4% to chloroplast DNA, and 15% to the seven repetitive DNA motifs. The remaining 71.4% of the sequence was unique to the cucumber mitochondrial genome. There was <4% sequence colinearity surrounding the watermelon and cucumber atp9 coding regions, and the much smaller watermelon mitochondrial genome possessed no significant amounts of cucumber repetitive DNAs. Our results demonstrate that the expanded cucumber mitochondrial genome is in part due to extensive duplication of short repetitive sequences, possibly by recombination and/or replication slippage.

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