Expansion of Microsatellites on Evolutionary Young Y Chromosome

Kejnovský, Eduard; Michalovová, Monika; Šteflová, Pavlína; Kejnovská, Iva; Manzano, Susana; Hobza, Roman; Kubát, Zdeněk; Kovařík, J; Jamilena, Manuel; Vyskot, Boris

doi:10.1371/journal.pone.0045519

Cited by 52 publications

(48 citation statements)

References 48 publications

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“…B B chromosome. Bar=5 μm rapidly increasing genomic microsatellite characterization in model and nonmodel species, but studies addressing their characterization at both genomic and chromosomal levels have not virtually been done (Kejnovský et al 2013). We have performed this combined approach in two grasshopper species with genomes of different size, that in E. plorans (11.11 Gb) being almost double that in L. migratoria (6.3 Gb).…”

Section: Discussionmentioning

confidence: 99%

“…However, physical mapping by fluorescent in situ hybridization (FISH) constitutes a quicker and easier strategy for ascertaining the abundance and chromosomal distribution of microsatellite and other repeated sequences, thus providing a means for determining, in detail, the precise chromosomal regions in which repeats are clustered, and this is the approach of choice in nonmodel species. The development of NGS technology has highlighted the need for combined genomic and chromosomal analyses for mapping new characterized sequences and confirming de novo genome assemblies, but these combined studies are still scarce (Soltis et al 2013;Kejnovský et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

et al. 2014

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Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, distribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshopper species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and association with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

et al. 2014

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“…Contrary to the accepted picture of Y chromosomes, high rates of colonization by DNA satellites prevented a significant expansion of the transposable elements within the Y chromosomes, although some transposable elements were able to compete with satellites for Y-linked niches, either by a higher insertion rate or a lower removal rate . Kejnovský et al [2013] have found evidence of microsatellite expansion on the Y chromosome of R. acetosa in contrast to other older Y chromosomes. They have also found that the abundance of microsatellites is higher in the neighborhood of transposable elements, suggesting that microsatellites are probably targets for insertions of transposable elements [Kejnovský et al, 2013].…”

Section: Satellite Dnas In Plant Sex Chromosomesmentioning

confidence: 91%

“…Kejnovský et al [2013] have found evidence of microsatellite expansion on the Y chromosome of R. acetosa in contrast to other older Y chromosomes. They have also found that the abundance of microsatellites is higher in the neighborhood of transposable elements, suggesting that microsatellites are probably targets for insertions of transposable elements [Kejnovský et al, 2013]. These authors have suggested that microsatellite expansion would be an early event that shaped Y chromosome evolution, while the accumulation of mobile elements and chromosome shrinkage would have occurred later.…”

Section: Satellite Dnas In Plant Sex Chromosomesmentioning

confidence: 91%

Satellite DNA in Plants: More than Just Rubbish

Garrido-Ramos

2015

Cytogenet Genome Res

145

149

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For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

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“…Our results revealed variability in the distribution of repetitive DNA sequences and their possible association with sex chromosome diversification in Characidium species. © 2015 S. Karger AG, Basel korná et al, 2011; Kejnovský et al, 2013;Milani and Cabral-de-Mello, 2014;Ruiz-Ruano et al, 2015;Ziemniczak et al, 2014]. In this context, cytogenetic studies have provided a better characterization of sex chromosomes by identifying distinctive degrees of heterochromatinization and differential accumulation of repetitive sequences [for a review, see .…”

Section: Chromosomal Mapping Of Repetitive Dnas Inmentioning

confidence: 99%

Chromosomal Mapping of Repetitive DNAs in <b><i>Characidium</i></b> (Teleostei, Characiformes): Genomic Organization and Diversification of ZW Sex Chromosomes

Scacchetti

Utsunomia

Pansonato-Alves

et al. 2015

Cytogenet Genome Res

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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.

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Expansion of Microsatellites on Evolutionary Young Y Chromosome

Cited by 52 publications

References 48 publications

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

Satellite DNA in Plants: More than Just Rubbish

Chromosomal Mapping of Repetitive DNAs in <b><i>Characidium</i></b> (Teleostei, Characiformes): Genomic Organization and Diversification of ZW Sex Chromosomes

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