Exploring Satellite DNAs: Specificities of Bivalve Mollusks Genomes

Šatović-Vukšić, Eva; Plohl, Miroslav

doi:10.1007/978-3-030-74889-0_3

Cited by 5 publications

(10 citation statements)

References 144 publications

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“…This finding suggests that amplifications from extant abundant sequences could play a key role in the evolution of the genomic landscape of the D. virilis group for reasons still to be elucidated. Moreover, the “hybrid” structure of mobile elements incorporating tandem repeats in Drosophila , such as Helitrons ( Dias et al 2015 ), results in complications in the precise classification and quantification of SatDNA sequences (see Results, Šatović Vukšić and Plohl 2021 ). Therefore, meticulous sequence characterization of RepeatExplorer outputs is required to surpass this significant classification challenge ( Montiel et al 2021 ; Cintra et al 2022 ).…”

Section: Discussionmentioning

confidence: 99%

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

Ruiz‐Ruano

2022

Genome Biology and Evolution

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Satellite DNAs (SatDNA) are ubiquitously present in eukaryotic genomes and have been recently associated with several biological roles. Understanding the evolution and significance of SatDNA requires an extensive comparison across multiple phylogenetic depths. We combined the RepeatExplorer pipeline and cytogenetic approaches to conduct a comprehensive identification and analysis of the satellitome in 37 species from the genus Drosophila. We identified 188 SatDNA-like families, 112 of them being characterized for the first time. Repeat analysis within a phylogenetic framework has revealed the deeply divergent nature of SatDNA sequences in the Drosophila genus. The SatDNA content varied from 0.54% of the D. arizonae genome to 38.8% of the D. albomicans genome, with the SatDNA content often following a phylogenetic signal. Monomer size and GC-content also showed extreme variation ranging 2-570 bp and 9.1-71.4%, respectively. SatDNA families are shared among closely related species, consistent with the SatDNA library hypothesis. However, we uncovered the emergence of species-specific SatDNA families through amplification of unique or low abundant sequences in a lineage. Finally, we found that genome sizes of the Sophophora subgenus are positively correlated with transposable element content, whereas genome size in the Drosophila subgenus is positively correlated with SatDNA. This finding indicates genome size could be driven by different categories of repetitive elements in each subgenus. Altogether, we conducted the most comprehensive satellitome analysis in Drosophila from a phylogenetic perspective and generated the largest catalog of SatDNA sequences to date, enabling future discoveries in SatDNA evolution and Drosophila genome architecture.

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Section: Discussionmentioning

confidence: 99%

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

Ruiz‐Ruano

2022

Genome Biology and Evolution

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“…Satellite DNA (SatDNA) sequences, in the traditional view, appear as megabase-long arrays of many thousands of highly similar head-to-tail tandemly repeated units (monomers) localized in heterochromatic chromosomal segments [ 7 , 8 , 9 , 10 ]. They were discovered in experiments of density gradient centrifugation in which an accompanying “satellite” band appeared due to differences in nucleotide composition with regard to the bulk genomic DNA [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…They were discovered in experiments of density gradient centrifugation in which an accompanying “satellite” band appeared due to differences in nucleotide composition with regard to the bulk genomic DNA [ 11 , 12 ]. This generic name continued to be used, irrespective of the method of detection or characteristics of sequences repeated in tandem [ 8 , 10 ]. The other class is made up of interspersed repeats formed as a result of transposition processes, introducing transposable elements (TEs) into new locations, changing, in this process, genome structure, adaptability and evolution [ 13 , 14 , 15 , 16 ].…”

Section: Introductionmentioning

confidence: 99%

“…This is not an easy task, and, in general, we are still far from full comprehension regarding repetitive DNA genomics and their diversity (for example, [ 21 ]). Nevertheless, the burst of methodological approaches in recent years significantly accelerated the accumulation of previously inaccessible data, broadened the number of attended species and detected repetitive DNA families, changing the views and established concepts (reviewed in [ 6 , 8 , 10 , 18 , 22 , 23 ]). The result are satellitomes and repeatomes, defined as collections of all satDNAs and repetitive DNAs, respectively [ 24 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

“…A growing number of studied species and data accumulated on the genomics scale emphasized extreme variations in the general architecture of satDNAs, not only in the number and abundance of families but also in their genomic distribution, heterochromatin/euchromatin localization, array length and association with TEs. Differences indicate conceptual specificities in repetitive DNA organization, in particular, taxonomic groups and the need to expand the number of model systems [ 10 ]. In the present review, we compare data in the light of different organizational forms of satDNAs and repetitive DNAs, in general, in an attempt to summarize conceptual differences in repetitive DNA landscapes and evolutionary processes that may cause their diversity.…”

Section: Introductionmentioning

confidence: 99%

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Satellite DNAs—From Localized to Highly Dispersed Genome Components

Šatović-Vukšić

Plohl

2023

Genes

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According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes’ diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.

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