Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups

Kuhn, Gustavo C. S.; Heringer, Pedro; Dias, Guilherme B.

doi:10.1007/978-3-030-74889-0_2

Cited by 8 publications

(4 citation statements)

References 106 publications

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“…One might hypothesize that some of the low-copy satDNAs arrays scattered along euchromatic regions represent "satDNA seeds" that have the potential to be amplified into more extensive satDNA families and that euchromatin, being less inert than heterochromatin, may even facilitate their propagation. In Drosophila virilis and Drosophila americana, the transition zones between densely condensed heterochromatin and lightly packed euchromatin were detected as regions of recently formed, abundant tandem repeats derived from DNA transposons, suggesting that the less compacted environment of the higher recombination rates may favor amplification of satDNA arrays [59,60].…”

Section: Discussionmentioning

confidence: 99%

The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum

Gržan

Dombi

Despot-Slade

et al. 2023

Genes

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The red flour beetle Tribolium castaneum is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderate-copy-number satellite DNAs (satDNAs) have been described in the assembled part of its genome. In this work, we aimed to catalog the entire collection of T. castaneum satDNAs. We resequenced the genome using Illumina technology and predicted potential satDNAs via graph-based sequence clustering. In this way, we discovered 46 novel satDNAs that occupied a total of 2.1% of the genome and were, therefore, considered low-copy-number satellites. Their repeat units, preferentially 140–180 bp and 300–340 bp long, showed a high A + T composition ranging from 59.2 to 80.1%. In the current assembly, we annotated the majority of the low-copy-number satDNAs on one or a few chromosomes, discovering mainly transposable elements in their vicinity. The current assembly also revealed that many of the in silico predicted satDNAs were organized into short arrays not much longer than five consecutive repeats, and some of them also had numerous repeat units scattered throughout the genome. Although 20% of the unassembled genome sequence masked the genuine state, the predominance of scattered repeats for some low-copy satDNAs raises the question of whether these are essentially interspersed repeats that occur in tandem only sporadically, with the potential to be satDNA “seeds”.

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Section: Discussionmentioning

confidence: 99%

The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum

Gržan

Dombi

Despot-Slade

et al. 2023

Genes

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“…An increasing number of reports show that satDNAs and TEs are tightly connected in many different ways, and TEs, in general, were proposed to facilitate the dispersal of satDNA repeats (reviewed in [ 17 , 20 , 52 , 53 ]). Tandemization of TEs or their parts can be accomplished through different mechanisms, resulting in arrays of repeats characteristic for a satDNA [ 54 ].…”

Section: Functional Importance Of Satellite Dnas and Partnership With...mentioning

confidence: 99%

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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“…Several models aim to explain generation of tandem repeats from TEs (Grabundzija et al 2016 ; Hikosaka and Kawahara 2004 ; McGurk and Barbash 2018 ; Xiong et al 2016 ,). TEs not only serve as origin for satDNA but were proposed to be facilitators/drivers of their dispersal (Cohen et al 2010 ; Grabundzija et al 2016 ; Hofstatter et al 2022 ; Kuhn et al 2021 ; Paço et al 2019 ; Tunjić-Cvitanić et al 2021 ; Zattera and Bruschi 2022 ). Whether tandem repeats are derived from TEs by tandemization of their parts or TEs capture parts of satDNA arrays and continue propagating them is probably situation- and genome-dependent.…”

Section: Discussionmentioning

confidence: 99%

Dominance of transposable element-related satDNAs results in great complexity of “satDNA library” and invokes the extension towards “repetitive DNA library”

Tunjić-Cvitanić,

García-Souto,

Pasantes

et al. 2024

Mar Life Sci Technol

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Research on bivalves is fast-growing, including genome-wide analyses and genome sequencing. Several characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome organization. Here we characterize the satellitomes of five species in the family Ostreidae (Crassostrea angulata, C. virginica, C. hongkongensis, C. ariakensis, Ostrea edulis), revealing a substantial number of satellite DNAs (satDNAs) per genome (ranging between 33 and 61) and peculiarities in the composition of their satellitomes. Numerous satDNAs were either associated to or derived from transposable elements, displaying a scarcity of transposable element-unrelated satDNAs in these genomes. Due to the non-conventional satellitome constitution and dominance of Helitron-associated satDNAs, comparative satellitomics demanded more in-depth analyses than standardly employed. Comparative analyses (including C. gigas, the first bivalve species with a defined satellitome) revealed that 13 satDNAs occur in all six oyster genomes, with Cg170/HindIII satDNA being the most abundant in all of them. Evaluating the “satDNA library model” highlighted the necessity to adjust this term when studying tandem repeat evolution in organisms with such satellitomes. When repetitive sequences with potential variation in the organizational form and repeat-type affiliation are examined across related species, the introduction of the terms “TE library” and “repetitive DNA library” becomes essential.

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Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups

Cited by 8 publications

References 106 publications

The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum

The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum

Satellite DNAs—From Localized to Highly Dispersed Genome Components

Dominance of transposable element-related satDNAs results in great complexity of “satDNA library” and invokes the extension towards “repetitive DNA library”

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