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Classification Problems of Repetitive DNA Sequences

Šatović-Vukšić, Eva; Plohl, Miroslav (2021) Classification Problems of Repetitive DNA Sequences. DNA, 1 (2). pp. 84-90. ISSN 2673-8856

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Repetitive DNA sequences, satellite DNAs (satDNAs) and transposable elements (TEs) are essential components of the genome landscape, with many different roles in genome function and evolution. Despite significant advances in sequencing technologies and bioinformatics tools, detection and classification of repetitive sequences can still be an obstacle to the analysis of genomic repeats. Here, we summarize how specificities in repetitive DNA organizational patterns can lead to an inability to classify (and study) a significant fraction of bivalve mollusk repetitive sequences. We suggest that the main reasons for this inability are: the predominant association of satDNA arrays with Helitron/Helentron TEs ; the existence of many complex loci ; and the unusual, highly scattered organization of short satDNA arrays or single monomers across the whole genome. The specificities of bivalve genomes confirm the need for introducing diverse organisms as models in order to understand all aspects of repetitive DNA biology. It is expected that further development of sequencing techniques and synergy among different bioinformatics tools and databases will enable quick and unambiguous characterization and classification of repetitive DNA sequences in assembled genomes.

Item Type: Article
Uncontrolled Keywords: repetitive DNA classification ; satellite DNA ; transposable element ; Helitron/Helentron ; bivalves ; genome assemblies
Subjects: NATURAL SCIENCES > Biology
Divisions: Division of Molecular Biology
Project titleProject leaderProject codeProject type
Rasvjetljavanje evolucije satelitnih DNA visokoprotočnim analizama satelitoma srodnih vrstaMravinac, BrankicaIP-2019-04-5522HRZZ
Depositing User: Miroslav Plohl
Date Deposited: 27 Dec 2021 14:37
DOI: 10.3390/dna1020009

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