Transposons and satellite DNA: on the origin of the major satellite DNA family in the  Chenopodium  genome

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Abstract

Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.

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Alignment-free sequence comparison-a review.

Susana Vinga, Jonas Almeida, John Osborne (2003)

Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments. A variety of theoretical foundations are being used to derive alignment-free methods that overcome this limitation. The formulation of alternative metrics for dissimilarity between sequences and their algorithmic implementations are reviewed. The overwhelming majority of work on alignment-free sequence has taken place in the past two decades, with most reports published in the past 5 years. Two main categories of methods have been proposed-methods based on word (oligomer) frequency, and methods that do not require resolving the sequence with fixed word length segments. The first category is based on the statistics of word frequency, on the distances defined in a Cartesian space defined by the frequency vectors, and on the information content of frequency distribution. The second category includes the use of Kolmogorov complexity and Chaos Theory. Despite their low visibility, alignment-free metrics are in fact already widely used as pre-selection filters for alignment-based querying of large applications. Recent work is furthering their usage as a scale-independent methodology that is capable of recognizing homology when loss of contiguity is beyond the possibility of alignment. Most of the alignment-free algorithms reviewed were implemented in MATLAB code and are available at http://bioinformatics.musc.edu/resources.html

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YASS: enhancing the sensitivity of DNA similarity search

Laurent Noé, Gregory Kucherov (2005)

YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous sequences, combined with a flexible hit criterion used to identify groups of seeds that are likely to exhibit significant alignments. A web interface () is available to upload input sequences in fasta format, query the program and visualize the results obtained in several forms (dot-plot, tabular output and others). A standalone version is available for download from the web page.

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Repetitive DNA in eukaryotic genomes.

Maria Biscotti, Ettore Olmo, J. Heslop-Harrison (2015)

Repetitive DNA--sequence motifs repeated hundreds or thousands of times in the genome--makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest contrasting modes of evolution of repetitive DNA of different types, including selfish sequences that propagate themselves and may even be transferred horizontally between species rather than by descent, through to sequences that have a tendency to amplification because of their sequence motifs, to those that have structural significance because of their bulk rather than precise sequence. Functional consequences of repeats include generation of variability by movement and insertion in the genome (giving useful genetic markers), the definition of centromeres, expression under stress conditions and regulation of gene expression via RNA moieties. Molecular cytogenetics and bioinformatic studies in a comparative context are now enabling understanding of the nature and behaviour of this major genomic component.

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Author and article information

Contributors

Alexander Belyayev:

ORCID: http://orcid.org/0000-0002-8933-6197

alexander.belyayev@ibot.cas.cz

Journal

Journal ID (nlm-ta): Mob DNA

Journal ID (iso-abbrev): Mob DNA

Title: Mobile DNA

Publisher: BioMed Central (London )

ISSN (Electronic): 1759-8753

Publication date (Electronic): 26 June 2020

Publication date PMC-release: 26 June 2020

Publication date Collection: 2020

Volume: 11

Electronic Location Identifier: 20

Affiliations

[1 ]GRID grid.424923.a, ISNI 0000 0001 2035 1455, Czech Academy of Sciences, , Institute of Botany, ; Zámek 1, CZ-252 43 Průhonice, Czech Republic

[2 ]GRID grid.15866.3c, ISNI 0000 0001 2238 631X, Faculty of Environmental Sciences, , Czech University of Life Sciences Prague, ; Kamýcká 129, 165 00 Praha, Suchdol Czech Republic

Author information

Alexander Belyayev http://orcid.org/0000-0002-8933-6197

Article

Publisher ID: 219

DOI: 10.1186/s13100-020-00219-7

PMC ID: 7320549

PubMed ID: 32607133

SO-VID: 496551fe-4dda-4568-9dbb-bdde672e5e9a

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Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 24 March 2020

Date accepted : 19 June 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001824, Grantová Agentura České Republiky;

Award ID: 20-20286S

Award Recipient : Karol Krak

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: cacta transposons,satellite dna,transposase,chenopodium,next generation sequencing,oxford nanopore sequencing

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ScienceOpen disciplines: Genetics

Keywords: cacta transposons, satellite dna, transposase, chenopodium, next generation sequencing, oxford nanopore sequencing

Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome

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Genome Integrity

Most cited references 30

Alignment-free sequence comparison-a review.

YASS: enhancing the sensitivity of DNA similarity search

Repetitive DNA in eukaryotic genomes.

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