Adjacent sequences disclose potential for intra-genomic dispersal of satellite DNA repeats and suggest a complex network with transposable elements

Abstract

BackgroundSatellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape.ResultsWe explored sets of randomly selected satDNA-harboring genomic fragments in four mollusc species to examine satDNA transition sites, and the nature of adjacent sequences. All examined junctions are characterized by abrupt transitions from satDNAs to other sequences. Among them, junctions of only one examined satDNA mapped non-randomly (within the palindrome), indicating that well-defined sequence feature is not a necessary prerequisite in the junction formation. In the studied sample, satDNA flanking sequences can be roughly classified into two groups. The first group is composed of anonymous DNA sequences which occasionally include short segments of transposable elements (TEs) as well as segments of other satDNA sequences. In the second group, satDNA repeats and the array flanking sequences are identified as parts of TEs of the Helitron superfamily. There, some array flanking regions hold fragmented satDNA monomers alternating with anonymous sequences of comparable length as missing monomer parts, suggesting a process of sequence reorganization by a mechanism able to excise short monomer parts and replace them with unrelated sequences.ConclusionsThe observed architecture of satDNA transition sites can be explained as a result of insertion and/or recombination events involving short arrays of satDNA monomers and TEs, in combination with hypothetical transposition-related ability of satDNA monomers to be shuffled independently in the genome. We conclude that satDNAs and TEs can form a complex network of sequences which essentially share the propagation mechanisms and in synergy shape the genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3347-1) contains supplementary material, which is available to authorized users.

Dissecting the Satellite DNA Landscape in Three CactophilicDrosophilaSequenced Genomes

“…In contrast to TEs, satDNAs do not have the ability to transpose by themselves. However, there are some reported examples showing that TEs may act as a substrate for satDNA emergence and mobility ( Dias et al 2015 ; Meštrović et al 2015 ; Satović et al 2016 ). We created a database containing the 500-bp sequences immediately before and after each CDSTR198 array (37 in total; Table S6 in File S1 ) found in the assembled scaffolds of D. buzzatii .…”

“…SatDNAs do not have the ability to transpose by themselves as transposable elements (TEs) do. However, there are some reported examples showing that TEs may act as a substrate for satDNA emergence and mobility ( Dias et al 2015 ; Meštrović et al 2015 ; Satović et al 2016 ).…”

Satellite DNA: An Evolving Topic

“…Conversely, tandem repeats have also been found as integral components of TEs [ 109 ] and some satDNA were probably derived from tandem repeats present in a hypothetical miniature inverted–repeat transposable element (MITE)-like element [ 109 , 110 , 111 , 112 ]. Thus, it has been suggested that mobile elements may be an important source of satDNAs in diverse genomes [ 109 , 113 , 114 , 115 ].…”

Long-read single-molecule maps of the functional methylome

“…5D). The repetitive region of the consensus map displays 22 labels; however, as the first or last repeat may be truncated and unlabeled (Dini and Lipsick 1993;Satovićet al 2016), these 22 labels indicate 22 ± 1 D4Z4 repeats. The exact size of the array can be validated by measuring the length of the array directly from the consensus map.…”