2019
DOI: 10.1111/tpj.14546
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Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats

Abstract: Summary Amplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly‐free approach that utilizes ultra‐long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities. Using the … Show more

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Cited by 87 publications
(101 citation statements)
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“…Thirteen satellite DNA families whose genome abundance differ ~10–1000 times have been recorded in the pea centromeres [ 7 ], confirming that tandem organization is favorable, while abundance of a tandem repeat could be less determinative criteria for centromeric assortment. In addition to satellites, retroelements can be equally important or even dominant centromere components [ 43 ], and contribution of retrotransposons to functional centromeres have been documented in different animal, plant and fungal lineages [ 43 47 ]. In T .…”
Section: Discussionmentioning
confidence: 99%
“…Thirteen satellite DNA families whose genome abundance differ ~10–1000 times have been recorded in the pea centromeres [ 7 ], confirming that tandem organization is favorable, while abundance of a tandem repeat could be less determinative criteria for centromeric assortment. In addition to satellites, retroelements can be equally important or even dominant centromere components [ 43 ], and contribution of retrotransposons to functional centromeres have been documented in different animal, plant and fungal lineages [ 43 47 ]. In T .…”
Section: Discussionmentioning
confidence: 99%
“…The presence of long tandem arrays in currently available sequence assemblies is limited by the assemblies being based on short-read DNA sequencing approaches, which can tend to pile up tandem repeats. As assemblies based on the newer long-read sequencing techniques such as those of Oxford Nanopore or Pacific Biosciences [32,33] appear, the problem of under-representation of repeat numbers in tandem arrays should decrease. Table 1.…”
Section: Introductionmentioning
confidence: 99%
“…Novel satDNAs can arise from the amplification of unique sequences through replication slippage [19,20], unequal exchange, rolling circle replication [4,[21][22][23], or even from transposable elements (TEs) [24][25][26]. However, much of the species-level differences in satDNA arises through movement and divergence of ancestral satellites inherited through common decent [27].…”
Section: Introductionmentioning
confidence: 99%