Abstract
SummaryAmplification 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 satellite DNA‐rich legume plant Lathyrus sativus as a model, we demonstrated this approach by analyzing 11 major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73× genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR‐retrotransposons that occasionally expanded in length. While the corresponding LTR‐retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of the L. sativus chromosomes, which suggests that these genome regions are favourable for satellite DNA accumulation.
Highlights
Satellite DNA is a class of highly repeated genomic sequences characterized by its occurrence in long arrays of almost identical, tandemly arranged units called monomers
We chose a set of 16 putative satellites with estimated genome proportions exceeding a threshold of 0.1% and reaching up to 2.6% of the L. sativus genome (Table 1)
These sequences were selected as the most abundant from a broader set of 23 tandem repeats that were previously identified in L. sativus using graph-based clustering of Illumina reads (Macas et al, 2015)
Summary
Satellite DNA (satDNA) is a class of highly repeated genomic sequences characterized by its occurrence in long arrays of almost identical, tandemly arranged units called monomers. Thanks to a number of studies in diverse groups of organisms, the initial view of satellite DNA as genomic ‘junk’ has gradually shifted to an appreciation of its roles in chromosome organization, replication and segregation, gene expression, disease phenotypes and reproductive isolation between species (reviewed in Plohl et al, 2014; Garrido-Ramos, 2015, 2017; Hartley et al, 2019) Despite this progress, there are still serious limitations in our understanding of the biology of satDNA, especially with respect to the molecular mechanisms underlying its evolution and turnover in the genome
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