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[Preprint]. 2023 Apr 19:arXiv:2304.09729v1.

De novo reconstruction of satellite repeat units from sequence data

Yujie Zhang  1 , Justin Chu  2   3 , Haoyu Cheng  2   3 , Heng Li  2   3
Affiliations

De novo reconstruction of satellite repeat units from sequence data

Yujie Zhang et al. ArXiv. .

Update in

Abstract

Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats either require the complete assembly of satellites or only work for simple repeat structures without HORs. Here we describe Satellite Repeat Finder (SRF), a new algorithm for reconstructing satellite repeat units and HORs from accurate reads or assemblies without prior knowledge on repeat structures. Applying SRF to real sequence data, we showed that SRF could reconstruct known satellites in human and well-studied model organisms. We also found satellite repeats are pervasive in various other species, accounting for up to 12% of their genome contents but are often underrepresented in assemblies. With the rapid progress on genome sequencing, SRF will help the annotation of new genomes and the study of satellite DNA evolution even if such repeats are not fully assembled.

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Conflict of interest statement

6COMPETING INTEREST STATEMENT H.L. is a consualtant for Integrated DNA Technologies, Inc.

Figures

Fig. 1.
Fig. 1.
Normalized counts of 179-mers in three A. thaliana read datasets. Raw 179-mer counts in reads are normalized by coverage. A 179-mer is selected in the plot if it matches the CEN180 satellite and if its normalized count is at least 50 in one of the datasets. (a) Counts between two different samples from the same strain. (b) Counts between two different strains.
Fig. 2.
Fig. 2.
Abundance of satellite DNA in 21 species.
See this image and copyright information in PMC

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