Satellite DNA evolution: old ideas, new approaches

Abstract

A substantial portion of the genomes of most multicellular eukaryotes consists of large arrays of tandemly repeated sequence, collectively called satellite DNA. The processes generating and maintaining different satellite DNA abundances across lineages are important to understand as satellites have been linked to chromosome mis-segregation, disease phenotypes, and reproductive isolation between species. While much theory has been developed to describe satellite evolution, empirical tests of these models have fallen short because of the challenges in assessing satellite repeat regions of the genome. Advances in computational tools and sequencing technologies now enable identification and quantification of satellite sequences genome-wide. Here, we describe some of these tools and how their applications are furthering our knowledge of satellite evolution and function.

Figure 1. Assembly-free strategies for identifying and analyzing repetitive sequences

A) Alignment based approaches generally collapse repeat-derived reads onto known repeat consensus sequences (ConTExt, McGurk and Barbash, bioRxiv doi: 10.1101/158386). Copy number can be inferred from the alignment depth, while sequence polymorphism can be assessed from the collapsed reads. The large gray rectangle represents consensus sequence, while smaller black rectangles represent individual sequencing reads. Red positions within reads indicate sequence polymorphism. B) Kmer-based approaches decompose sequencing reads into overlapping subsequences of length k. Reads derived from simple satellites will be enriched for a small set of kmers. These kmers can be quantified (k-Seek [22]) or used in more abstract representations of reads [23]. C) Graph-based methods construct representations of repeats using sequence similarity. The nodes in such graphs are sequences: kmers (De Bruijin graphs), sequencing reads (e.g. RepeatExplorer [19]), or entire repeats [44]. The edges reflect neighboring relationships (sequence composition similarity). Because of their tandem nature, satellites often present as as circular graphs. Distinct repeat families can be identified as clusters of nodes. Here, two distinct satellites (the separate circular graphs, left and center) as well as a non-tandem sequence (right) are depicted.

Ectopic recombination between arrays results in copy number and sequence