Compressed Synteny Plots: a Tool for Visualizing Repeated Genomic Sequences

摘要

Repeated sequences are ubiquitous in eukaryotic genomes. Useful information about the number of copies, their degree of similarity, and their position in the genome can be visualized by matching each 1000bp segment of the genome against the rest of the genome using BLAST or MUMmer, and then plotting the coordinates of each hit. The x-axis, representing the query sequence., is plotted at 30bp per pixel, a scale that shows each gene as a well-separated entity. The y-axis, representing the subject sequences (i.e. repeats in other regions of the genome), is plotted at a very compressed scale that allows the entire genome to be seen at once. For the Arabidopsis thaliana genome we used a y-axis scale of 200,000bp per pixel. On these plots, repeats are seen as horizontal lines above and below the main chromosome line. The technique is demonstrated with several examples from the Arabidopsis genome.