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Representing GC variation along eukaryotic chromosomes

Jan Pac̀es, Radek Zı́ka, Václav Pac̀es, Adam Pavlı́c̀ek, Oliver Clay, and Giorgio Bernardi

Gene (2004) PMID 15177688

Genome sequencing now permits direct visual representation, at any scale, of GC heterogeneity along the chromosomes of several higher eukaryotes. Plots can be easily obtained from the chromosomal sequences, yet sequence releases of mammalian or plant chromosomes still tend to use small scales or window sizes that obscure important large-scale compositional features. To faithfully reveal, at one glance, the compositional variation at a given scale, we have devised a simple scheme that combines line plots with color-coded shading of the regions underneath the plots. The scheme can be applied to different eukaryotic genomes to facilitate their comparison, as illustrated here for a sample of chromosomes chosen from seven selected species. As a complement to a previously published compact view of isochores in the human genome sequence [FEBS Lett. 511 (2002a) 165], we include here an analogous map for the recently sequenced mouse genome, and discuss the contribution of repetitive DNA to the GC variation along the plots. Supplementary information, including a database of color-coded GC profiles for all recently sequenced eukaryotes and the program draw_chromosomes_gc.pl used to obtain them, are available at http://genomat.img.cas.cz.

Copyright © 2004 Elsevier Ltd. All rights reserved.

DOI: 10.1016/j.gene.2004.02.041
Version: za2963e q8za7 q8zbe q8zcf q8zdc q8ze5 q8zfd q8zg3

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