Eukaryotic genomes, particularly animal genomes, have a complex, nonuniform, and nonrandom internal compositional organization. The compositional organization of animal genomes can be described as a mosaic of discrete genomic regions, called “compositional domains,” each with a distinct GC content that significantly differs from those of its upstream and downstream neighboring domains. A typical animal genome consists of a mixture of compositionally homogeneous and nonhomogeneous domains of varying lengths and nucleotide compositions that are interspersed with one another. We have devised IsoPlotter, an unbiased segmentation algorithm for inferring the compositional organization of genomes. IsoPlotter has become an indispensable tool for describing genomic composition and has been used in the analysis of more than a dozen genomes. Applications include describing new genomes, correlating domain composition with gene composition and their density, studying the evolution of genomes, testing phylogenomic hypotheses, and detect regions of potential interbreeding between human and extinct hominines. To extend the use of IsoPlotter, we designed a completely automated pipeline, called IsoPlotter+ to carry out all segmentation analyses, including graphical display, and built a repository for compositional domain maps of all fully sequenced vertebrate and invertebrate genomes. The IsoPlotter+ pipeline and repository offer a comprehensive solution to the study of genome compositional architecture. Here, we demonstrate IsoPlotter+ by applying it to human and insect genomes. The computational tools and data repository are available online. 1. Introduction While the genome sizes of multicellular eukaryotes are generally larger and more variable in length than those of prokaryotes, guanine and cytosine (GC) content exhibits a much smaller variation in eukaryotes than in prokaryotes. In particular, vertebrate genomes show quite a uniform GC content, distributing over a very narrow range from about 40% to 45% [1]. Despite the uniformity of their genomic GC content, vertebrate genomes have a much more complex compositional organization than prokaryotic genomes. Recent studies have shown that this narrow distribution cloaks a complex mosaic of homogeneous and nonhomogeneous compositional domains whose sizes range from 3 kilobases (kb) to more than 10 Mega bases (Mb) and whose GC contents range from ~7% to ~72% (e.g., [2, 3]). Molecular evolutionists have had a long-standing interest in deciphering the internal compositional organization of genomes, describing their
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