Abstract
BackgroundOne of the most striking features of mammalian and birds chromosomes is the variation in the guanine-cytosine (GC) content that occurs over scales of hundreds of kilobases to megabases; this is known as the "isochore" structure. Among other vertebrates the presence of isochores depends upon the taxon; isochore are clearly present in Crocodiles and turtles but fish genome seems very homogeneous on GC content. This has suggested a unique isochore origin after the divergence between Sarcopterygii and Actinopterygii, but before that between Sauropsida and mammals. However during more than 30 years of analysis, isochore characteristics have been studied and many important biological properties have been associated with the isochore structure of human genomes. For instance, the genes are more compact and their density is highest in GC rich isochores.ResultsThis paper shows in teleost fish genomes the existence of "GC segmentation" sharing some of the characteristics of isochores although teleost fish genomes presenting a particular homogeneity in CG content. The entire genomes of T nigroviridis and D rerio are now available, and this has made it possible to check whether a mosaic structure associated with isochore properties can be found in these fishes. In this study, hidden Markov models were trained on fish genes (T nigroviridis and D rerio) which were classified by using the isochore class of their human orthologous. A clear segmentation of these genomes was detected.ConclusionThe GC content is an excellent indicator of isochores in heterogeneous genomes as mammals. The segmentation we obtained were well correlated with GC content and other properties associated to GC content such as gene density, the number of exons per gene and the length of introns. Therefore, the GC content is the main property that allows the detection of isochore but more biological properties have to be taken into account. This method allows detecting isochores in homogeneous genomes.
Highlights
One of the most striking features of mammalian and birds chromosomes is the variation in the guanine-cytosine (GC) content that occurs over scales of hundreds of kilobases to megabases; this is known as the "isochore" structure
The segmentation we obtained were well correlated with GC content and other properties associated to GC content such as gene density, the number of exons per gene and the length of introns
Preliminary results obtained in the chicken genome In this study, we assume that orthologous genes remain approximately in the same isochore class over evolutionary time between human and fish genomes
Summary
One of the most striking features of mammalian and birds chromosomes is the variation in the guanine-cytosine (GC) content that occurs over scales of hundreds of kilobases to megabases; this is known as the "isochore" structure. Among other vertebrates the presence of isochores depends upon the taxon; isochore are clearly present in Crocodiles and turtles but fish genome seems very homogeneous on GC content. The isochore has been classified as a "fundamental level of genome organization" [2], and this concept has increased our appreciation of the complexity and variability of the composition of eukaryotic genomes [3]. The genomes of amphibians and fishes (cold-blooded vertebrates) are characterized by a much lower level of compositional heterogeneity [7]. From these observations, a correlation between isochore structure and body temperature pattern is assumed [8]. Even if only partial dataset are available, it seems that almost all cold-blooded vertebrates show substantially less variability in GC3 within their genomes than warm-blooded species
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