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The GC-heterogeneity of teleost fishes.

Melodelima C, Gautier C - BMC Genomics (2008)

Bottom Line: 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.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.This method allows detecting isochores in homogeneous genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J, Fourier, 38041 Grenoble Cedex 9, France. christelle.melo-de-lima@ujf-grenoble.fr

ABSTRACT

Background: 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. 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.

Results: This 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.

Conclusion: The 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.

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Distribution of isochores along D rerio chromosomes 7 and 16. The H, L and M isochores detected are shown in red, green and blue respectively. To check the consistency of isochore prediction, the graph is shown alongside a plot of the GC content along the chromosome.
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Figure 5: Distribution of isochores along D rerio chromosomes 7 and 16. The H, L and M isochores detected are shown in red, green and blue respectively. To check the consistency of isochore prediction, the graph is shown alongside a plot of the GC content along the chromosome.

Mentions: The T nigroviridis and D rerio genome segmentations obtained by our method are shown in Figures 4 and 5. Maps of all the chromosomes of the T nigroviridis and D rerio genomes are available online at .


The GC-heterogeneity of teleost fishes.

Melodelima C, Gautier C - BMC Genomics (2008)

Distribution of isochores along D rerio chromosomes 7 and 16. The H, L and M isochores detected are shown in red, green and blue respectively. To check the consistency of isochore prediction, the graph is shown alongside a plot of the GC content along the chromosome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651174&req=5

Figure 5: Distribution of isochores along D rerio chromosomes 7 and 16. The H, L and M isochores detected are shown in red, green and blue respectively. To check the consistency of isochore prediction, the graph is shown alongside a plot of the GC content along the chromosome.
Mentions: The T nigroviridis and D rerio genome segmentations obtained by our method are shown in Figures 4 and 5. Maps of all the chromosomes of the T nigroviridis and D rerio genomes are available online at .

Bottom Line: 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.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.This method allows detecting isochores in homogeneous genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J, Fourier, 38041 Grenoble Cedex 9, France. christelle.melo-de-lima@ujf-grenoble.fr

ABSTRACT

Background: 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. 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.

Results: This 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.

Conclusion: The 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.

Show MeSH