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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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GC contents of intergenic regions and GC3 content of CDS contained respectively in H, M and L isochore predicted in vertebrates by our HMMs.
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Figure 8: GC contents of intergenic regions and GC3 content of CDS contained respectively in H, M and L isochore predicted in vertebrates by our HMMs.

Mentions: The GC content for H, M and L isochores from the two Teleost fishes and human (from [17]) are shown in figure 7 and 8. The D rerio genome is more homogeneous compared with the T nigroviridis genome but the segmentation of the two fish genomes was related to the GC content.


The GC-heterogeneity of teleost fishes.

Melodelima C, Gautier C - BMC Genomics (2008)

GC contents of intergenic regions and GC3 content of CDS contained respectively in H, M and L isochore predicted in vertebrates by our HMMs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: GC contents of intergenic regions and GC3 content of CDS contained respectively in H, M and L isochore predicted in vertebrates by our HMMs.
Mentions: The GC content for H, M and L isochores from the two Teleost fishes and human (from [17]) are shown in figure 7 and 8. The D rerio genome is more homogeneous compared with the T nigroviridis genome but the segmentation of the two fish genomes was related to the GC content.

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
Related in: MedlinePlus