The Decline of Isochores in Mammals: An Assessment of the GC ContentVariation Along the Mammalian Phylogeny

Belle, Elise M. S.; Duret, Laurent; Galtier, Nicolas; Eyre‐Walker, Adam

doi:10.1007/s00239-004-2587-x

Cited by 64 publications

(70 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The erosion of GC-rich isochores in primates was again confirmed by the analysis of substitutions in introns and intergenic regions (Webster et al 2003;Meunier and Duret 2004). This erosion of GC-rich isochores has also been noted in carnivores, but not in lagomorphs or perissodactyls (Belle et al 2004). …”

mentioning

confidence: 57%

“…The latter result was criticized because the cetartiodactyls species that we had analyzed were too distantly related and, therefore, the parsimony approach that we had used was not reliable (Alvarez-Valin et al 2004). Indeed, the analysis of synonymous substitutions by a maximum likelihood approach confirmed the erosion of GC-rich isochores in primates and in rodents, but not in cetartiodactyles (Belle et al 2004). The erosion of GC-rich isochores in primates was again confirmed by the analysis of substitutions in introns and intergenic regions (Webster et al 2003;Meunier and Duret 2004).…”

mentioning

confidence: 95%

See 1 more Smart Citation

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium: A Reply to Antezana

Duret

2006

J Mol Evol

Self Cite

View full text Add to dashboard Cite

To study the patterns of neutral substitutions in the human genome, we have recently analyzed a large data set of alignments of orthologous noncoding DNA sequences from human, chimpanzee, and baboon (Meunier and Duret 2004). We observed that the base composition of the human genome is not at equilibrium: substitutions from G or C to A or T (hereafter referred to as GC fi AT substitutions) are more numerous than AT fi GC substitutions. Antezana (2005) has re-analyzed the genomic alignment data that we had compiled. In contradiction to our results, he found that the GC-content of the human genome is close to the equilibrium. The explanation he proposed for this discrepancy is that Meunier and Duret ''used a malfunctioning dinucleotide-level simulation procedure out of concern for contextdependent mutation effects.'' I show here that in fact, Antezana (2005) used an erroneous procedure to count substitutions that ignored the hypermutability of CpG dinucleotides, and therefore led to systematically overestimating the number of AT fi GC substitutions.Antezana (2005) used parsimony to count substitutions in alignments of orthologous human, chimpanzee, and baboon nongenic DNA sequences: substitutions to human or chimpanzee were retrieved from sites at which the baboon base and the base in one of the two nonbaboon sequences were identical but different from the base in the other nonbaboon sequence. It is well established that because of multiple substitutions, parsimony may be erroneous when patterns of substitutions are biased (EyreWalker 1998). It is also well known that in mammals, CpG dinucleotides are mutational hot spots: the rate of transition (C fi T or G fi A) at CpG sites is about 10 times higher than at non-CpG sites (Giannelli et al. 1999). Thus, although the average rate of divergence (excluding indels) between human and chimpanzee is 1.2%, the divergence at CpG sites is about 15.2% (CSAC 2005). Hence, as mentioned in our article (Meunier and Duret 2004), there is an important frequency of homoplasy at CpG sites, and therefore parsimony must be used with caution.To illustrate this problem of homoplasy at CpG sites, let us take a simple example, very similar to the real situation in our human/chimp/baboon alignments: two species (species1 and species2) and an outgroup, such that the evolutionary distance at nonCpG sites is 0.01 substitutions/site between species1 and species2 and 0.05 substitutions/site between the outgroup and the two other species (Fig. 1a), and the rate of substitution at CpG sites is 10 times higher than at non-CpG sites. Let us consider a site that corresponds to a T in species1, a C in species2, a T in the outgroup and that is followed by a C, conserved in the three species (Fig. 1b, c). The scenario proposed by the simple parsimony method predicts that the ancestral sequence was TC and that a single T fi C substitution occurred in the species2 lineage. The probability of that scenario is 5 · 10 )3 (Fig. 1b). The second most likely scenario involves two independent substitutions, and i...

show abstract

mentioning

confidence: 57%

mentioning

confidence: 95%

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium: A Reply to Antezana

Duret

2006

J Mol Evol

Self Cite

View full text Add to dashboard Cite

show abstract

“…The isochore structure is vanishing in mammalian genomes, according to recent studies (Duret et al 2002;Arndt et al 2003b;Belle et al 2004). Moreover, Meunier and Duret (2004) have demonstrated that the current substitution pattern in human genome should lead to a new isochore structure, with a lower GC mean and a lower variance.…”

Section: Evolution Of Isochore Structure In Mammalian Genomesmentioning

confidence: 95%

“…Kauppi and colleagues (2004) have demonstrated that the rate of gene conversion outside CO is 4 to 15 times higher than the rate of gene conversion inside CO. Recent works have demonstrated that GC-BGC can increase GC content very quickly (Belle et al 2004;Kudla et al 2003;Galtier 2004;Webster et al 2005). The rate of gene conversion is 100 times higher than the rate of neutral substitutions in mammalian genomes (Kudla et al 2004), which could be enough to induce a tremendous change in GC content and in isochore structure.…”

Section: The Impact Of Recombination On Gc Content Evolutionmentioning

confidence: 99%

GC Content Evolution of the Human and Mouse Genomes: Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates

et al. 2006

Self Cite

View full text Add to dashboard Cite

Abstract. Processed pseudogenes are generated by reverse transcription of a functional gene. They are generally nonfunctional after their insertion and, as a consequence, are no longer subjected to the selective constraints associated with functional genes. Because of this property they can be used as neutral markers in molecular evolution. In this work, we investigated the relationship between the evolution of GC content in recently inserted processed pseudogenes and the local recombination pattern in two mammalian genomes (human and mouse). We confirmed, using original markers, that recombination drives GC content in the human genome and we demonstrated that this is also true for the mouse genome despite lower recombination rates. Finally, we discussed the consequences on isochores evolution and the contrast between the human and the mouse pattern.

show abstract

“…S6). The wider distribution of GþC content in human and dog is thus likely to reflect the boreoeutherian ancestor 44,45 , with the more homogeneous composition in rodents having arisen primarily through lineagespecific changes in substitution patterns 46,47 rather than deletion of sequences with high GþC content. Rate of nucleotide divergence.…”

Section: Generating a Draft Genome Sequencementioning

confidence: 99%

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Lindblad‐Toh¹,

Wade²,

Mikkelsen³

et al. 2005

Nature

2,234

2,079

View full text Add to dashboard Cite

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

show abstract

The Decline of Isochores in Mammals: An Assessment of the GC ContentVariation Along the Mammalian Phylogeny

Cited by 64 publications

References 31 publications

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium: A Reply to Antezana

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium: A Reply to Antezana

GC Content Evolution of the Human and Mouse Genomes: Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Contact Info

Product

Resources

About