Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes - PubMed (original) (raw)

Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes

Jonathan Romiguier et al. Genome Res. 2010 Aug.

Abstract

The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconstructed their ancestral isochore organization in the maximum likelihood framework, and explored the evolution of third-codon position GC content in representatives of 16 orders and 27 families. We showed that the previously reported erosion of GC-rich isochores is not a general trend. Several species (e.g., shrew, microbat, tenrec, rabbit) have independently undergone a marked increase in GC content, with a widening gap between the GC-poorest and GC-richest classes of genes. The intensively studied apes and (especially) murids do not reflect the general placental pattern. We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene conversion model.

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Figures

Figure 1.

Genomic third-codon position GC-content (GC3) evolution in placental mammals. Colors reflect current or estimated average GC3 on 1138 orthologous genes (green, low GC; yellow, medium GC; red, high GC). current or estimated average GC3 on 1138 orthologous genes. Branch lengths quantify the amount of GC3 divergence: the branch connecting nodes i and j has a length proportional to Di,j (Equation 2). The estimated ancestral GC content of the placental ancestor is 46.2%.

Figure 2.

Gene GC-content distribution in three representative placental species. (A) Third-codon position GC content (GC3); (B) 5′- and 3′-flanking GC content. (Curved line) Estimated GC distribution of the common placental ancestor. (Gray histogram) Observed distributions of extant species. As compared to the estimated ancestral state, humans show a conservative pattern, tenrecs (Echinops telfairi) a global enrichment in GC, and mice (Mus musculus) a decreased variance in GC across genes.

Figure 3.

Relationship between genomic average and standard deviation of GC3.

Figure 4.

GC3 dynamics in GC3-rich versus GC3-poor genes. Genes are divided into five categories, depending on their ancestral GC3%. Blue, green, orange, red, and brown are used from the least GC-rich to the most GC-rich categories. Within each category, the average GC3 of each placental species is plotted against Di,anc (i.e., the average amount of GC3 divergence among the 1138 genes since the placental ancestor). Dotted lines represent the average ancestral GC3 within each category.

Figure 5.

Relationship between adult body mass and GC3 (left) and Di,anc (right).

Figure 6.

Relationship between genome size and GC3.

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Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes - PubMed (original) (raw)