Fujita MK et al. (2011), The Anolis lizard genome: an amniote genome wit...

XB-ART-44341

Genome Biol Evol 2011 Jan 01;3:974-84. doi: 10.1093/gbe/evr072.

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The Anolis lizard genome: an amniote genome without isochores.

Fujita MK , Edwards SV , Ponting CP .

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Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to have the most compositionally homogeneous genome of all amniotes sequenced thus far, a homogeneity exceeding that for the frog Xenopus. Based on a Bayesian algorithm, Anolis has smaller and less GC-rich isochores compared with human and chicken. Correlates generally associated with GC-rich isochores, including shorter introns and higher gene density, have all but disappeared from the Anolis genome. Using genic GC as a proxy for isochore structure so as to compare with other vertebrates, we found that GC content has substantially decreased in the lineage leading to Anolis since diverging from the common ancestor of Reptilia ∼275 Ma, perhaps reflecting weakened or reversed GC-biased gene conversion, a nonadaptive substitution process that is thought to be important in the maintenance and trajectory of isochore evolution. Our results demonstrate that GC composition in Anolis is not associated with important features of genome structure, including gene density and intron size, in contrast to patterns seen in mammal and bird genomes.

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Species referenced: Xenopus
Genes referenced: acta4

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	FIG. 1. Distributions of GC content in vertebrate genomes. Distributions are based on GC contents of 3-kb windows for genomes of human, chicken, Xenopus frog, and Anolis.
	FIG. 2. Observed and expected reduction of genomic GC spread for increasing window size. SDs were calculated for increasing window lengths (x axis) in human (+), chicken (â¡), Xenopus frog (Î), and Anolis (Ã). The expected curve (O) is based on calculations from human mean GC content (see Materials and Methods), but it is nearly identical for those of the other genomes.
	FIG. 3. GC composition along Anolis macrochromosomes. Graphs are based on GC contents of 3-kb windows, ignoring windows with >20% missing data. The bars above the plots represent classical isochores (>300 kb in length).
	FIG. 4. Amniote phylogeny with branch lengths proportional to Di,j. Di,j is the divergence of GC3 between two nodes of a branch. Black branches represent decreases of GC3, whereas gray branches represent increases of GC3. The current GC3 and the equilibrium GC3* are also shown and demonstrate the expected continued trajectory of GC content evolution.
	FIG. 5. Correlations with flanking GC content. (A) Flanking GC content exhibits greater correlation with GC3 (genic GC at third codon positions) in human and chicken (higher r2) than in Anolis. (B) Flanking GC content correlate between human and chicken, implying conserved isochore structure in mammals and birds, but less so between Anolis and human or chicken. Sample sizes (N) include genes with long open-reading frame (length > 1,000 bp) that were not saturated (dS < 1) or undergoing positive selection (dN/dS < 1).
	FIG. 6. GC content decreases as noncoding sequence length increases. Noncoding sequences were divided into ten bins based on length. The line connects median GC values from each bin. In human and chicken, GC content decreases as (A) intergenic and (B) intron sequence length increases but exhibits a flat relationship with noncoding sequence length in Anolis.

References [+] :

Alföldi, The genome of the green anole lizard and a comparative analysis with birds and mammals. 2011, Pubmed