Article

Effects of GC content and mutational pressure on the lengths of exons and coding sequences

Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
Journal of Molecular Evolution (Impact Factor: 1.86). 03/2003; 56(3):362-70. DOI: 10.1007/s00239-002-2406-1
Source: PubMed

ABSTRACT It has been hypothesized that the length of an exon tends to increase with the GC content because stop codons are AT-rich and should occur less frequently in GC-rich exons. This prediction assumes that mutation pressure plays a significant role in the occurrence and distribution of stop codons. However, the prediction is applicable not to all exons, but only to the last coding exon of a gene and to single-exon CDS sequences. We classified exons in multiexon genes in eight eukaryotic species into three groups-the first exon, the internal, and the last exon-and computed the Spearman correlation between the exon length and the percentage GC (%GC) for each of the three groups. In only five of the species studied is the correlation for the last coding exon greater than that for the first or internal exons. For the single-exon CDS sequences, the correlation between CDS length and %GC is mostly negative. Thus, eukaryotic genomes do not support the predicted relationship between exon length and %GC. In prokaryotic genomes, CDS length and %GC are positively correlated in each of the 68 completely sequenced prokaryotic genomes in GenBank with genomic GC contents varying from 25 to 68%, except for the wall-less Mycoplasma genitalium and the syphilis pathogen Treponema pallidum. Moreover, the average CDS length and the genomic GC content are also positively correlated. After correcting for genome size, the partial correlation between the average CDS length and the genomic GC content is 0.3217 ( p < 0.025).

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    • "The sequences were aligned in Geneious 5.6 (Biomatters, Auckland, New Zealand) and substitution saturation in different codon position for coding regions was detected using Xia et al. (2003) test performed in DAMBE5 (Xia 2013). Appropriate models of evolution for each gene partition were determined in jModelTest 2.1.4 "
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    • "They suggested that the longest coding sequences/exons in vertebrates are GC rich, while the shortest ones are GC-poor. Subsequently, Xia et al. (2003) described positive correlations between GC content and coding regions (CDS) lengths in 68 genomes. It was later shown that highly expressed rice and human GC-rich genes have significantly more and longer introns than lowly expressed genes, whereas their average exon length per gene is significantly lower. "
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    • "We analyzed the first, internal, and last exons separately. If exon length is different because of ATbiased mutations leading to a gain of stop codons and thus a shortening of the transcript, then a significant difference in GC content of those longer transcripts should be primarily found in the last exon (Xia et al. 2003). The average percent GC content was used for genes with multiple internal exons. "
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