Number Of Introns In The Drosophila Genome And Codon Usage Bias Relationship

Codon usage bias is the phenomenon of non-uniformity use of the synonymous codons that many codons code for the same amino acid. In the post-genome era, a lot of investigations indicate that codon usage bias is widespread in both eukaryotic and prokaryotic genomes, and the "selection-mutation-drift" theory has been put forward to explaining the evolutionary mechanism of the codon usage bias. In the genomes of some organisms such as the bacteria, yeast and drosophile, synonymous codons tend to use codons that the third base is G or C. These codons may have a little advantage, because they correspond to the tRNA abundance distribution in the genome and hence may facilitate synthesis of the gene production. An important prediction of "selection-mutation-drift" theory is that if a gene experiences a highly selective pressure, such as high expression, it may be inclined to stronger codon usage bias.Eukaryotic gene is more complex than prokaryotic one. Most of coding regions in the eukaryotic gene are non-continuous, and coding regions are often split to many small segments by introns. Recently a population genetics research revealed that the insertion of the intron may be slightly deleterious (Lynch 2002). So, if a gene experiences a strong selective pressure, it may have fewer introns. According to the above two deductions, one can predict that the number of introns in a gene may have negative relationship with codon usage bias. The purpose of this paper is to validate the speculation by using the genome information of a model organism, Drosophila melanogaster.The results revealed that the amount of the introns have a significantly negative correlation with codon usage bias. As the increase of the introns, the contents of the GC and codon usage bias (the scaled x~2 and N_C) decrease. But the values of GC3, GC3s and codon adaptation index (CAI) increase with intron number, and become maximum until it has 2 introns, and then decrease with the increase of intron number. When a gene only has one intron, the difference of the intron insertion positions may have influence on GC contents and codon usage bias. The more distant from the start codon, the lower the GC contents of CDS is and the less codon usage bias is.For stop codons which are the termination signal in protein translation, the results reveal that for the genes without intron, the usage of the stop codons has a strong preference. However, as the number of introns per gene increases, the preference becomes weak. The most commonly used stop codon is TAA, the next is TAG and the usage of TGA is the fewest. This preference is more evident in the highly expressed genes. Additionally, it was found that the length ratio of intron to CDS also has a significant relationship with the GC contents and codon usage bias.Our results are consistent with the predictions of "selection-mutation-drift" theory, implying that in the eukaryotic genomes, such as Drosophila, the structure of the gene (the number of introns) and codon usage bias might have coevolved and their evolution was driven not only by mutation and drift but also by selection.