Repetitive Sequence and Noncoding DNA Evolution in Eukaryotes

Abstract

The amount of haploid nuclear DNA (or C-value) among eukaryotes varies more than 4 orders of magnitude, with brewer's yeast Saccharomyces cerevisiae (1.2 × 107 bp) or the parasitic microsporidium Encephalitozoon intestinalis (3 × 106 bp) as prototypical examples of the smallest genomes and several amoebae mentioned as the eukaryotes with largest genomes with > 6 × 1011 bp (e.g. Amoeba dubia and Chaos chaos ). Differences in the amount of noncoding DNA are also observed within a given taxonomic group, with algae varying more than 5000-fold, more than 1000-fold among flowering plants or invertebrates, more than 300-fold among vertebrates, and 100-fold among amphibians and insects. An apparent “paradox” arises when the size of the nuclear genome is compared to organismal complexity (morphological or developmental) if we assume that the amount of genetic material (genome size) should somehow correspond to the amount of genetic information. The so-called C-value paradox or enigma was coined to describe this lack of correspondence. Later findings revealed that coding sequences account for only a small proportion of the genomic DNA in most eukaryotes. This observation does not solve the C-value paradox, but shifts the debate from the number of genes responsible for a given degree of complexity (the G-value paradox) to the amount of noncoding DNA and the causes for its tremendous variation. In fact, recent studies based on fully sequenced genomes and expression data in model eukaryotes, including humans, have shown that complex gene regulation and the number of different transcripts—with a high fraction of genes having multiple transcripts—and not the number of genes, would better represent biological “complexity,” hence explaining the G-value paradox. Keywords: Deletion Bias; Effective Population Size (Ne)