Codon usage in the siliceous sponge Geodia cydonium: highly expressed genes in the simplest multicellular animals prefer C- and G-ending codons

Among a sample of 39 Geodia cydonium (Demospongiae, Porifera) genes, with a n average G + C content of 51.2%, extensive structural heterogeneity and co nsiderable variations in synonymous codon usage were found. The G + C conte nt of coding sequences and G + C content at silent codon positions (GC3S) v aried from 42.4 to 59.2% and from 35.6 to 76.5%, respectively. Corresponden ce analysis of 39 genes revealed that putative highly expressed genes prefe rentially use a limited subset of codons, which were therefore defined as p referred codons in C. cydonium. A total of 22 preferred codons for 18 amino acids with synonyms in codons were identified and they all (with one excep tion) end with C or G. Among these codons there are also C- and G-ending co dons which were previously identified as codons optimal for translation in a variety of eukaryotes, including metazoans and plants. The bias in synony mous codon usage in putative highly expressed G. cyonium genes is moderate, indicating that these genes are not shaped under strong natural selection. We postulate that the preference for C- and G-ending codons was already es tablished in the ancestor of all Metazoa, including also sponges. This ance stor most probably also had a G + C rich genome. The selection toward C- an d G-ending codons has been largely conserved throughout eukaryote evolution exceptions are, for example, mammals for which strong mutational biases ca used switches from that rule,