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Highly Expressed Genes in Marine Sponge Suberites domuncula Prefer C- and G-Ending Codons 

Drago Perina1, Matija Harcet1, Andreja Mikoč1, Kristian Vlahoviček2, Werner E. G. Müller3 and Helena Ćetković1*


1
Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia

2Faculty of Science, Division of Biology, Molecular Biology Department, Horvatovac 102a, HR-10000 Zagreb, Croatia
3Institute for Physiological Chemistry, Department for Applied Molecular Biology, Johannes Gutenberg University, Duesbergweg 6, D-55099 Mainz, Germany

Article history:

Received November 11, 2008
Accepted May 27, 2009

Key words:

porifera, Suberites domuncula, codon usage

Summary:

Sponges are the simplest extant phylum of Metazoa; they are closest to the common ancestor of all multicellular animals. A total of 223 coding sequences from Suberites domuncula (Demospongiae) represent the dataset for the codon usage analysis. A total of 46038 codons had an average guanine and cytosine (G+C) content of 45.8 % and an average content of guanine and cytosine at the synonymous third position of codons (GC3S) of 43.4 %. In this sample of genes considerable variations in synonymous codon usage were found. The G+C content of the coding sequences varied from 34 to 56.1 % and GC3S from 19 to 58.7 %. Correspondence analysis revealed that highly expressed genes preferentially use a limited subset of codons (preferred codons). A total of 15 preferred codons were found and they all, with one exception, end with C or G. The preferential use of C- or G-ending codons in highly expressed genes was possibly developed in a common ancestor of sponges and other Metazoa and it has remained conserved throughout the sponge evolution.

 


*Corresponding author:           cetkovic@irb.hr
                                               ++385 1 4571 239
                                               ++385 1 4561 177

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