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Comparative and Functional Genomics
Volume 2010, Article ID 138538, 9 pages
Research Article

Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data

1Graduate Institute of Marine Biotechnology, National Dong Hwa University, Pingtung 944, Taiwan
2Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan
3Department of Bioresources, Da-Yeh University, Da Tsuen, Chang hua 515, Taiwan
4Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
5Bioinformatics Program, Department of Biology, The University of Memphis, Memphis, TN 38152, USA

Received 10 August 2010; Accepted 1 October 2010

Academic Editor: John Parkinson

Copyright © 2010 Yi-Yuong Hsiao et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


We have analyzed synonymous codon usage in the genome of A. tamarense CCMP 1598 for protein-coding sequences from 10865 expressed sequence tags (ESTs). We reconstructed a total of 4284 unigenes, including 74 ribosomal protein and 40 plastid-related genes, from ESTs using FrameDP, an open reading frame (ORF) prediction program. Correspondence analysis of A. tamarense genes based on codon usage showed that the GC content at the third base of synonymous codons (GC3s) was strongly correlated with the first axis ( with ). On the other hand, the second axis discriminated between presumed highly and low expressed genes, with expression levels being confirmed by the analysis of EST frequencies ( with ). Our results suggest that mutational bias is the major factor in shaping codon usage in A. tamarense genome, but other factors, namely, translational selection, hydropathy, and aromaticity, also appear to influence the selection of codon usage in this species.