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Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data
Joint Authors
Lin, Chorng-Horng
Wong, Tit-Yee
Hsiao, Yi-Yuong
Liu, Jong-Kang
Kuo, Jimmy
Source
International Journal of Genomics
Issue
Vol. 2010, Issue 2010 (31 Dec. 2010), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2010-10-05
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
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 (r=0.93 with P<.001).
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 (r=−0.89 with P<.001).
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.
American Psychological Association (APA)
Hsiao, Yi-Yuong& Lin, Chorng-Horng& Liu, Jong-Kang& Wong, Tit-Yee& Kuo, Jimmy. 2010. Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data. International Journal of Genomics،Vol. 2010, no. 2010, pp.1-9.
https://search.emarefa.net/detail/BIM-989226
Modern Language Association (MLA)
Hsiao, Yi-Yuong…[et al.]. Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data. International Journal of Genomics No. 2010 (2010), pp.1-9.
https://search.emarefa.net/detail/BIM-989226
American Medical Association (AMA)
Hsiao, Yi-Yuong& Lin, Chorng-Horng& Liu, Jong-Kang& Wong, Tit-Yee& Kuo, Jimmy. Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data. International Journal of Genomics. 2010. Vol. 2010, no. 2010, pp.1-9.
https://search.emarefa.net/detail/BIM-989226
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-989226