Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Hsiao YY

PROVIDER: S-EPMC2967832 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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

Hsiao Yi-Yuong YY Lin Chorng-Horng CH Liu Jong-Kang JK Wong Tit-Yee TY Kuo Jimmy J

Comparative and functional genomics 20101101

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 th ...[more]

PMID: 21052492

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Project description:The eastern Bering Sea has a vast continental shelf, which contains various endangered marine mammals and large fishery resources. Recently, high numbers of toxic A. tamarense resting cysts were found in the bottom sediment surface of the eastern Bering Sea shelf, suggesting that the blooms have recently occurred. However, little is known about the presence of A. tamarense vegetative cells in the eastern Bering Sea. This study's goals were to detect the occurrence of A. tamarense vegetative cells on the eastern Bering Sea shelf and to find a relationship between environmental factors and their presence. Inter-annual field surveys were conducted to detect A. tamarense cells and environmental factors, such as nutrients, salinity, chlorophyll a, and water temperature, along a transect line on the eastern Bering Sea shelf during the summers of 2004, 2005, 2006, 2009, 2012, and 2013. A. tamarense vegetative cells were detected during every sampling year, and their quantities varied greatly from year to year. The maximum cell densities of A. tamarense observed during the summers of 2004 and 2005 were much higher than the Paralytic shellfish poisoning warning levels, which are greater than 100-1,000 cells L-1, in other subarctic areas. Lower quantities of the species occurred during the summers of 2009, 2012, and 2013. A significant positive correlation between A. tamarense quantity and water temperature and significant negative correlations between A. tamarense quantity and nutrient concentrations (of phosphate, silicate, and nitrite and nitrate) were detected in every sampling period. The surface- and bottom-water temperatures varied significantly from year to year, suggesting that water temperatures, which have been known to affect the cell growth and cyst germination of A. tamarense, might have affected the cells' quantities in the eastern Bering Sea each summer. Thus, an increase in the Bering Sea shelf's water temperature during the summer will increase the frequency and scale of toxic blooms and the toxin contamination of plankton feeders. This poses serious threats to humans and the marine ecosystem.

Dataset Information

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

Publications

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

Similar Datasets

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