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Open Access Highly Accessed Research article

Evolution of complete proteomes: guanine-cytosine pressure, phylogeny and environmental influences blend the proteomic architecture

Wanping Chen3, Yanchun Shao23 and Fusheng Chen123*

Author Affiliations

1 Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China

2 National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China

3 College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China

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BMC Evolutionary Biology 2013, 13:219  doi:10.1186/1471-2148-13-219

Published: 3 October 2013

Additional files

Additional file 1:

Correlation coefficients between the frequencies of 11 amino acids in the three domains. The correlation between 20 standard amino acid frequencies was studied. Pearson correlation coefficients were used to evaluate the correlation between amino acid frequencies. The figure presents the correlations of 11 amino acids, which had significant correlations in frequency.

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Additional file 2:

Principal component analysis of the 20-dimentional amino acid frequency matrix. Prin1, Prin2 and Prin3 were the top three components, accounting for 43.91%, 16.84% and 11.06% of the total information, respectively. (a) Factorial plane of Prin1 and Prin2. (b) Factorial plane of Prin1 and Prin3. (c) Factorial plane of Prin2 and Prin3.

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Additional file 3:

Comparison of the features of amino acid distribution in the 11 main branches of the clustering tree. The values were expressed as averages and reflected by rectangle lengths. (a) The frequency distribution of the 20 amino acids in the 11 main branches (groups A–K). (b) The frequency distribution of charged, hydrophobic, and polar and uncharged amino acids. (c) The frequency distribution of aliphatic, aromatic and heterocyclic amino acids. (d) Boxplot of Pearson correlation coefficients between the 20 amino acid frequencies and their corresponding synonymous codon frequencies in the 11 groups.

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Additional file 4:

Correlation analysis of physico-chemical properties of amino acids with genomic GC content in 461 species. Pearson correlation coefficients were used to evaluate the correlation between composition of physico-chemical groups and genomic GC content in 461 species.

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Additional file 5:

Comparison of the distribution of the 20 amino acid frequencies in different taxonomic groups. Archaea groups (Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota and Thaumarchaeota), Bacteria groups (Actinobacteria, Aquificae, Bacteroidetes/Chlorobi, Chlamydiae/Verrucomicrobia, Chloroflexi, Chrysiogenetes, Cyanobacteria, Deferribacteres, Deinococcus-Thermus, Dictyoglomi, Elusimicrobia, Fibrobacteres/Acidobacteria, Firmicutes, Fusobacteria, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Spirochaetes, Synergistetes, Tenericutes, Thermode sulfobacteria and Thermotogae) and Eukaryota groups (Animals, Fungi, Plants and Protists). The taxonomy information was extracted from NCBI classification. The amino acid frequencies in different taxonomic groups were represented as averages plus standard deviations and their expected values based on the universal genetic code were indicated by dash lines.

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Additional file 6:

List of the 461 species from Archaea, Bacteria, and Eukaryota analyzed in this study.

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