Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha - PubMed (original) (raw)

Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha

Sudeesh Karumathil et al. Bioinform Biol Insights. 2016.

Abstract

Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman's rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from mutational pressure and selection, certain unknown selective forces might be acting on the PCGs in the analyzed mitogenomes as the phenomenon of SCUB could not be explained by mutational pressure, by selection, or by both.

Keywords: Chaetognatha; bilaterian lineage; evolution; mitogenomes; synonymous codon usage.

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Figures

Figure 1

Figure 1

ENC vs. GC3 plots for the quantification of SCUB. The SCUB of genes lying on or close to the expected GC3 is dictated by GC compositional constraints.

Figure 2

Figure 2

Neutrality plot. If correlation exists between GC3 and GC12, GC compositional constraints may have profound influence in shaping SCUB. If no correlation exists between GC3 and GC12, selection may have significant role in framing SCUB.

Figure 3

Figure 3

Parity rule 2 bias plot. This plot reveals the proportionate usage of A and T contents in comparison with that of G and C contents.

Figure 4

Figure 4

Correspondence analysis. Axis 1 accounts for the majority of variations. COA–RSCU plot reveals various factors that are responsible for the variations in RSCU values.

Figure 5

Figure 5

Cluster analysis. All examined species were grouped into two clusters based on the variations in RSCU values. All chaetognaths were grouped with species belonging to protostomes.

Figure 6

Figure 6

Identified major forces driving SCUB in mitogenomes of chaetognaths and other closely related phyla. The intensity of these forces vary and terms such as strong, moderate, and weak are used to express it.

References

    1. Hershberg R, Petrov DA. Selection on codon bias. Annu Rev Genet. 2008;42:287–99. - PubMed
    1. Shields DC, Sharp PM. Synonymous codon usage in Bacillus subtilis reflects both traditional selection and mutational biases. Nucleic Acids Res. 1987;15:8023–40. - PMC - PubMed
    1. Shields DC, Sharp PM, Higgins DG, Wright F. “Silent” sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol. 1988;5:704–16. - PubMed
    1. Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics. 1991;129:897–907. - PMC - PubMed
    1. Duret L. Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev. 2002;12:640–9. - PubMed

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