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

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.

Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus

“…The existence of positive correlations between homogeneous nucleotide contents and negative correlations between heterogeneous nucleotide contents implies that mutational pressure due to compositional constraints might play a crucial role in shaping the codon usage. 64 In the case of viral genomes, the positively correlated heterogeneous contents and the negatively correlated homogeneous contents indicate natural selection by the host. 24 In this study, significant positive correlations were found between A and A 3 , T and T 3 , G and G 3 , and C and C 3 .…”

Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

“…In this study, patterns of SCUB and various factors which influence the formation of SCUB patterns in selected individuals of MCV-1 and MCV-2 were examined in detail. Positively correlated homogeneous base contents and negatively correlated heterogeneous base contents in MCV-1 and MCV-2 indicate the major influence of mutational pressure [66]. However, correlation analyses revealed the existence of positive heterogenous correlations (T and A3; C and G3) in all selected MC viruses.…”