Abstract
BackgroundHirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data.ResultsWe identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species.ConclusionsCodon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection.
Highlights
Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications
To better understand the nucleotide base composition in H. manillensis, we measured the number of Coding sequences (CDS) with different GC content levels
Almost all CDSs contained 30–60% GC content (Fig. 1a); CDSs having GC contents lower than 30% or higher than 60% were considered as CDSs with extreme GC content
Summary
Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. The most popular and widely accepted hypothesis that explains codon usage bias is mutation-selection balance, which proposes that codon usage reflects the combined effects of three evolutionary forces: mutation pressure, selection constraints, and genetic drift within a. Selection constraints are the major influence on codon usage, as demonstrated in taxa such as Drosophila melanogaster, Bemisia tabaci, and Taenia pisiformis [7, 12, 13]. These studies demonstrate that characterising codon usage and other relevant indices provides simple and intuitive strategies for examining complex evolutionary forces in many different species
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