Abstract
The biological meaning of low complexity regions in the proteins of Plasmodium species is a topic of discussion in evolutionary biology. There is a debate between selectionists and neutralists, who either attribute or do not attribute an effect of low-complexity regions on the fitness of these parasites, respectively. In this work, we comparatively study 22 Plasmodium species to understand whether their low complexity regions undergo a neutral or, rather, a selective and species-dependent evolution. The focus is on the connection between the codon repertoire of the genetic coding sequences and the occurrence of low complexity regions in the corresponding proteins. The first part of the work concerns the correlation between the length of plasmodial proteins and their propensity at embedding low complexity regions. Relative synonymous codon usage, entropy, and other indicators reveal that the incidence of low complexity regions and their codon bias is species-specific and subject to selective evolutionary pressure. We also observed that protein length, a relaxed selective pressure, and a broad repertoire of codons in proteins, are strongly correlated with the occurrence of low complexity regions. Overall, it seems plausible that the codon bias of low-complexity regions contributes to functional innovation and codon bias enhancement of proteins on which Plasmodium species rest as successful evolutionary parasites.
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taken from GitHub-Matlab. c Trend of the sample averages of the distributions of b with respect to the average Guanine and Cytosine content of each parasite (Table 1)
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Data are retrievable from public archives as mentioned in methods. Supplementary files are provided as electronically.
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Scripts are available, upon request, from the corresponding author.
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The authors want to thank the anonymous referees whose corrections and questions have allowed us to greatly improve the work. Furthermore, we thank our Editor, prof. Horacio Naveira, for the extraordinary editing service and management of the entire peer review process.
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AC and AG conceived the study. AC conducted the analyses and conceived the original manuscript. AC, SF and AG read, edited, and approved the final manuscript.
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Cappannini, A., Forcelloni, S. & Giansanti, A. Evolutionary pressures and codon bias in low complexity regions of plasmodia. Genetica 149, 217–237 (2021). https://doi.org/10.1007/s10709-021-00126-6
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DOI: https://doi.org/10.1007/s10709-021-00126-6