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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00771

Compositional analysis of flatworm genomes shows strong codon usage biases across all classes

  • 1Department of Genetics, Faculty of Medicine, University of the Republic, Uruguay
  • 2Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Uruguay
  • 3Laboratory of Molecular Interactions, Faculty of Sciences, University of the Republic, Uruguay

In the present work, we performed a comparative genome wide analysis of 22 species representative of the main clades and lifestyles of the phylum Platyhelminthes. We selected a set of 700 orthologous genes conserved in all species, measuring changes in GC content, codon and amino acid usage in orthologous positions. Values of 3rd codon position GC spanned over a wide range allowing to discriminate two distinctive clusters within fresh-water turbellarians, Cestodes and Trematodes respectively. Furthermore, a hierarchical clustering of codon usage data differs remarkably from the phylogenetic tree. Additionally, we detected a synonymous codon usage bias that was more dramatic in extreme GC poor or rich genomes, i.e. GC poor Schistosomes preferred to use AT rich terminated synonymous codons, while GC rich M. lignano showed the opposite behavior. Interestingly, these biases impacted the amino acidic usage, with preferred amino acids encoded by codons following the GC content trend. These are associated with non-synonymous substitutions at orthologous positions. The detailed analysis of the synonymous and non-synonymous changes provides evidence for a two hit mechanism where both mutation and selection forces drive the diverse coding strategies of flatworms.

Keywords: Flatworms, GC content, synonymous codons, codon usage, Non-synonymous substitutions, amino acid usage, Mutation, selection

Received: 24 May 2019; Accepted: 22 Jul 2019.

Edited by:

Daniel Yero, Department of Genetics and Microbiology, Autonomous University of Barcelona, Spain

Reviewed by:

Deng-Feng Xie, Sichuan University, China
Arif Uddin, Assam University, India  

Copyright: © 2019 Lamolle, Fontenla, Rijo, Tort and Smircich. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Mx. Jose F. Tort, Department of Genetics, Faculty of Medicine, University of the Republic, Montevideo, Uruguay, jtort@fmed.edu.uy
Dr. Pablo Smircich, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay, psmircich@gmail.com