Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes
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 orth...
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doaj-81f2485b996c47059f5cfb2f181ccabf2020-11-24T22:21:01ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-09-011010.3389/fgene.2019.00771474422Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All ClassesGuillermo Lamolle0Santiago Fontenla1Gastón Rijo2Jose F. Tort3Pablo Smircich4Pablo Smircich5Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, UruguayDepartamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, UruguayDepartamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, UruguayDepartamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, UruguayDepartamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, IIBCE, MEC, Montevideo, UruguayLaboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la Republica, UDELAR, Montevideo, UruguayIn 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 freshwater 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 GC-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.https://www.frontiersin.org/article/10.3389/fgene.2019.00771/fullflatwormsGC contentsynonymous codonscodon usagenon-synonymous substitutionsamino acid usage |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Guillermo Lamolle Santiago Fontenla Gastón Rijo Jose F. Tort Pablo Smircich Pablo Smircich |
spellingShingle |
Guillermo Lamolle Santiago Fontenla Gastón Rijo Jose F. Tort Pablo Smircich Pablo Smircich Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes Frontiers in Genetics flatworms GC content synonymous codons codon usage non-synonymous substitutions amino acid usage |
author_facet |
Guillermo Lamolle Santiago Fontenla Gastón Rijo Jose F. Tort Pablo Smircich Pablo Smircich |
author_sort |
Guillermo Lamolle |
title |
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes |
title_short |
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes |
title_full |
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes |
title_fullStr |
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes |
title_full_unstemmed |
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes |
title_sort |
compositional analysis of flatworm genomes shows strong codon usage biases across all classes |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2019-09-01 |
description |
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 freshwater 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 GC-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. |
topic |
flatworms GC content synonymous codons codon usage non-synonymous substitutions amino acid usage |
url |
https://www.frontiersin.org/article/10.3389/fgene.2019.00771/full |
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