COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences

Jérôme Bourret (1) , Samuel Alizon (2, 3) , Ignacio Bravo (4)

1 MIVEGEC - Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle
2 MIVEGEC-ETE - Evolution Théorique et Expérimentale
3 CIRB - Centre interdisciplinaire de recherche en biologie
4 MIVEGEC-Virostyle - Virostyle

Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been developed to evaluate CUPrefs, either in absolute terms or with respect to a reference. We introduce the normalized index COUSIN (for COdon Usage Similarity INdex), that compares the CUPrefs of a query against those of a reference and normalizes the output over a Null Hypothesis of random codon usage. The added value of COUSIN is to be easily interpreted, both quantitatively and qualitatively. An eponymous software written in Python3 is available for local or online use (http://cousin.ird.fr). This software allows for an easy and complete analysis of CUPrefs via COUSIN, includes seven other indices, and provides additional features such as statistical analyses, clustering, and CUPrefs optimization for gene expression. We illustrate the flexibility of COUSIN and highlight its advantages by analyzing the complete coding sequences of eight divergent genomes. Strikingly, COUSIN captures a bimodal distribution in the CUPrefs of human and chicken genes hitherto unreported with such precision. COUSIN opens new perspectives to uncover CUPrefs specificities in genomes in a practical, informative, and user-friendly way.

Mots clés: codon usage bias; mutational bias; translational selection; nucleotide composition; amino acid composition; codon adaptation index; bioinformatics; mutation-selection

Domaines: Sciences du Vivant [q-bio]; Informatique [cs]

Jérôme Bourret, Samuel Alizon, Ignacio Bravo. COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences. Genome Biology and Evolution, 2019, 11 (12), pp.3523-3528. ⟨10.1093/gbe/evz262⟩. ⟨hal-02957623⟩