Comprehensive profiling of codon usage signatures and codon context variations in the genus Ustilago

  • Ayan Roy
  • Johannes van StadenEmail author
Original Article


The fungal genus Ustilago consists of intimidating pathogens associated with disease manifestations in plants of agricultural importance and gravity. Rapid progress of genome sequencing has opened the floodgates for biological research. Availability of Ustilago genomes provides a scope to explore complex codon and amino acid usage patterns in the genus. An extensive scrutiny of the factors underlying the complex modalities of codon and amino acid usage in Ustilago has been executed in the present analysis. Multivariate statistical analysis revealed a dominant effect of natural selection pressure, aimed at translational accuracy, to be operative on the codon usage behavior. Subtle impact of GC compositional constraint was also evident on the codon usage patterns. Gene expressivity was inferred to be the most crucial determinant governing observed codon usage variations. Amino acid usage patterns were found to be significantly governed by aromatic and hydrophobic characters of the encoded proteins. GC content and length of protein coding sequences also had considerable influence on the amino acid usage signatures. Extensive analysis of codon context variations revealed that UpA dinucleotides were strictly avoided at the codon–codon junctions (cP3–cA1) which might be attributed to reduce the risk of nonsense mutations and subsequently, improve translational finesse. Identification of the optimal codons, employed preferentially among the genes with high expressivity, and estimation of preferred and avoided codon pairs in Ustilago promises to be useful pertaining to mutational experiments at the codonic level, targeted to thwart the growth of Ustilago and combat associated pathogenesis.


Ustilago Relative synonymous codon usage Relative amino acid usage Correspondence analysis Dinucleotide frequency Codon context patterns 



The authors would like to thank the University of KwaZulu-Natal for providing a postdoctoral fellowship to AR to execute this research work.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11274_2019_2693_MOESM1_ESM.pdf (1.3 mb)
Supplementary file1 (PDF 1256 kb)


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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Research Centre for Plant Growth and Development, School of Life SciencesUniversity of KwaZulu-NatalScottsvilleSouth Africa

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