Environmental implications of codon usage bias in Crocus sativus and its impact on host pathogen interactions

Abstract

Codon usage bias (CUB) is a ubiquitous phenomenon perseveres in genome of all the organisms. It impinges the gene expression and other genetic intricacies within a genome. The present study explains the pattern of codon usage in the protein coding sequence of Crocus sativus and its relation with gene expression. Gene expression analysis in C. sativus showed genes with high expression had a preference of G base at third position. CUB had an inverse relation with gene expression. Coding sequences with effective number of codons (ENC) < 50 had low Fragments Per Kilobase Million (FPKM) value while low codon bias group ENC >50 possessed high FPKM value. The low tAI values showed the low translation efficiency of genes in C. sativus. The non-significant MILC-based expression level predictor (MELP) and ENC correlation analysis suggested that expression of genes might not be associated with codon usage bias. ENC and PR-2 plot revealed mutation pressure and natural selection played role in shaping Codon usage patterns. However, neutrality plot conclusively depicted the dominance of natural selection in regulating the configuration of codons in all the selected species. In addition, the role of Codon usage bias regarding the predilection of fungal pathogens Aspergillus fumigatus, Fusarium oxysporum, Aspergillus niger and Aspergillus flavus towards host plant C. sativus has also been expounded. We found a similar trend of codon usage operative in plant and fungal pathogens as all the fungal pathogens and host plant showed similar GC rich genomic content as well as preference for GC ending codons at third codon position. This concurrence might be attributed for the colonization of fungal pathogens in C. sativus. Overall, different indices reflected a weak codon bias in the C. sativus, and its associated pathogens.