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

Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens

“…Implication of C/G-ending codon optimization might favor the high expression of genes involved in the invasion of pathogens inside the host and, thus, helps in establishing parasitism. Previous studies have reported similar bias in fungal genomes toward G and C nucleotides (Roy and Staden 2019;Muthabathula et al 2018). In fungal genomes, GC content close to 50% indicates the influence of mutational bias (Lloyd and Sharp 1991;Muthabathula et al 2018).…”

“…Although plant kingdom represents the AT-rich genome, however, in the present study, we found that except two codons GAA (Glutamate) and GCU (Alanine), rest all the preferred codons are GC rich similar to fungal pathogens. GC-rich amino acids are considered to cause a lower metabolic burden on the fungal community (Roy and staden 2019). The similarity in codon usage pattern could help the pathogens to synthesize the amino acids and corresponding proteins more efficiently that helps pathogens to thrive in the host (Qian et al 2012;Biswas et al 2019).…”

“…The study on codon usage patterns has been reported in different fungal genera like Aspergillus, Neurospora, Epichole, Utialago, Volvariella, etc. (Chen et al 2012;Iriarte et al 2012;Li et al 2016;Zhou et al 2016;Song et al 2017;Roy and Staden 2019). Moreover, the link between the translational regulation and variation in the host range through codon optimization has been reported in several fungal kingdoms (Badet et al 2017).…”

“…Optimization of protein translation is of utmost importance as this process is considered as the largest consumer of energy during cellular proliferation. It has been reported that translational efficiency is greatly affected by the synonymous codon usage pattern (Li et al 2019;Roy and Staden 2019;Sahoo et al 2019). Further, the codon usage pattern can be regarded as the outcome of the balance between two important factors, i.e., directional mutation pressure, and natural selection (Wang et al 2018;Biswas et al 2019).…”

“…Investigations on codon usage pattern have helped us to understand the molecular organization of genomes. Study in CUB has gained more impetus after the advancement in sequencing technology as many genomes were sequenced (Roy and Staden 2019), following which codon usage patterns were studied in many eukaryotic and prokaryotic organisms. The study on codon usage patterns has been reported in different fungal genera like Aspergillus, Neurospora, Epichole, Utialago, Volvariella, etc.…”