Analysis of synonymous codon usage patterns in the edible fungus Volvariella volvacea

Abstract

In this study, trends in synonymous codons usage of Volvariella volvecea have been first examined by analysis of complete coding sequences and gene chip data. The results showed that GC content at three codon positions are obviously different and there were several factors shaping the codon usage of V. volvacea genes, including base composition. The comparison of codon usage among four edible fungi such as V. volvacea, Agaricus bisporus, Coprinopsis cinerea, and Pleurotus ostreatus indicated that the similar codon usage pattern was used among V. volvacea, A. bisporus and P. ostreatus, but there was significantly different codon usage pattern of C. cinerea. Two arrays of optimal codons were determined by effective number of codons (ENC) values and gene chip database separately, resulting that most of the ENC-predicted optimal codons were included in the array of gene chip resulted optimal codons. This study can provide useful information for codon usage pattern analysis and gene transformation of V. volvacea.

Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia, a persistent threat to global agriculture

“…Codon usage signatures in the genus Puccinia appeared to be a complex interplay of natural selection aimed at translational precision and AT compositional bias. Similar instances have earlier been reported where codon usage variations resulted as consequences of both the aforesaid factors instrumental on the genes/genomes . However, selection pressure aimed at translational accuracy was observed to be more commanding than compositional constraint in Puccinia .…”

“…Similar instances have earlier been reported where codon usage variations resulted as consequences of both the aforesaid factors instrumental on the genes/ genomes. 19,20 However, selection pressure aimed at translational accuracy was observed to be more commanding than compositional constraint in Puccinia. Interestingly, gene expression level was observed to be F I G U R E 5 Dinucleotide bias at codon-codon junctions for the members of Puccinia.…”

“…10,11 Other imperative factors involving gene expression level, 12,13 transfer RNA abundance, 14 gene length, 15 and codon-anticodon interactions 16 have also been observed to have significant impact on the codon usage patterns of genes and genomes. Natural selection for translation and genomic compositional bias have been observed to be the dictating factors governing the fashion of codon usage in various fungi like Aspergillus, 17 Neurospora, 18 Volvariella, 19 Epichloë, 20 and Encephalitozoon. 21 Availability of complete genome sequences of various Puccinia species like Pso, 6 Pgr, 4 Ptr, 5 Pst, 3 and Pco 7 has opened up floodgates to explore their genomic niceties and investigate the complex strategies that they opt to infect their target host plants.…”

“…Availability of complete genome sequences of various Puccinia species like Pso, Pgr, Ptr, Pst, and Pco has opened up floodgates to explore their genomic niceties and investigate the complex strategies that they opt to infect their target host plants. Tremendous advancements have been made pertaining to comparative genomics, phylogenetic analyses and pathogenesis of Puccinia . Valuable information regarding interaction of various Puccinia species with their susceptible host plants has been mined efficiently, providing thorough know‐how about their infective policies .…”

“…Other imperative factors involving gene expression level, transfer RNA abundance, gene length, and codon–anticodon interactions have also been observed to have significant impact on the codon usage patterns of genes and genomes. Natural selection for translation and genomic compositional bias have been observed to be the dictating factors governing the fashion of codon usage in various fungi like Aspergillus , Neurospora , Volvariella , Epichloë , and Encephalitozoon …”