title: 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.
authors.affiliation: Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.|Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
authors.affiliation: Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.|Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, People's Republic of China.
authors.forename: Beibei
authors.initials: B
authors.lastname: Lv
authors.affiliation: Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.|Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, People's Republic of China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wu
authors.affiliation: Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.|Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, People's Republic of China.
authors.forename: Jinbin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.|Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, People's Republic of China.
authors.forename: Guogan
authors.initials: G
authors.lastname: Wu
authors.affiliation: Forestry and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.
authors.forename: Chunhui
authors.initials: C
authors.lastname: Shi
authors.affiliation: Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China.|Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, People's Republic of China.
authors.forename: Xueming
authors.initials: X
authors.lastname: Tang
mesh_terms: D001482:Base Composition / Q000235:genetics; D003062:Codon / Q000235:genetics*; D010945:Plants, Edible / Q000235:genetics; D055367:Volvariella / Q000235:genetics*
chemical_list: D003062:Codon
keywords: Volvariella volvacea; codon usage bias; optimal codons