title: [Codon usage bias in the straw mushroom Volvariella volvacea].
abstract: We analyzed the whole genome coding sequence of Volvariella volvacea to study the pattern utilization of codons by Codon W 1.4.2. As results, 24 optimal codons were identified. Moreover, the frequency of codons usage was calculated by CUSP program. We compared the frequency of codons usage of V. volvacea with other organisms including 6 modal value species (Homo sapiens, Saccharomys cerevisiae, Arabidopsis thalian, Mus musculus, Danio rerio and Drosophila melanogaster) and 4 edible fungi (Coprinopsis cinerea, Agaricus bisporus, Lentinula edodes and Pleurotus ostreatus). We found that there were less differences in 3 edible fungi (excluding Pleurotus ostreatus) than 6 modal value species, comparing with the frequency of codons usage of V. volvacea. With software SPSS16.0, cluster analysis which showed differences in the size of codon bias, reflects the evolutionary relationships between species, which can be used as a reference of evolutionary relationships of species. This was the first time for analysis the codon preference among the whole coding sequences of edible fungi, serving as theoretical basis to apply genetic engineering of V. volvacea.
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
authors.forename: Beibei
authors.initials: B
authors.lastname: Lü
authors.forename: Jianhua
authors.initials: J
authors.lastname: He
authors.forename: Jinbin
authors.initials: J
authors.lastname: Wang
authors.forename: Xiao
authors.initials: X
authors.lastname: Wu
authors.forename: Guogan
authors.initials: G
authors.lastname: Wu
authors.forename: Dapeng
authors.initials: D
authors.lastname: Bao
authors.forename: Mingjie
authors.initials: M
authors.lastname: Chen
authors.forename: Jinsong
authors.initials: J
authors.lastname: Zhang
authors.forename: Qi
authors.initials: Q
authors.lastname: Tan
authors.forename: Xueming
authors.initials: X
authors.lastname: Tang
mesh_terms: D000363:Agaricales / Q000235:genetics; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D016000:Cluster Analysis; D003062:Codon; D004271:DNA, Fungal / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D006801:Humans; D051379:Mice; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D055367:Volvariella / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics
chemical_list: D003062:Codon; D004271:DNA, Fungal