Wei Jiang
1 Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; 2 Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, ChinaBeibei Lü
2 Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, ChinaJianhua He
1 Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; 2 Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, ChinaJinbin Wang
1 Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; 2 Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, ChinaXiao Wu
1 Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; 2 Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, ChinaGuogan Wu
1 Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; 2 Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, ChinaDapeng Bao
3 National Engineering Research Center of Edible Fungi, Shanghai 201106, ChinaMingjie Chen
3 National Engineering Research Center of Edible Fungi, Shanghai 201106, ChinaJinsong Zhang
3 National Engineering Research Center of Edible Fungi, Shanghai 201106, ChinaQi Tan
3 National Engineering Research Center of Edible Fungi, Shanghai 201106, ChinaThe Shanghai Academy of Agricultural Sciences (No. 2013(23)), the China Postdoctoral Science Foundation Grant (No. 2013M531197), Shanghai Postdoctoral Sustentation Fund Grant (No. 13R21421000), the Key Project of Developing Agriculture through Science and Technology of Shanghai Municipal Agricultural Commission (No. (2011) 1-2).
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.
蒋玮,吕贝贝,何建华,王金斌,吴潇,武国干,鲍大鹏,陈明杰,张劲松,谭琦,唐雪明. 草菇密码子偏好性分析[J]. Chinese Journal of Biotechnology, 2014, 30(9): 1424-1435
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