草菇密码子偏好性分析

Codon usage bias in the straw mushroom Volvariella volvacea

摘要:

以草菇全基因组编码序列为研究对象，利用软件CodonW1.4.2分析草菇基因组密码子使用模式，确定了草菇的24个最优密码子。利用Create a condon usage table (CUSP)程序分析计算草菇密码子使用频率，并将它与人、酵母、拟南芥、小鼠、斑马鱼、果蝇6个代表性物种及灰盖鬼伞、双孢蘑菇、香菇、平菇4个食用菌进行比较。结果显示草菇密码子偏好性与人、酵母、拟南芥、小鼠、斑马鱼、果蝇和平菇都有较大的差异，与灰盖鬼伞、双孢蘑菇、香菇的密码子偏好性差异较小。利用软件SPSS16.0聚类分析表明密码子偏好性差异大小在一定程度上反映物种间的进化关系，可作为研究物种进化关系的参考。首次以食用菌全基因组为分析对象，解析草菇的密码子偏好性，并将其与其他生物进行比较，这些将为不同来源的外源基因在草菇中的异源表达提供重要参考。

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.