Codon usage bias amongst plant viruses
Codon usage bias amongst plant viruses
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DOI：
10.1007/s00705-003-0186-6
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发表时间：
2004-01-01
影响因子：
2.7
通讯作者：
Antoniw, JF
中科院分区：
文献类型：
--
作者：
Adams, MJ;Antoniw, JF
建立了一个互联网数据库(DPVweb)，其中包含完整或至少包含一个完整基因的所有病毒、类病毒和植物卫星序列的详细信息(n>；4600)。记录每个特征(基因、非翻译区等)的开始和结束位置，并检查其准确性。编写了客户端软件，以便于选择所选病毒的序列和特征，并分析密码子使用偏向。对每个完全测序的植物病毒的一个例子的每个基因的密码子使用进行了分析。密码子偏好有很大的差异，这与基因组的核苷酸组成有关，特别是第三密码子位置的GC含量。基因大小对密码子偏好性没有影响。来自同一基因组的基因通常有相似的编码策略，除非受到阅读框架重叠的限制。尽管一些同义密码子一直被植物和病毒使用频率很低，但病毒通常不适应使用(或避免)寄主植物最频繁使用的密码子，而且与传播类型没有明显的联系。突变偏向，而不是翻译选择似乎解释了检测到的大部分变异。该软件在http://www.dpvweb.net/analysis/codons.php.上有售
An internet database (DPVweb) was established containing details of all sequences of viruses, viroids and satellites of plants that are complete or that contain at least one complete gene (n>4600). The start and end positions of each feature (genes, non-translated regions etc) were recorded and checked for accuracy. Client software was written to enable easy selection of sequences and features of a chosen virus and to analyse codon usage bias. Codon usage was analysed for each gene of one example of each fully-sequenced plant virus. There were large differences in codon preferences, related to the nucleotide composition of the genome, particularly the GC content of the third codon position. There was no effect of gene size on codon bias. Genes from the same genome usually had similar coding strategies except where constrained by the overlap of reading frames. Although some synonymous codons were consistently used with low frequency by both plants and viruses, viruses were not generally adapted to use (or avoid) those codons most frequently used by their host plants and there was no obvious association with the type of transmission. Mutational bias, rather than translational selection appears to account for the majority of the variation detected. The software is available at http://www.dpvweb.net/analysis/codons.php.