James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China.
Genomics Proteomics Bioinformatics. 2009 Dec;7(4):175-84. doi: 10.1016/S1672-0229(08)60047-9.
Transposable elements (TEs) are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of Oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa (r=0.944 and 0.839, respectively, P<0.0001) but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species.
转座元件（TEs）是广泛分布于几乎所有基因组中的可移动遗传实体。先前在一些物种中观察到 TE 中的终止密码子 A/T 出现高频率。在这项研究中，在富含 A/T 的拟南芥和富含 GC 的水稻基因组中，研究了 TE 转座酶和宿主核基因的核苷酸组成和密码子使用偏好。与宿主核基因相比，TE 中终止密码子 A/T 的使用频率更高。在水稻中，高表达的核基因与 C/G 结尾的密码子之间存在显著的正相关（r 分别为 0.944 和 0.839，均 P<0.0001），但在拟南芥中则没有，这表明单子叶植物的 GC 含量与基因表达水平之间存在密切关联。在这两个物种中，TE 的密码子使用偏好与弱表达基因相似。TE 的表达和活性可能在植物基因组中受到严格控制。突变偏向和选择压力同时作用于拟南芥和水稻中 TE 的进化。TE 的核苷酸组成和密码子使用偏好的一致性观察结果也可能为在不同物种中准确检测 TE 序列提供有用线索。
