Jiang Rays H Y, Govers Francine
Laboratory of Phytopathology, Plant Sciences Group, and Graduate School of Experimental Plant Sciences, Wageningen University, Binnenhaven 5, NL-6709 PD, Wageningen, The Netherlands.
J Mol Evol. 2006 Oct;63(4):458-72. doi: 10.1007/s00239-005-0211-3. Epub 2006 Sep 4.
Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.
疫霉属完全由具有破坏性的植物病原体组成。它属于不等鞭毛类，是真核生物中的一个独特分支，在系统发育上与植物、动物或真菌不同。疫霉属基因对以G或C结尾的密码子（高GC3）的使用表现出强烈偏好。基因中高GC3的存在可用于区分基因组中的编码区和非编码区。我们发现，选择压力和突变偏向都驱动疫霉属中的密码子偏向。不同疫霉属物种中高表达基因的GC3值较高，这表明存在选择压力。非编码区的谱系特异性GC增加让人联想到全基因组突变偏向，而疫霉属GC3升高主要是翻译效率驱动的选择的结果。疫霉属基因组中存在异质逆转座子，其中许多在GC含量上有所不同。有趣的是，疫霉属中最广泛分布的逆转座子群体显示出高GC3和与宿主基因相似的密码子偏向。显然，选择压力已作用于逆转座子的密码子使用，而这种对宿主密码子偏向的模仿可能有利于逆转座子的传播。
