Gómez-Valero Laura, Latorre Amparo, Silva Francisco J
Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, 46071 Valencia, Spain.
Mol Biol Evol. 2004 Nov;21(11):2172-81. doi: 10.1093/molbev/msh232. Epub 2004 Aug 18.
Reduction of the genome size in endosymbiotic bacteria is the main feature linked to the adaptation to a host-associated lifestyle. We have analyzed the fate of the nonfunctional DNA in Buchnera aphidicola, the primary endosymbiont of aphids. At least 164 gene losses took place during the recent evolution of three B. aphidicola strains, symbionts of the aphids Acyrthosiphon pisum (BAp), Schizaphis graminum (BSg), and Baizongia pistacia (BBp). A typical pattern starts with the inactivation of a gene, which produces a pseudogene, and is followed by the progressive loss of its DNA. Our results show that during the period from the separation of the Aphidinae and Pemphiginae lineages (86-164 MYA) to the divergence of BAp and BSg (50-70 MYA) the half-life of a pseudogene was 23.9 Myr. For the remaining periods of evolution, the ranges of values obtained for this parameter are of the same order of magnitude. These results have revealed that a gene inactivated during B. aphidicola evolution requires 40-60 Myr to become almost completely disintegrated. Moreover, we have shown a positive correlation between the decrease in the GC content and the DNA loss for these nonfunctional DNA regions. When gene losses are classified, based on the detection of a pseudogene or otherwise of an absent gene in the modern B. aphidicola genomes, we have observed a drastic reduction of DNA length in the latter versus the former relative to the functional gene. Finally, we have also detected a slight reduction in size of the intergenic regions in the three B. aphidicola strains, when they are compared with the size of the close relative Escherichia coli.
内共生细菌基因组大小的缩减是与适应宿主相关生活方式相关的主要特征。我们分析了蚜虫主要内共生菌——蚜虫内共生菌（Buchnera aphidicola）中无功能DNA的命运。在最近三种蚜虫内共生菌菌株（豌豆蚜（Acyrthosiphon pisum）的共生菌BAp、麦二叉蚜（Schizaphis graminum）的共生菌BSg和黄连木蚜（Baizongia pistacia）的共生菌BBp）的进化过程中，至少发生了164次基因丢失。一种典型模式始于基因失活，产生假基因，随后其DNA逐渐丢失。我们的结果表明，在蚜亚科和瘿蚜亚科谱系分离（86 - 164百万年前）到BAp和BSg分化（50 - 70百万年前）的期间，假基因的半衰期为2390万年。对于其余的进化时期，该参数获得的值范围处于相同数量级。这些结果表明，在蚜虫内共生菌进化过程中失活的基因需要40 - 60百万年才能几乎完全解体。此外，我们还表明这些无功能DNA区域的GC含量下降与DNA丢失之间存在正相关。当根据现代蚜虫内共生菌基因组中假基因或缺失基因的检测对基因丢失进行分类时，我们观察到相对于功能基因，后者的DNA长度相对于前者急剧减少。最后，当将三种蚜虫内共生菌菌株与亲缘关系较近的大肠杆菌的大小进行比较时，我们还检测到它们基因间区域的大小略有减小。
