The balance of driving forces during genome evolution in prokaryotes
The balance of driving forces during genome evolution in prokaryotes
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DOI：
10.1101/gr.1092603
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发表时间：
2003-07-01
期刊：
影响因子：
7
通讯作者：
Ouzounis, CA
中科院分区：
文献类型：
--
作者：
Kunin, V;Ouzounis, CA
基因组是由基因发生、水平基因转移（HGT）和基因丢失等进化过程形成的。为了量化这些过程的相对贡献，我们分析了来自41种细菌和10种古细菌全基因组的12,762个蛋白质家族在系统发育树上的分布。我们发现基因丢失是形成基因组内容的最重要因素，其频率是HGT的三倍，其次是基因发生，其贡献的基因数量可能是HGT的两倍。我们认为原核生物的基因获得和基因损失是平衡的；因此，平均而言，原核生物基因组的大小是保持不变的。尽管HGT很重要，但我们的研究结果表明，大多数蛋白质家族仅通过垂直遗传传播。为了验证我们的方法，我们对幽门螺杆菌的菌株特异性基因进行了研究，并在至少81%的验证病例中证明了基因丢失和HGT的正确预测。这种方法表明，有可能追踪基因组内容的历史，并量化塑造当代原核生物基因组的因素。
Genomes are shaped by evolutionary processes such as gene genesis, horizontal gene transfer (HGT), and gene loss. To quantify the relative contributions of these processes, we analyze the distribution of 12,762 protein families on a phylogenetic tree, derived from entire genomes of 41 Bacteria and 10 Archaea. We show that gene loss is the most important factor in shaping genome content, being up to three times more frequent than HGT, followed by gene genesis, which may contribute up to twice as many genes as HGT. We suggest that gene gain and gene loss in prokaryotes are balanced; thus, on average, prokaryodic genome size is kept constant. Despite the importance of HGT, our results indicate that the majority of protein families have only been transmitted by vertical inheritance. To test our method, we present a study of strain-specific genes of Helicobacter pylori, and demonstrate correct predictions of gene loss and HGT for at least 81% of validated cases. This approach indicates that it is possible to trace genome content history and quantify the factors that shape contemporary prokaryotic genomes.