Lassalle Florent, Périan Séverine, Bataillon Thomas, Nesme Xavier, Duret Laurent, Daubin Vincent
Université de Lyon, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France; CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, Villeurbanne, France; Ecole Normale Supérieure de Lyon, Lyon, France.
Université de Lyon, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
PLoS Genet. 2015 Feb 6;11(2):e1004941. doi: 10.1371/journal.pgen.1004941. eCollection 2015 Feb.
The characterization of functional elements in genomes relies on the identification of the footprints of natural selection. In this quest, taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic signatures of selection. In mammals, and probably in many eukaryotes, another such confounding factor called GC-Biased Gene Conversion (gBGC) has been documented. This mechanism generates patterns identical to what is expected under selection for higher GC-content, specifically in highly recombining genomic regions. Recent results have suggested that a mysterious selective force favouring higher GC-content exists in Bacteria but the possibility that it could be gBGC has been excluded. Here, we show that gBGC is probably at work in most if not all bacterial species. First we find a consistent positive relationship between the GC-content of a gene and evidence of intra-genic recombination throughout a broad spectrum of bacterial clades. Second, we show that the evolutionary force responsible for this pattern is acting independently from selection on codon usage, and could potentially interfere with selection in favor of optimal AU-ending codons. A comparison with data from human populations shows that the intensity of gBGC in Bacteria is comparable to what has been reported in mammals. We propose that gBGC is not restricted to sexual Eukaryotes but also widespread among Bacteria and could therefore be an ancestral feature of cellular organisms. We argue that if gBGC occurs in bacteria, it can account for previously unexplained observations, such as the apparent non-equilibrium of base substitution patterns and the heterogeneity of gene composition within bacterial genomes. Because gBGC produces patterns similar to positive selection, it is essential to take this process into account when studying the evolutionary forces at work in bacterial genomes.
基因组中功能元件的特征描述依赖于对自然选择印记的识别。在这一探索过程中，考虑诸如突变和遗传漂变等中性进化过程至关重要，因为这些力量会产生可能掩盖或模仿选择特征的模式。在哺乳动物中，可能在许多真核生物中，另一个这样的混杂因素——GC偏向性基因转换（gBGC）已被记录在案。这种机制产生的模式与在选择更高GC含量时预期的模式相同，特别是在高度重组的基因组区域。最近的结果表明，细菌中存在一种有利于更高GC含量的神秘选择力，但gBGC的可能性已被排除。在这里，我们表明gBGC可能在大多数（如果不是全部）细菌物种中起作用。首先，我们在广泛的细菌类群中发现基因的GC含量与基因内重组证据之间存在一致的正相关关系。其次，我们表明导致这种模式的进化力独立于密码子使用的选择作用，并且可能潜在地干扰有利于最佳AU结尾密码子的选择。与人类群体数据的比较表明，细菌中gBGC的强度与哺乳动物中报道的强度相当。我们提出gBGC不仅限于有性真核生物，在细菌中也广泛存在，因此可能是细胞生物体的一个祖先特征。我们认为，如果gBGC发生在细菌中，它可以解释以前无法解释的观察结果，例如碱基替换模式的明显非平衡和细菌基因组内基因组成的异质性。由于gBGC产生与正选择相似的模式，在研究细菌基因组中起作用的进化力时考虑这个过程至关重要。
