The Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes. These genes tend to be hyper-variable, highly recombinogenic and variantly expressed. The best-characterized family is the var genes, exclusively found in the Laveranian subgenus of malaria parasites infecting humans and great apes. Var genes encode major virulence factors involved in immune evasion and the maintenance of chronic infections. In the human parasite P. falciparum, var gene recombination and diversification appear to be promoted by G-quadruplex (G4) DNA motifs, which are strongly associated with var genes in P. falciparum. Here, we investigated how this association might have evolved across Plasmodium species – both Laverania and also more distantly related species which lack vars but encode other, more ancient variant gene families. The association between var genes and G4-forming motifs was conserved across Laverania, spanning ~ 1 million years of evolutionary time, with suggestive evidence for evolution of the association occurring within this subgenus. In rodent malaria species, G4-forming motifs were somewhat associated with pir genes, but this was not conserved in the Laverania, nor did we find a strong association of these motifs with any gene family in a second outgroup of avian malaria parasites. Secondly, we compared two different G4 prediction algorithms in their performance on extremely A/T-rich Plasmodium genomes, and also compared these predictions with experimental data from G4-seq, a DNA sequencing method for identifying G4-forming motifs. We found a surprising lack of concordance between the two algorithms and also between the algorithms and G4-seq data. G4-forming motifs are uniquely strongly associated with Plasmodium var genes, suggesting a particular role for G4s in recombination and diversification of these genes. Secondly, in the A/T-rich genomes of Plasmodium species, the choice of prediction algorithm may be particularly influential when studying G4s in these important protozoan pathogens.

中文翻译：

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疟原虫中 G-四链体形成 DNA 基序与毒力基因家族之间的保守关联

疟原虫属的疟原虫编码几个抗原编码基因家族。这些基因往往是高度可变的、高度重组的和变异表达的。最具特征的家族是 var 基因，它仅存在于感染人类和类人猿的疟原虫的 Laveranian 亚属中。Var 基因编码参与免疫逃避和维持慢性感染的主要毒力因子。在人类寄生虫恶性疟原虫中，与恶性疟原虫中的 var 基因密切相关的 G-四链体 (G4) DNA 基序似乎促进了 var 基因重组和多样化。在这里，我们研究了这种关联是如何在疟原虫物种中进化的——包括紫薇和更远亲的物种，它们缺乏 vars 但编码其他更古老的变异基因家族。var 基因和 G4 形成基序之间的关联在 Laverania 中是保守的，跨越了约 100 万年的进化时间，有证据表明该关联发生在该亚属内的进化。在啮齿动物疟疾物种中，G4 形成基序与 pir 基因有些相关，但这在 Laverania 中并不保守，我们也没有发现这些基序与第二类禽疟疾寄生虫中的任何基因家族有很强的关联。其次，我们比较了两种不同的 G4 预测算法在极其富含 A/T 的疟原虫基因组上的性能，并将这些预测与来自 G4-seq 的实验数据进行了比较，G4-seq 是一种用于识别 G4 形成基序的 DNA 测序方法。我们发现这两种算法之间以及算法与 G4-seq 数据之间缺乏一致性令人惊讶。G4 形成基序与疟原虫 var 基因密切相关，表明 G4 在这些基因的重组和多样化中具有特殊作用。其次，在富含 A/T 的疟原虫基因组中，在研究这些重要原生动物病原体中的 G4 时，预测算法的选择可能特别有影响。