Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil.
Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil.
FEMS Yeast Res. 2023 Jan 4;23. doi: 10.1093/femsyr/foad032.
In eukaryotes, the ribosome machinery is encoded by repeats of the ribosomal RNA genes: 26/28S, 18S, 5.8S, and 5S, structured in tandem arrays and frequently homogenized within a genome. This homogenization is thought to be driven by concerted evolution, evolving as a unit, which contributes to its target as the species barcode in modern taxonomy. However, high heterogeneity of rDNA genes has been reported, including in Saccharomycotina yeasts. Here, we describe the polymorphisms and heterogeneity of D1/D2 domains (26S rRNA) and the intergenic transcribed spacer of a new yeast species with affinities to the genus Cyberlindnera and their evolution. Both regions are not homogenized, failing the prediction of concerted evolution. Phylogenetic network analysis of cloned sequences revealed that Cyberlindnera sp. rDNAs are diverse and evolved by reticulation rather than by bifurcating tree evolution model. Predicted rRNA secondary structures also confirmed structural differences, except for some conserved hairpin loops. We hypothesize that some rDNA is inactive within this species and evolves by birth-and-death rather than concerted evolution. Our findings propel further investigation into the evolution of rDNA genes in yeasts.
在真核生物中，核糖体机器由核糖体 RNA 基因的重复序列编码：26/28S、18S、5.8S 和 5S，它们以串联数组的形式排列，并经常在基因组内同质化。这种同质化被认为是由协同进化驱动的，作为一个整体进化，这有助于它成为现代分类学中物种条形码的目标。然而，已经报道了 rDNA 基因的高度异质性，包括 Saccharomycotina 酵母。在这里，我们描述了与 Cyberlindnera 属亲缘关系密切的一种新型酵母的 D1/D2 结构域（26S rRNA）和基因间转录间隔区的多态性和异质性及其进化。这两个区域都没有同质化，与协同进化的预测相悖。克隆序列的系统发育网络分析表明，Cyberlindnera sp. 的 rDNAs 是多样化的，并且是通过网状而不是分支树进化模型进化的。预测的 rRNA 二级结构也证实了结构上的差异，除了一些保守的发夹环。我们假设该物种中的一些 rDNA 是无活性的，并且通过诞生和死亡而不是协同进化进化。我们的发现推动了对酵母中 rDNA 基因进化的进一步研究。
