Sipiczki Matthias, Horvath Eniko, Pfliegler Walter P
Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary.
Front Microbiol. 2018 Jun 12;9:1193. doi: 10.3389/fmicb.2018.01193. eCollection 2018.
The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high degree of sequence diversity in the D1/D2 domains of two pulcherrimin-producing (Saccharomycotina) species which appeared to evolve by reticulation. The major goals of this study were the examination of the diversity of the ITS segments and their evolution. We show that the ITS sequences of these species are not homogenized either, differ from each other by up to 38 substitutions and indels which have dramatic effects on the predicted secondary structures of the transcripts. The high intragenomic diversity makes the D1/D2 domains and the ITS spacers unsuitable for barcoding of these species and therefore the taxonomic position of strains previously assigned to them needs revision. By analyzing the genome sequence of the type strain, we also show that the rDNA of this species is fragmented, contains pseudogenes and thus evolves by the birth-and-death mechanism rather than by homogenisation, which is unusual in yeasts. The results of the network analysis of the sequences further indicate that the ITS regions are also involved in reticulation. and can form interspecies hybrids and their hybrids segregate, providing thus possibilities for reticulation of the rDNA repeats.
内部转录间隔区（ITS）区域（ITS1、5.8S rDNA和ITS2）将编码小亚基18S和大亚基26S基因的基因分隔开，这些基因在绝大多数真菌中以长串联阵列的形式组织在核糖体DNA（rDNA）单元中。作为一个多基因家族的成员，这些单元经历协同进化，使它们的序列趋于同质化。在某些植物群体和少数真菌物种中观察到了例外情况。在我们之前的研究中，我们描述了两种产腐殖质菌素的（子囊菌纲）物种的D1/D2结构域中异常高的序列多样性，这些物种似乎通过网状进化。本研究的主要目标是检查ITS片段的多样性及其进化。我们发现这些物种的ITS序列也没有同质化，彼此之间相差多达38个替换和插入缺失，这对转录本的预测二级结构有显著影响。高基因组内多样性使得D1/D2结构域和ITS间隔区不适用于这些物种的条形码分析，因此先前归属于它们的菌株的分类地位需要修订。通过分析模式菌株的基因组序列，我们还表明该物种的rDNA是片段化的，包含假基因，因此通过生死机制进化，而不是通过同质化，这在酵母中是不常见的。序列的网络分析结果进一步表明，ITS区域也参与了网状进化，并且可以形成种间杂种，其杂种会分离，从而为rDNA重复序列的网状进化提供了可能性。
