5S Ribosomal DNA in the Family Plumbaginaceae

Pub Date : 2023-12-04 DOI:10.3103/s0095452723060099

Y. O. Tynkevich, M. O. Valin, I. I. Moysiyenko, I. I. Panchuk, R. A. Volkov

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Abstract

Tandemly arranged repetitive regions (repeats) that encode 5S rRNA (5S rDNA) are an indispensable component of eukaryotic genomes. Typically, 5S rDNA repeats within a genome are very similar due to the concerted nature of the evolution of this type of repeats. Each 5S rDNA repeat consists of an evolutionarily conserved coding sequence (CDS) and a variable intergenic spacer (IGS). 5S rDNA is a popular model for studying the molecular evolution of repetitive sequences, and the high rate of IGS mutations determines its wide use in phylogenetic analysis of closely related taxa. Nevertheless, 5S rDNA remains unexplored for many groups of higher plants, especially for the Plumbaginaceae family. Some taxa of this family are endemic to southern Ukraine and listed in the Red Book. However, their taxonomic status is controversial, and its clarification requires the use of molecular phylogenetic methods. In this work, we examined the molecular organization of 5S rDNA for representatives of four genera of the tribe Limonieae, the largest in the family Plumbaginaceae. It was shown that the CDS of 5S rDNA of representatives of the genera Limonium, Armeria, and Ceratolimon possess single mutations that do not affect the formation of the secondary structure of 5S rRNA. In contrast, in the genomes of Goniolimon species, in addition to functionally normal 5S rDNA repeats, numerous pseudogenes were found that do not evolve in a concerted manner and contain numerous mutations in the CDS that disrupt the secondary structure of 5S rRNA. A significant phylogenetic distance between representatives of the subgenera Pteroclados and Limonium of the genus Limonium indicates that Pteroclados can be considered a separate genus. The high rate of molecular evolution makes 5S rDNA IGS a convenient tool for the reconstruction of phylogenetic relationships within the studied genera of the tribe Limonieae and the barcoding of Ukrainian endemics of the genus Limonium.

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白桦科的5S核糖体DNA

编码5S rRNA (5S rDNA)的随机排列重复区(repeats)是真核生物基因组不可缺少的组成部分。通常，基因组内的5S rDNA重复序列非常相似，这是由于这种重复序列进化的协同性。每个5S rDNA重复序列由一个进化上保守的编码序列(CDS)和一个可变的基因间间隔序列(IGS)组成。5S rDNA是研究重复序列分子进化的常用模型，IGS的高突变率决定了其在近缘类群系统发育分析中的广泛应用。然而，在许多高等植物类群中，特别是在白桦科中，5S rDNA仍未被发现。这个科的一些分类群是乌克兰南部特有的，并被列入红皮书。然而，它们的分类地位是有争议的，它的澄清需要使用分子系统发育方法。在这项工作中，我们研究了4个属的代表人物的5S rDNA的分子组织，Limonieae tribe是Plumbaginaceae科中最大的。结果表明，Limonium属、Armeria属和Ceratolimon属代表植物的5S rDNA CDS具有单突变，不影响5S rRNA二级结构的形成。相比之下，在Goniolimon物种的基因组中，除了功能正常的5S rDNA重复序列外，还发现了许多假基因，这些假基因不能以协调一致的方式进化，并且在CDS中包含许多突变，这些突变破坏了5S rRNA的二级结构。Pteroclados亚属的代表与Limonium属的Limonium之间存在显著的系统发育距离，表明Pteroclados可以被认为是一个单独的属。5S rDNA IGS具有较高的分子进化率，可用于所研究的Limonieae部落属内系统发育关系的重建和Limonium属乌克兰特有植物的条形码鉴定。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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