Fehrer Judith, Slavíková Renáta, Paštová Ladislava, Josefiová Jiřina, Mráz Patrik, Chrtek Jindřich, Bertrand Yann J K
Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia.
Department of Botany, Charles University, Prague, Czechia.
Front Plant Sci. 2021 Mar 12;12:647375. doi: 10.3389/fpls.2021.647375. eCollection 2021.
Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera , , , and and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between and was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In , some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in . No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.
核糖体DNA的分子进化可能高度动态。基因组中数百到数千个拷贝会经历协同进化，这种进化会使序列变异在不同程度上同质化。如果同质化良好，序列就适合用于系统发育重建；如果不是，就必须适当处理序列多态性。在这里，我们研究了亚族鹰爪草亚科二倍体中非编码rDNA序列（ITS/ETS、5S-NTS）及其各自位点（45S和5S rDNA）的染色体组织。该亚族由[具体属名1]、[具体属名2]、[具体属名3]和[具体属名4]属组成，具有复杂的进化历史，其特征是古老的属间杂交、物种间的等位基因共享以及不完全的谱系分选。对直接或克隆的桑格序列以及来自Illumina基因组测序的分阶段等位基因进行了系统发育分析。比较了基于这三个区域的同质化模式和树形拓扑结构。与大多数其他植物类群不同，5S-NTS序列通常比ITS和ETS序列同质化程度更高。推断出[具体属名1]和[具体属名2]之间存在一个新的古老属间杂交案例，并发现树形之间存在一些进一步的不一致，表明这些区域是独立进化的。在一些物种中，尽管5S rDNA位点总是与一个45S rDNA位点位于同一条染色体上，但ITS/ETS和5S-NTS序列的同质化方向不同。鹰爪草亚科的祖先rDNA组织包括每个二倍体基因组末端位置的4个45S rDNA位点和中间位置的2个5S rDNA位点。在[具体属名1]中，发现了一些与这种一般模式的偏差（45S rDNA有3、6或7个位点；5S rDNA有3个位点）。其中一些偏差涉及种内变异，并且大多数发生在树形的末端或在不同谱系中独立出现。这表明rDNA位点的组织比其中包含的序列进化更具动态性，因此位点数量在很大程度上不适用于说明鹰爪草亚科中的物种关系。在序列同质化程度和45S rDNA位点数量上未发现一致的差异，表明位点间存在协同进化。
