Tynkevich Yurij O, Shelyfist Antonina Y, Kozub Liudmyla V, Hemleben Vera, Panchuk Irina I, Volkov Roman A
Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine.
Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany.
Front Plant Sci. 2022 Apr 13;13:852406. doi: 10.3389/fpls.2022.852406. eCollection 2022.
The genus, being one of the largest among high plants, is distributed worldwide and comprises about 1,200 species. The genus includes numerous agronomically important species such as (potato), (tomato), and (eggplant) as well as medical and ornamental plants. The huge genus is a convenient model for research in the field of molecular evolution and structural and functional genomics. Clear knowledge of evolutionary relationships in the genus is required to increase the effectiveness of breeding programs, but the phylogeny of the genus is still not fully understood. The rapidly evolving intergenic spacer region (IGS) of 5S rDNA has been successfully used for inferring interspecific relationships in several groups of angiosperms. Here, combining cloning and sequencing with bioinformatic analysis of genomic data available in the SRA database, we evaluate the molecular organization and diversity of IGS for 184 accessions, representing 137 species of the genus. It was found that the main mechanisms of IGS molecular evolution was step-wise accumulation of single base substitution or short indels, and that long indels and multiple base substitutions, which arose repeatedly during evolution, were mostly not conserved and eliminated. The reason for this negative selection seems to be association between indels/multiple base substitutions and pseudogenization of 5S rDNA. Comparison of IGS sequences allowed us to reconstruct the phylogeny of the genus. The obtained dendrograms are mainly congruent with published data: same major and minor clades were found. However, relationships between these clades and position of some species (, and ) were different from those of previous results and require further clarification. Our results show that 5S IGS represents a convenient molecular marker for phylogenetic studies on the genus. In particular, the simultaneous presence of several structural variants of rDNA in the genome enables the detection of reticular evolution, especially in the largest and economically most important sect. . The origin of several polyploid species should be reconsidered.
该属是高等植物中最大的属之一，分布于全球，约有1200个物种。该属包括许多具有重要农艺价值的物种，如（马铃薯）、（番茄）和（茄子），以及药用植物和观赏植物。庞大的该属是分子进化以及结构和功能基因组学领域研究的便利模型。为提高育种计划的有效性，需要清楚了解该属中的进化关系，但该属的系统发育仍未完全明晰。5S核糖体DNA快速进化的基因间隔区（IGS）已成功用于推断几组被子植物的种间关系。在此，我们将克隆和测序与SRA数据库中可用基因组数据的生物信息学分析相结合，评估了代表该属137个物种的184份种质的IGS分子组织和多样性。研究发现，IGS分子进化的主要机制是单碱基替换或短插入缺失的逐步积累，而在进化过程中反复出现的长插入缺失和多碱基替换大多未被保留并被淘汰。这种负选择的原因似乎是插入缺失/多碱基替换与5S核糖体DNA的假基因化之间的关联。IGS序列的比较使我们能够重建该属的系统发育。所得的树状图与已发表的数据基本一致：发现了相同的主要和次要分支。然而，这些分支之间的关系以及一些物种（、和）的位置与先前的结果不同，需要进一步阐明。我们的结果表明，5S IGS是该属系统发育研究的便利分子标记。特别是，基因组中同时存在几种核糖体DNA的结构变体能够检测网状进化，尤其是在最大且经济上最重要的组中。几个多倍体物种的起源应重新考虑。
