Episodic and ongoing mechanisms drive plastid-derived nuclear DNA evolution in angiosperms.

IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
Juan Pablo Marczuk-Rojas, Ana D Maldonado, Lorenzo Carretero-Paulet
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引用次数: 0

Abstract

NUPTs are DNA sequences of plastid origin present in plant nuclear genomes to varying, though typically low, amounts. It is assumed that they are continuously formed and, due to their potentially mutagenic effect, removed at a constant turnover rate, which should result in an exponential decay of their age distributions and a negative correlation between age and size. However, these assumptions are based on analysis from a limited number of species and have never been explicitly tested. To gain insight into the mechanisms driving the origin and evolution of NUPTs, here we surveyed the plastid and nuclear genomes of 30 species representing the main angiosperm (flowering plants) lineages. By modeling the distribution of ages and sizes, examining their linear arrangement across the plastid genome, and statistically assessing spatial biases with respect to other genomic features, we showed that NUPTs are i) formed by both continuous and episodic mechanisms; ii) unevenly represented across the plastid genome; iii) consistently associated with certain classes of RNA genes, in particular rRNA, tRNA and regulatory RNA genes; iv) differentially contributing to structural genes; and v) closer than expected to different superfamilies of transposons in a species-specific manner. Our results reveal the unexpected complexity in the mechanisms driving the origin of NUPTs, which do not only involve their continuous formation but also episodic, highlight their role as a major source of non-coding RNA genes and other genomic features and provide a more complete picture of the different drivers of evolutionary change at the genome level.

在被子植物中,偶发和持续的机制驱动质体衍生的核DNA进化。
nupt是存在于植物核基因组中质体起源的DNA序列,虽然数量通常很低。假设它们是连续形成的,由于其潜在的诱变作用,它们以恒定的周转率被移除,这应该导致它们的年龄分布呈指数衰减,年龄与尺寸之间呈负相关。然而,这些假设是基于对有限物种的分析,从未经过明确的测试。为了深入了解nupt的起源和进化机制,我们调查了30种主要被子植物(开花植物)谱系的质体和核基因组。通过建模年龄和大小的分布,检查它们在质体基因组中的线性排列,并统计评估相对于其他基因组特征的空间偏差,我们发现nupt是由连续和偶发机制形成的;Ii)在质体基因组中不均匀分布;iii)始终与某些类别的RNA基因相关,特别是rRNA、tRNA和调控RNA基因;Iv)对结构基因的差异贡献;v)以物种特异性的方式与不同的转座子超家族更接近。我们的研究结果揭示了驱动nupt起源机制的意想不到的复杂性,这不仅涉及它们的连续形成,而且还涉及它们的偶发性,突出了它们作为非编码RNA基因和其他基因组特征的主要来源的作用,并提供了基因组水平上进化变化的不同驱动因素的更完整的图景。
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来源期刊
Genome Biology and Evolution
Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY
CiteScore
5.80
自引率
6.10%
发文量
169
审稿时长
1 months
期刊介绍: About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.
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