Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

中文翻译：

---

比较分析揭示轮虫群体内基因组大小的变化是由具有高度丰富的卫星DNA重复元件的大型基因组元件驱动的


众所周知，真核生物基因组在大小上表现出巨大的差异，但这种现象的进化原因仍然知之甚少。为了获得对这种变异的机制见解，以前的研究经常采用比较基因组学方法，涉及密切相关的物种或物种内地理上孤立的种群。迄今为止，同一种群个体之间的基因组比较仍然没有得到充分研究，尽管它们在为基因组大小进化提供微观进化视角方面具有巨大潜力。轮虫 Brachionus asplanchnoidis 是真核生物群体内基因组大小变异最极端的例子之一，在地理群体内表现出几乎两倍的变异。在这里，我们使用全基因组测序方法，通过为人群中的一个个体组装高质量的参考基因组草图，并比对来自同一地理人群（包括参考个体）的 15 个个体的短读段，来识别潜在的 DNA 序列差异。我们鉴定了几个大的、连续的拷贝数可变区（CNV），大小高达兆碱基，它们在个体之间表现出显着的覆盖范围差异，并且其覆盖范围总体上随基因组大小而变化。 CNV 的复杂性非常低，主要由串联重复的卫星 DNA 组成，只有少数散布的基因或其他序列，其特点是 GC 含量显着升高。基因组大小不同的两个亲本的后代中的 CNV 模式以及来自基因组大小不同的近交系的几个个体中的 CNV 模式表明了 CNV 的跨代遗传和积累。 通过识别导致种群内基因组大小变异的确切基因组元件，我们的研究为研究当代种群基因组大小进化铺平了道路，而不是从物种比较中推断模式和处理后验。