Owing to their nutritional and commercial values, the genomes of several citrus plants have been sequenced, and the genome of one close relative in the Rutaceae family, atalantia (Atalantia buxifolia), has also been sequenced. Here, we show a family-level comparative analysis of Rutaceae genomes. By using grape as the outgroup and checking cross-genome gene collinearity, we systematically performed a hierarchical and event-related alignment of Rutaceae genomes, and produced a gene list defining homologous regions based on ancestral polyploidization or speciation. We characterized genome fractionation resulting from gene loss or relocation, and found that erosion of gene collinearity could largely be described by a geometric distribution. Moreover, we found that well-assembled Rutaceae genomes retained significantly more genes (65-82%) than other eudicots affected by recursive polyploidization. Additionally, we showed divergent evolutionary rates among Rutaceae plants, with sweet orange evolving faster than others, and by performing evolutionary rate correction, re-dated major evolutionary events during their evolution. We deduced that the divergence between the Rutaceae family and grape occurred about 81.15-91.74 million years ago (mya), while the split between citrus and atalantia plants occurred <10 mya. In addition, we showed that polyploidization led to a copy number expansion of key gene families contributing to the biosynthesis of vitamin C. Overall, the present effort provides an important comparative genomics resource and lays a foundation to understand the evolution and functional innovation of Rutaceae genomes.

中文翻译：

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芸苔科基因组的比对显示比受额外多倍体化影响的Eudicot基因组更低的基因组分级水平。

由于它们的营养和商业价值，已经对几种柑橘类植物的基因组进行了测序，还对芸香科的一个近缘亲戚Atalantia（Atalantia buxifolia）的基因组进行了测序。在这里，我们显示了芸香科基因组的家庭水平比较分析。通过使用葡萄作为外群并检查跨基因组基因的共线性，我们系统地进行了芸香科基因组的分级和事件相关比对，并基于祖先多倍体化或物种形成产生了定义同源区域的基因列表。我们表征了基因丢失或重定位导致的基因组分级分离，发现基因共线性的侵蚀很大程度上可以通过几何分布来描述。此外，我们发现，组装良好的芸香科基因组比受递归多倍体化影响的其他双子叶植物保留了更多的基因（65-82％）。此外，我们显示了芸香科植物之间的进化速率不同，甜橙的进化速度比其他植物快，并且通过执行进化速率校正，可以重新确定其进化过程中的主要进化事件。我们推论，芸香科和葡萄之间的分歧发生在大约81.15-91.74百万年前（mya），而柑桔和atalantia植物之间的分裂发生了<10 mya。此外，我们发现多倍体化导致关键基因家族的拷贝数扩展，从而促进了维生素C的生物合成。