Multiple Fragaria species sequenced to evaluate octoploid progenitors Phenotype or Genotype

Whole-genome duplications are radical evolutionary events that drive speciation and adaptation in many taxa. The hybrid origins and dynamic restructuring of polyploid genomes are poorly understood due to the challenge of distinguishing homeologous sequences. We use dense targeted-capture-based linkage maps to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the octoploid subgenomes of F. virginiana and F. chiloensis. Our novel approach, POLiMAPS, associates informative inter-homeolog phylogenetic markers with linkage groups and reference genome positions. Upending a widely accepted model, we find that three subgenomes originate with F. iinumae and only one with F. vesca. Extensive unidirectional gene conversion has made the F. iinumae-like subgenomes more F. vesca-like and divergent from each other, likely for adaptive reasons. Divergence among homeologs is also facilitated by interchromosome transpositions. We reveal the complex genomic exchanges underlying polyploid evolution and present a path to unravel other polyploid genomes of agricultural and evolutionary importance.

全基因组复制是驱动众多生物类群物种形成与适应性进化的根本性演化事件。由于难以区分同源序列，关于杂种起源和倍性基因组动态重构的理解尚显不足。我们利用基于密集靶向捕获的连锁图谱，旨在优化二倍体草莓（Fragaria vesca）参考基因组，并解析弗吉尼亚草莓（F. virginiana）和智利草莓（F. chiloensis）的八倍体亚基因组。我们的创新方法，即POLiMAPS，将具有信息量的跨同源系统发育标记与连锁群和参考基因组位置关联。颠覆了广泛接受的模型，我们发现三个亚基因组起源于弗吉尼亚草莓属（F. iinumae），而只有一个起源于草莓属（F. vesca）。广泛的单向基因转换使得弗吉尼亚草莓属样亚基因组更趋近于草莓属样，并彼此分化，这可能是出于适应性进化的原因。同源序列间的分化也得益于染色体重排。我们揭示了倍性演化背后的复杂基因组交换，并开辟了解开其他具有农业和演化重要性的倍性基因组的新途径。