Over the decades, evolutionists and ecologists have shown intense interest in the role of polyploidization in plant evolution. Without clear knowledge of the diploid ancestor(s) of polyploids, we would not be able to answer fundamental ecological questions such as the evolution of niche differences between them or its underlying genetic basis. Here, we explored the evolutionary history of two Fragaria tetraploids, Fragaria corymbosa and Fragaria moupinensis. We de novo assembled five genomes including these two tetraploids and three diploid relatives. Based on multiple lines of evidence, we found no evidence of subgenomes in either of the two tetraploids, suggesting autopolyploid origins. We determined that Fragaria chinensis was the diploid ancestor of F. corymbosa while either an extinct species affinitive to F. chinensis or an unsampled population of F. chinensis could be the progenitor of F. moupinensis. Meanwhile, we found introgression signals between F. chinensis and Fragaria pentaphylla, leading to the genomic similarity between these two diploids. Compared to F. chinensis, gene families related to high ultraviolet (UV)-B and DNA repair were expanded, while those that responded towards abiotic and biotic stresses (such as salt stress, wounding, and various pathogens) were contracted in both tetraploids. Furthermore, the two tetraploids tended to down-regulate defense response genes but up-regulate UV-B response, DNA repairing, and cell division gene expression compared to F. chinensis. These findings may reflect adaptions toward high-altitude habitats. In summary, our work provides insights into the genome evolution of wild Fragaria tetraploids and opens up an avenue for future works to answer deeper evolutionary and ecological questions regarding the strawberry genus.

中文翻译：

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基因组数据提供了对两个四倍体草莓的进化历史和适应性分化的见解


几十年来，进化论者和生态学家对多倍体化在植物进化中的作用表现出了浓厚的兴趣。如果没有对多倍体的二倍体祖先的明确了解，我们将无法回答基本的生态学问题，例如它们之间生态位差异的进化或其潜在的遗传基础。在这里，我们探讨了两种 Fragaria 四倍体 Fragaria corymbosa 和 Fragaria moupinensis 的进化历史。我们从头组装了 5 个基因组，包括这两个四倍体和 3 个二倍体亲戚。基于多条证据线，我们在两个四倍体中的任何一个都没有发现亚基因组的证据，这表明自体多倍体起源。我们确定 Fragaria chinensis 是 F. corymbosa 的二倍体祖先，而与 F. chinensis 相关的已灭绝物种或未采样的 F. chinensis 种群可能是 F. moupinensis 的祖先。同时，我们发现了 F. chinensis 和 Fragaria pentaphylla 之间的渗入信号，导致这两个二倍体之间的基因组相似性。与中华镰刀菌相比，与高紫外线 （UV）-B 和 DNA 修复相关的基因家族扩大，而对非生物和生物胁迫 （如盐胁迫、损伤和各种病原体） 有反应的基因家族在两个四倍体中收缩。此外，与中华镰刀菌相比，这两个四倍体倾向于下调防御反应基因，但上调 UV-B 反应、DNA 修复和细胞分裂基因表达。这些发现可能反映了对高海拔栖息地的适应。 总之，我们的工作为野生 Fragaria 四倍体的基因组进化提供了见解，并为未来的工作开辟了一条途径，以回答有关草莓属的更深层次的进化和生态问题。