Fan Zhen, Liston Aaron, Soltis Douglas E, Soltis Pamela S, Ashman Tia-Lynn, Hummer Kim E, Whitaker Vance M
Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Horticultural Sciences Department, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
Horticultural Sciences Department, University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, FL 33597.
Proc Natl Acad Sci U S A. 2025 Jun 24;122(25):e2502814122. doi: 10.1073/pnas.2502814122. Epub 2025 Jun 18.
The evolutionary histories of many polyploid plant species are difficult to resolve due to a complex interplay of hybridization, incomplete lineage sorting, and missing diploid progenitors. In the case of octoploid strawberry with four subgenomes designated ABCD, the identities of the diploid progenitors for subgenomes C and D have been subject to much debate. By integrating new sequencing data from North American diploids with reticulate phylogeny and admixture analyses, we uncovered introgression from an extinct or unsampled species in the clade of , , and into the donor of subgenome A of octoploid prior to its divergence from subsp. We also detected an introgression event from into an ancestor of and Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports of and as donors of the C and D subgenomes and suggest a greater role than previously thought for homoploid hybridization in the diploid progenitors of octoploid strawberry. The integrated set of approaches used here can help advance polyploid genome analysis in other species where hybridization and incomplete lineage sorting obscure evolutionary relationships.
由于杂交、不完全谱系分选和缺失二倍体祖先的复杂相互作用，许多多倍体植物物种的进化历史难以解析。在具有四个亚基因组（命名为ABCD）的八倍体草莓中，亚基因组C和D的二倍体祖先的身份一直存在诸多争议。通过将来自北美二倍体的新测序数据与网状系统发育和混合分析相结合，我们发现，在八倍体草莓的亚基因组A的供体与弗州草莓亚种分化之前，一个已灭绝或未采样的物种（属于弗州草莓、智利草莓和饭沼草莓分支）的基因渗入到了该供体中。我们还检测到一次从饭沼草莓到弗州草莓和智利草莓共同祖先的基因渗入事件。使用基于LTR年龄分布的方法，我们估计八倍体草莓及其中间的六倍体和四倍体祖先分别大约在80万、200万和300万年前出现。这些结果为之前关于饭沼草莓和智利草莓作为C和D亚基因组供体的报道提供了解释，并表明在八倍体草莓的二倍体祖先中，同倍体杂交所起的作用比之前认为的更大。这里使用的这套综合方法有助于推动其他物种的多倍体基因组分析，在这些物种中，杂交和不完全谱系分选模糊了进化关系。
