The members of the tribe Brassiceae share a whole genome triplication (WGT), and one proposed model for its formation is a "two-step" pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using POInT (the Polyploidy Orthology Inference Tool). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring prior to the arrival of the third. We also, for the 90,000 individual genes in our study, make parental "subgenome" assignments, inferring, with measured uncertainty, which of the progenitor genomes of the allohexaploidy each gene derives from. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, where subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

中文翻译：

---

芸苔属中倍体祖细胞基因组的贡献在进化上是截然不同的，但在功能上是兼容的

芸苔属的成员共享一个完整的基因组三倍体（WGT），其形成的一个提议模型是产生六倍体后代的“两步”杂交对。但是，该模型的证据不完整，甚至在六倍体之后驱动进化的进化和功能限制还很少被理解。在这里，我们报告了Crambe hispanica的新基因组序列，是大多数已测序的芸苔科的姊妹物种。使用这个新的基因组和其他三个共有六倍体的基因组，我们使用POInT（多倍体正畸推断工具）追踪了WGT后基因丢失的历史。我们确认了两步形成模型，并推断这两个同种多倍体化之间存在明显的时间间隙，前两个亚基因组的基因损失中约有三分之一发生在第三个亚基因组到达之前。对于我们研究中的90,000个个体基因，我们还要进行父母的“亚基因组”分配，并在不确定的情况下推断出每个基因来自同种六倍体的祖细胞基因组。我们进一步表明，每个亚基因组都有统计上可区分的同源损失率。几乎没有迹象表明这三个亚基因组之间在功能上有所区别：各个亚基因组没有显示功能性富集的模式，其成员之间没有过多的共享蛋白质-蛋白质或代谢相互作用，并且在经历最近的选择性扫描时没有偏见。我们提出异源多倍体的“混合与匹配”模型，其中亚基因组起源驱动同源丢失的倾向，而来自不同亚基因组的基因一起发挥作用却没有困难。