Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, C. amara and C. rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified by using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.

中文翻译：

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最近形成的三倍体Cardamine insueta遗传了父母的叶片活力和淹没耐受性状

当代物种形成提供了独特的机会，可以直接观察新物种的特征和环境响应。腰果豆蔻是一种异三倍体物种，在过去的150年中出现在瑞士村庄Urnerboden。与它的两个祖先物种C. amara和C. rivularis分别生活在潮湿和开放的生境中不同，在其生境之间发现了C. insueta，其中水位随时间发生波动。该三倍体物种克隆繁殖，并作为三倍体桥形成更高的倍性物种。虽然在田间研究中观察到了利基分离，但是尚不清楚印度棕榈梭菌的环境稳健性的潜在机制。为了表征对波动环境的响应，我们在C中进行了同源基因表达的时程分析。insueta对淹没处理的反应。为此，使用参考指导的方法组装了两个亲本（C. amara和C. rivularis）基因组序列，并使用HomeoRoq软件对同源同源物特异性基因表达进行了定量。我们发现C. insueta和C. rivularis通过在叶子上形成异位分生组织来启动营养繁殖，而C. amara则没有。我们在治疗期间的九个时间点检查了三种物种的同源同源物特异性基因表达。同源基因对的全基因组表达率在整个时间过程中为2：1，与倍性数一致。通过搜索随时间变化的转录组数据具有高表达变异系数的基因，我们发现了许多已知的与两个分生组织发育和形成上调有关的关键转录因子。C. insueta的小叶和小叶-同源物，但在C. amara中没有。此外，在三倍体中，这些基因的一些同源同源物也被上调，表明反式调节。反过来，基因本体论分析表明三倍体中的耐淹水基因的表达模式是从阿曼梭菌（C. amara）继承的。这些结果表明，三倍体C. insueta结合了亲本转录组的有利模式，有助于其沿着用水梯度在新的生态位中建立。