Sun Jianqiang, Shimizu-Inatsugi Rie, Hofhuis Hugo, Shimizu Kentaro, Hay Angela, Shimizu Kentaro K, Sese Jun
Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Japan.
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
Front Genet. 2020 Oct 6;11:567262. doi: 10.3389/fgene.2020.567262. eCollection 2020.
Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, and that live in wet and open habitats, respectively, 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 are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in in response to submergence treatment. For this purpose, the two parental ( and ) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that and initiated vegetative propagation by forming ectopic meristems on leaves, while 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 and -homeolog of , but not in . Moreover, some -homeologs of these genes were also upregulated in the triploid, suggesting -regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from . These results suggest that the triploid combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.
当代物种形成提供了一个独特的机会，可以直接观察新物种的特征和对环境的反应。[该物种名称未给出]是一个异源三倍体物种，在过去150年内出现在瑞士的一个村庄乌尔纳博登。与其两个分别生活在潮湿和开阔栖息地的亲本物种相比，[该物种名称未给出]出现在它们栖息地之间，水位有季节性波动。这个三倍体物种通过克隆繁殖，作为形成更高倍性物种的三倍体桥梁。尽管在野外研究中观察到了生态位分离，但[该物种名称未给出]环境适应性的潜在机制尚不清楚。为了表征对波动环境的反应，我们对[该物种名称未给出]进行了淹水处理的同源基因表达的时间进程分析。为此，使用参考引导方法组装了两个亲本（[亲本物种名称未给出]和[亲本物种名称未给出]）的基因组序列，并使用HomeoRoq软件对同源特异性基因表达进行了定量。我们发现[亲本物种名称未给出]和[亲本物种名称未给出]通过在叶片上形成异位分生组织开始营养繁殖，而[该物种名称未给出]则没有。我们在处理过程中的九个时间点检查了三个物种的同源特异性基因表达。在整个时间进程中，同源基因对的全基因组表达比例为2:1，与倍性数量一致。通过在时间进程转录组数据中搜索表达变异系数高的基因，我们发现许多已知的与分生组织发育和形成相关的关键转录因子在[该物种名称未给出]的[亲本物种名称未给出]和[亲本物种名称未给出]同源基因中上调，但在[该物种名称未给出]中没有。此外，这些基因的一些[该物种名称未给出]同源基因在三倍体中也上调，表明[该物种名称未给出]调控。反过来，基因本体分析表明，三倍体中耐淹基因的表达模式是从[亲本物种名称未给出]遗传而来的。这些结果表明，三倍体[该物种名称未给出]结合了亲本转录组的有利模式，有助于其在沿用水梯度的新生态位中建立。
