On the origin of the seed habit

我们项目的最终目标是更好地了解在进化过程中带来种子的最接近的机制。在这项工作中，我们想要阐明胚珠和种子起源的分子机制，特别是基因调控网络(GRN)中的创新。我们将通过在新兴模式系统Ceratopteris richardii中研究生殖的分子发育遗传学来实现我们的目标。作为一种蕨类植物，里查迪亚是单子植物的一员，单子植物是现存种子植物中最接近的近亲。种子植物包括被子植物(开花植物)和裸子植物。我们将通过两种独立的方式来实现我们的目标，一种是“有针对性的候选基因方法”，另一种是“无偏见的转录切割方法”。在候选基因方法中，我们将首先重建陆地植物MIKCC型MADS-box基因的改进系统发育。通过这种方式，我们将确定蕨类植物中的基因，这些基因与种子植物中控制胚珠和种子发育的基因最接近。同时，我们将使用CRISPR-Cas9在里氏梭子蟹中建立基因组编辑。使用这种方法，我们将敲除花器官和种子识别基因的近亲，这些基因是通过系统发育重建鉴定出来的。基因敲除植物的突变表型将为深入了解这些基因在蕨类植物中的功能以及它们在种子起源过程中的潜在作用提供依据。在转录组学方法中，我们将首先提供里查迪孢子体几个信息性发育阶段的转录组数据。我们将把这些数据与不同种子植物的数据进行比较，包括裸子植物，如挪威云杉(Picea Abies)，以及开花植物，如拟南芥、番茄和水稻。为了更好地区分祖先和派生的特征状态，我们还将把苔藓模式多态地衣和丛生苔藓的合适转录纳入我们的比较中。我们和ICIPS研究单位的其他几名成员获得的数据将用于开发基因调控网络模型，使我们能够识别种子进化起源期间调控基因的关键变化。

The ultimate goal of our project is to better understand the proximate mechanisms that brought about seeds during evolution. During the course of this work we want to clarify the molecular mechanisms, especially innovations in gene regulatory networks (GRN), that were involved in the origin of ovules and seeds. We will pursue our goal by studying the molecular developmental genetics of reproduction in the emerging model system Ceratopteris richardii. As a fern, C. richardii is a member of the monilophytes, which represent the closest living relatives of extant seed plants. Seed plants are comprised of angiosperms (flowering plants) and gymnosperms. We will pursue our goal in two independent ways, a ‘targeted candidate gene approach’, and an ‘unbiased transcriptomic approach’. In the candidate gene approach we will first reconstruct improved phylogenies of MIKCC-type MADS-box genes of land plants. This way we will identify the genes in ferns which are the closest relatives to the genes that control ovule and seed development in seed plants. In parallel, we will establish genome editing in C. richardii employing CRISPR-Cas9. Using this method we will knockout the closest relatives of floral organ and seed identity genes, as identified using the phylogeny reconstructions, in C. richardii. The mutant phenotypes of the knockout plants will provide insights into the function of these genes in ferns and their potential role during the origin of the seed. In the transcriptomics approach we will first provide transcriptome data of several informative developmental stages of the C. richardii sporophyte. We will compare this data with those of diverse seed plants, including gymnosperms such as Norway spruce (Picea abies) and flowering plants such as Arabidopsis, tomato and rice. To better distinguish ancestral from derived character states, we will also include suitable transcriptomes of the bryophyte models Marchantia polymorpha and Physcomitrium patens into our comparisons. The data obtained by us and several other members of the research unit ICIPS will be used to develop models of gene regulatory networks that will enable us to identify critical changes in regulatory genes during the origin of the seed in evolution.