NSF Postdoctoral Fellowship in Biology: Investigating Fractionation in Land Plants with Comparative Genomics

这一行动为2022财年NSF植物基因组生物学博士后研究奖学金提供了资金。该奖学金支持在东道主实验室为该研究员制定的研究和培训计划，该研究员还提出了扩大生物学参与度的计划。为西尔维娅·基诺西安博士提供的这项研究和培训计划的标题是“用比较基因组学研究陆地植物的分裂”。该奖学金的主办机构是亚利桑那大学，赞助科学家是迈克尔·巴克博士。遗传变异是自然选择等进化过程所依据的原材料。产生新的遗传变异的一种方式是通过全基因组复制。这一过程在植物中很常见，通常伴随着不必要的重复材料的损失。重复基因组的缩小在开花植物中发生得非常快，但在非开花植物(如蕨类植物)中似乎进行得更慢，而且可能是通过不同的机制进行的。这个项目将研究影响蕨类植物基因组缩小的进化机制，由于获得了新测序的蕨类植物基因组，这项研究现在成为可能。这项研究不仅将使我们了解陆地植物基因组进化的驱动因素，还将有助于确定哪些领域需要未来的工作。研究陆地植物的基因组进化对于了解农作物、濒危物种和生态系统如何进化，以及它们将如何适应不断变化的气候至关重要。更广泛的影响包括指导和培训本科生，以及与图森市(亚利桑那州)的一家当地组织合作，开发植物学和生态学的K-12实地课程，并与在线科学交流系列We‘s Botanize合作提供科学外展教育，该系列利用植物生命教授生态学、进化和生物多样性。培训目标包括获得比较基因组学、生物信息学、机器学习以及基因组序列组装和注释方面的专业知识。多倍化后不必要的重复遗传物质的丢失，并返回到二倍体遗传，称为二倍化。二倍化的一种机制是分离，在一个或两个同源基因(多倍体中不同亲本分类群具有共同同源性的染色体)中基因丢失或沉默。这会影响二倍化后出现的遗传变异量，影响血统如何随着时间的推移而进化。尽管它在进化上很重要，但关于不同的陆地植物谱系，特别是蕨类植物和石蒜(蕨类植物)中的分离如何发生，人们知之甚少。该项目将首次在分馏比较工作中包括蕨类植物。它将利用新获得的蕨类植物基因组以及现有的种子植物基因组，来研究多倍化后的基因组分离是如何在陆地植物中发生的。具体地说，将比较不同陆生植物谱系之间以及不同生活史特征之间的分离机制。所有全基因组和转录组序列将在GenBank上公开可用；整个项目使用的代码和工作流程将在GitHub(githeb.com/sylviakinosian)上获得。关键词：蕨类、多倍体、基因组结构、基因组缩减、分裂、全基因组复制该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2022. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Dr. Sylvia Kinosian is "Investigating Fractionation in Land Plants with Comparative Genomics" The host institution for the fellowship is the University of Arizona and the sponsoring scientist is Dr. Michael Barker.Genetic variation is the raw material that evolutionary processes, such as natural selection, act upon. One way novel genetic variation is generated is via whole-genome duplication. This process is common in plants and is typically followed by a loss of unnecessary duplicated material. The downsizing of a duplicated genome can occur very rapidly in flowering plants, but appears to proceed much slower, and potentially by different mechanisms, in non-flowering plants such as ferns. This project will investigate the evolutionary mechanisms that affect genome downsizing in ferns, a study now possible due to access to newly sequenced fern genomes. This research will inform not only our understanding of the drivers of genome evolution in land plants but will also aid in determining what areas are in need of future work. Studying genome evolution in land plants is critical for understanding how crops, endangered species, and ecosystems evolve, and how they will adapt to a changing climate. Broader impacts include mentoring and training undergraduate students as well as partnering with a local organization in Tucson (AZ) to develop a K-12 field course in botany and ecology and provide science outreach education in partnership with Let’s Botanize, an online science communication series using plant life to teach about ecology, evolution, and biodiversity. Training objectives include obtaining expertise in comparative genomics, bioinformatics, machine learning, and genome sequence assembly and annotation. The loss of unnecessary duplicated genetic material following polyploidization, and a return to diploid inheritance, is known as diploidization. One mechanism of diploidization is fractionation, where genes are lost or silenced in one or both homeologs (chromosomes with shared homology from different parental taxa in a polyploid). This affects the amount of genetic variation present following diploidization, influencing how a lineage will be able to evolve over time. Despite its evolutionary importance, little is known about how fractionation occurs in different lineages of land plants, particularly in ferns and lycophytes (pteridophytes). This project will include pteridophytes for the first time in comparative work on fractionation. It will leverage newly available pteridophyte genomes, along with existing seed plant genomes, to investigate how genome fractionation following polyploidization occurs in land plants. Specifically, mechanisms of fractionation will be compared between lineages of land plants, and among different life-history traits. All whole-genome and transcriptome sequences will be publicly available on GenBank; the code and workflows used throughout this project will be available on GitHub (github.com/sylviakinosian).Keywords: ferns, polyploidy, genome structure, genome downsizing, fractionation, whole -genome duplicationThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.