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

这项行动为2022财年的NSF植物基因组博士后生物学研究奖学金提供资金。该研究金支持研究员在东道实验室的研究和培训计划，研究员还提出了扩大生物学参与的计划。Sylvia Kinosian博士的研究和培训计划的标题是“用比较基因组学研究陆生植物的分馏”。该奖学金的主办机构是亚利桑那大学，赞助科学家是Michael Barker博士。遗传变异是进化过程（如自然选择）作用的原材料。产生新的遗传变异的一种方式是通过全基因组复制。这个过程在工厂中很常见，通常会导致不必要的重复材料的损失。复制基因组的缩小在开花植物中可以非常迅速地发生，但在非开花植物如蕨类植物中似乎进行得慢得多，并且可能通过不同的机制进行。该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。这项研究不仅将为我们了解陆地植物基因组进化的驱动因素提供信息，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作物、濒危物种和生态系统如何进化以及它们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（亚利桑那州）的当地组织合作，开发K-12植物学和生态学实地课程，并与Let's Botanize合作提供科学推广教育，这是一个在线科学传播系列，使用植物生命来教授生态学，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，机器学习和基因组序列组装和注释方面的专业知识。 多倍体化后不必要的重复遗传物质的丢失，以及恢复到二倍体遗传，被称为二倍体化。二倍体化的一种机制是分馏，其中基因在一个或两个同源物中丢失或沉默（在多倍体中具有来自不同亲本分类群的共享同源性的染色体）。这会影响二倍体化后存在的遗传变异的数量，从而影响一个谱系如何能够随着时间的推移而进化。尽管它在进化上很重要，但人们对陆生植物的不同谱系，特别是蕨类植物和石松植物（蕨类植物）中的分馏是如何发生的知之甚少。该项目将首次将蕨类植物纳入分馏的比较工作。它将利用新获得的蕨类植物基因组，沿着现有的种子植物基因组，研究陆地植物多倍体化后的基因组分馏。具体而言，分馏机制将比较陆生植物的谱系之间，不同的生活史性状。所有全基因组和转录组序列将在GenBank上公开;整个项目使用的代码和工作流程将在GitHub上提供（github.com/sylviakinosian）.关键词：蕨类植物，多倍性，基因组结构，基因组缩小，分离，整个-基因组复制这个奖项反映了国家科学基金会的法定使命，并被认为是值得支持的，通过评估使用基金会的知识价值和更广泛的影响审查标准。

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.