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

本行动资助2022财年美国国家科学基金会植物基因组生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。西尔维娅·基诺西安博士的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异”。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。遗传变异是进化过程（如自然选择）赖以发生作用的原料。产生新的遗传变异的一种方法是通过全基因组复制。这个过程在植物中很常见，通常伴随着不必要的重复物质的损失。在开花植物中，重复基因组的缩小可以非常迅速地发生，但在蕨类等非开花植物中，缩小的过程似乎要慢得多，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，而且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）的一个当地组织合作，开发植物学和生态学的K-12实地课程，并与Let 's Botanize合作提供科学推广教育，Let 's Botanize是一个在线科学传播系列，利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。在多倍体化之后失去不必要的重复遗传物质，并返回到二倍体遗传，被称为二倍体化。二倍体化的一种机制是分化，基因在一个或两个同源体（多倍体中来自不同亲本类群的同源染色体）中丢失或沉默。这影响了二倍体化后出现的遗传变异的数量，影响了一个谱系如何随着时间的推移而进化。尽管分蘖在进化上具有重要意义，但人们对不同陆生植物谱系中分蘖是如何发生的知之甚少，尤其是蕨类植物和石松植物（蕨类植物）。本项目将首次将蕨类植物纳入分馏比较工作。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，来研究陆地植物多倍体化后的基因组分离是如何发生的。具体地说，将比较陆地植物谱系之间和不同生活史性状之间的分馏机制。所有全基因组和转录组序列将在GenBank上公开提供；整个项目中使用的代码和工作流程将在GitHub (github.com/sylviakinosian).Keywords：蕨类植物，多倍体，基因组结构，基因组缩小，分拣，全基因组复制)上提供。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值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.