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

Kinosian, Sylvia, Logan UT

Investigators

Abstract

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 duplication This 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.