Presentation Title

Pangenome Construction Pipeline for Eukaryotes

Format of Presentation

Poster to be presented the Friday of the conference

Abstract

In the field of plant genomics, there is an increasing trend towards the study of a species’ full complement of genes, termed the species’ pangenome, which can be used to capture the entire gene repertoire of a clade. This has created an expanding demand for tools relating to the construction of pangenomes for eukaryotes, especially for plants. The creation of a complete eukaryotic pangenome tool remains hindered due to the increased complexity placed on such a tool as a result of the large genetic duplicity and genome size within eukaryotes. Many tools capable of completing functions that are part of the pangenome construction process, such as genome assembly and annotations, already exist. This project explores how to employ and customize certain of these existing tools to create a pipeline that will serve as the complete pangenome construction. To identify these tools, numerous existing plant pangenome studies were reviewed to locate those tools common to multiple studies and then to combine them through experimentation to create the pipeline. By creating a complete pangenome construction pipeline for eukaryotes, pangenomes can be constructed for a larger number of and for more complex species. Through these pangenomes, biologists can identify which genes serve core functional needs or as a variable component between individuals and subspecies to further understand the variations of each subspecies.

Department

Computing Science

Faculty Advisor

Lingling Jin

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Pangenome Construction Pipeline for Eukaryotes

In the field of plant genomics, there is an increasing trend towards the study of a species’ full complement of genes, termed the species’ pangenome, which can be used to capture the entire gene repertoire of a clade. This has created an expanding demand for tools relating to the construction of pangenomes for eukaryotes, especially for plants. The creation of a complete eukaryotic pangenome tool remains hindered due to the increased complexity placed on such a tool as a result of the large genetic duplicity and genome size within eukaryotes. Many tools capable of completing functions that are part of the pangenome construction process, such as genome assembly and annotations, already exist. This project explores how to employ and customize certain of these existing tools to create a pipeline that will serve as the complete pangenome construction. To identify these tools, numerous existing plant pangenome studies were reviewed to locate those tools common to multiple studies and then to combine them through experimentation to create the pipeline. By creating a complete pangenome construction pipeline for eukaryotes, pangenomes can be constructed for a larger number of and for more complex species. Through these pangenomes, biologists can identify which genes serve core functional needs or as a variable component between individuals and subspecies to further understand the variations of each subspecies.