Presentation Title

Development and Application of a Software Tool/Package for Pan-genomic Analysis

Format of Presentation

15-minute lecture to be presented the Saturday of the conference

Presenter Information

Richard A. J. MartynFollow

Location

IB 1008

Start Date

30-3-2019 11:45 AM

End Date

30-3-2019 12:00 PM

Abstract

Continuing scientific progress in genetics allows us to better understand how structural variations in an organism’s gene content can lead to diversity within a species. By analyzing the sum of the genes for an entire species, we can construct a pan-genome for the species. The pan-genome of a species is the set of all genes present in all sub-species of a species. A pan-genome consists of the core genome, which represents the genes present in all sub-species of a species, and a variable genome, which refers to genes not present in all sub-species of a species. Micropan is an R package designed for the study of microbial pan-genomics. The genomes of prokaryotes (microbes) are relatively simple, leading to relatively simple construction of their pan-genome. However, plant genomes are highly repetitive and complex in comparison, and there is no general tool/package developed for pan-genome construction for plants. Due to the computational requirements of constructing such a pan-genome, the tool/package required needs to be more efficient and robust than Micropan. The objective of this project is to use Micropan as a guide to develop a pan-genome construction pipeline for single chromosome genomes. The design of this pipeline will allow it to adapt to different selections of gene annotation and ortholog clustering methods. With a more efficient and robust tool/package constructed, future research can discover how to extend it to multiple chromosome genomes.

Department

Computing Science

Faculty Advisor

Lingling Jin

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Mar 30th, 11:45 AM Mar 30th, 12:00 PM

Development and Application of a Software Tool/Package for Pan-genomic Analysis

IB 1008

Continuing scientific progress in genetics allows us to better understand how structural variations in an organism’s gene content can lead to diversity within a species. By analyzing the sum of the genes for an entire species, we can construct a pan-genome for the species. The pan-genome of a species is the set of all genes present in all sub-species of a species. A pan-genome consists of the core genome, which represents the genes present in all sub-species of a species, and a variable genome, which refers to genes not present in all sub-species of a species. Micropan is an R package designed for the study of microbial pan-genomics. The genomes of prokaryotes (microbes) are relatively simple, leading to relatively simple construction of their pan-genome. However, plant genomes are highly repetitive and complex in comparison, and there is no general tool/package developed for pan-genome construction for plants. Due to the computational requirements of constructing such a pan-genome, the tool/package required needs to be more efficient and robust than Micropan. The objective of this project is to use Micropan as a guide to develop a pan-genome construction pipeline for single chromosome genomes. The design of this pipeline will allow it to adapt to different selections of gene annotation and ortholog clustering methods. With a more efficient and robust tool/package constructed, future research can discover how to extend it to multiple chromosome genomes.