Brassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes

Abstract

Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population and the impact of climate change on agriculture, there is an increasing need to improve agronomically important traits of crops such as Brassica. The genomes of plant species have significant sequence presence absence variation (PAV), which is a source of genetic variation that can be used for crop improvement, and this species variation can be captured through the construction of pangenomes. Graph pangenomes are a recent reference format that represent the genomic variation with a species or population as alternate paths in a sequence graph. Graph pangenomes contain information on alignment, PAV, and annotation. Here we present the first multi-species graph pangenome for Brassica visualized with pangenome analyzer with chromosomal exploration (Panache).