Brassica napus Panache: A graph pangenome representing presence absence variation across ten B. napus genomes

Tessa R. MacNish; Connor McPhan; Philipp E. Bayer; Shengyi Liu; Hawlader A. Al-Mamun; Jacqueline Batley; David Edwards

doi:10.1016/j.agrcom.2026.100143

Brassica napus Panache: A graph pangenome representing presence absence variation across ten B. napus genomes

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Abstract

Brassica napus is an economically important oil crop with significant levels of gene presence absence variation (PAV) between individuals, providing a source of genetic diversity that can be applied for crop improvement. Graph pangenomes are a new format for representing pangenomes and can be used to identify and explore PAV for use in breeding to accelerate crop improvement. Here we present a graph pangenome constructed from ten high-quality B. napus genome assemblies. The pangenome is hosted and visualized online with the pangenome analyzer with chromosomal exploration (Panache) tool. This public resource provides a comprehensive map of genome variability in B. napus that can be applied to accelerate the breeding of this important crop.

Original language	English
Article number	100143
Journal	Agriculture Communications
Volume	4
Issue number	2
DOIs	https://doi.org/10.1016/j.agrcom.2026.100143
Publication status	Published - Jun 2026

Funding

Funders	Funder number
ARC Australian Research Council	DP200100762, DP210100296

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10.1016/j.agrcom.2026.100143Licence: CC BY-NC-ND

Cite this

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title = "Brassica napus Panache: A graph pangenome representing presence absence variation across ten B. napus genomes",

abstract = "Brassica napus is an economically important oil crop with significant levels of gene presence absence variation (PAV) between individuals, providing a source of genetic diversity that can be applied for crop improvement. Graph pangenomes are a new format for representing pangenomes and can be used to identify and explore PAV for use in breeding to accelerate crop improvement. Here we present a graph pangenome constructed from ten high-quality B. napus genome assemblies. The pangenome is hosted and visualized online with the pangenome analyzer with chromosomal exploration (Panache) tool. This public resource provides a comprehensive map of genome variability in B. napus that can be applied to accelerate the breeding of this important crop.",

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author = "MacNish, \{Tessa R.\} and Connor McPhan and Bayer, \{Philipp E.\} and Shengyi Liu and Al-Mamun, \{Hawlader A.\} and Jacqueline Batley and David Edwards",

note = "Publisher Copyright: {\textcopyright} 2026 The Authors",

year = "2026",

month = jun,

doi = "10.1016/j.agrcom.2026.100143",

language = "English",

volume = "4",

journal = "Agriculture Communications",

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T1 - Brassica napus Panache

T2 - A graph pangenome representing presence absence variation across ten B. napus genomes

AU - MacNish, Tessa R.

AU - McPhan, Connor

AU - Bayer, Philipp E.

AU - Liu, Shengyi

AU - Al-Mamun, Hawlader A.

AU - Batley, Jacqueline

AU - Edwards, David

PY - 2026/6

Y1 - 2026/6

N2 - Brassica napus is an economically important oil crop with significant levels of gene presence absence variation (PAV) between individuals, providing a source of genetic diversity that can be applied for crop improvement. Graph pangenomes are a new format for representing pangenomes and can be used to identify and explore PAV for use in breeding to accelerate crop improvement. Here we present a graph pangenome constructed from ten high-quality B. napus genome assemblies. The pangenome is hosted and visualized online with the pangenome analyzer with chromosomal exploration (Panache) tool. This public resource provides a comprehensive map of genome variability in B. napus that can be applied to accelerate the breeding of this important crop.

AB - Brassica napus is an economically important oil crop with significant levels of gene presence absence variation (PAV) between individuals, providing a source of genetic diversity that can be applied for crop improvement. Graph pangenomes are a new format for representing pangenomes and can be used to identify and explore PAV for use in breeding to accelerate crop improvement. Here we present a graph pangenome constructed from ten high-quality B. napus genome assemblies. The pangenome is hosted and visualized online with the pangenome analyzer with chromosomal exploration (Panache) tool. This public resource provides a comprehensive map of genome variability in B. napus that can be applied to accelerate the breeding of this important crop.

KW - Brassica napus

KW - Genetic diversity

KW - Graph pangenome

KW - Presence absence variation

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DO - 10.1016/j.agrcom.2026.100143

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Brassica napus Panache: A graph pangenome representing presence absence variation across ten B. napus genomes

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Understanding disease resistance gene evolution across the Brassicaceae

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Brassica napus Panache: A graph pangenome representing presence absence variation across ten B. napus genomes

Abstract

Funding

Access to Document

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Understanding disease resistance gene evolution across the Brassicaceae

Who’s who in the plant gene world?

Cite this