Wheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes

Abstract

Bread wheat is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence/absence variation between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate due to the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess presence/absence variation between bread wheat genomes. Database URL: http://www.appliedbioinformatics.com.au/wheat_panache .

ODGI: understanding pangenome graphs

“…With the increased adoption of long read sequencing we expect pangenomic tools to become increasingly common in the genomic studies at different taxonomic levels and in biomedical research. This progression is already afoot, particularly for targets that involve complex variation, such as cancer ( The Computational Pan-Genomics Consortium, 2016 ), plant pangenomics ( Bayer et al , 2020 , 2022 ; Li et al , 2022 ; Liu et al , 2020 ; Qin et al , 2021 ) and metagenomics ( Zhong et al , 2021 ). Also, when studying animals like bovines ( Bovine Pan-Genome Consortium, 2022 ; Leonard et al , 2021 ; Talenti et al , 2022 ).…”

ODGI: understanding pangenome graphs

“…With the increased adoption of long read sequencing we expect pangenomic tools to become increasingly common in the genomic studies at different taxonomic levels and in biomedical research. This progression is already afoot, particularly for targets that involve complex variation, such as cancer (The Computational Pan-Genomics Consortium, 2016), plant pangenomics (Bayer et al ., 2020; Liu et al ., 2020; Qin et al ., 2021; Li et al ., 2022; Bayer et al ., 2022), and metagenomics (Zhong et al ., 2021). Also, when studying animals like bovines (Leonard et al ., 2021; Talenti et al ., 2022; Bovine Pan-Genome Consortium, 2022).…”

Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis

“…Crop pangenomics resources are useful for plant breeding and improvement, revealing valuable information for breeders to tap into from the large diversity of a species (Golicz et al, 2016;Bayer et al, 2020Bayer et al, , 2022aZanini et al, 2022). For example, the soybean pangenome from the USDA collection revealed more genes with lower frequencies, such as those controlling plant architecture and seed composition, than those with higher frequencies, such as those controlling flowering time and stress tolerance traits; this gives breeders an idea of which genes to select from which accession during the selective breeding process ("smart" breeding) (Bayer et al, 2022b).…”