There is a wave of crop reference genomes being generated making it possible to improve navigation of important gene traits for crop improvement. A highly regarded approach toward assessing such traits is through the use of a pan-genome perspective for the genomes. Already there are over 100 reference genomes covering all the cereals: some are included here. For the cereals, genomes generally range in size from 6Gb to 15Gb in size each, depending on ploidy. Model genomes, such as Brachypodium spp. are smaller. Pan-genomes as a resource can begin the journey for evolutionary studies, tracking down individual traits, detecting genome variation by way of structure, tracking integrity of metabolic pathways, as well as leading to other studies in genomics, proteomics, and metabolomics. As many fully sequenced crop genomes quickly appear and multiply, the need for developing annotation pipelines for surveying pan-genomes and connecting them to traits and phenotypes in studied crop systems is imperative to secure our food future.

PanGenome Resources (with JBrowse 2)

These web interfaces provide several user-friendly tools, including micro-synteny visualization displays such as JBrowse2, genome-level synteny viewer through AccuSyn. Webpages also support a pan-genomic BLAST which facilitates sequence search against pan-genomic groups. Additionally, similar sequences across the pan-genome can be viewed and downloaded through Jalview.

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PanGenome Resources (with JBrowse 1)

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Informational Links