There are plans to include a suite of curated plant genomes. I'm not sure of the timing yet as it depends on a few other changes involving the inclusion of more genomes (in general) and standardizing those across usegalaxy.* servers.
A custom genome is just a fasta file. Sometimes the format needs to be manipulated but there is a Galaxy tool that can do that for most cases (NormalizeFasta). Double check that the remaining identifiers are all unique and are an exact match for the identifiers in any reference annotation you plan to use. Please see: https://galaxyproject.org/support/
- Preparing and using a Custom Reference Genome or Build https://galaxyproject.org/learn/custom-genomes/
- Mismatched Chromosome identifiers (and how to avoid them) https://galaxyproject.org/support/chrom-identifiers/
Thanks! Jen, Galaxy team