Dear all,
Can we construct single reference pangenome for different crops such as wheat, rice, maize or it is necessary to build separate pan genomes or genomes?
Thanks
We have only just started moving into super-pangenomes which include species within a genus, typically a cultivated variety with it's wild relatives. See a very important perspectives paper here.
You are suggesting mixing considerably different genomes into a single accession. Just to highlight some of the differences you would need to overcome, the wheat genome has ~100,000 coding genes and is 14.5Gb. Rice has ~36,000 coding genes and is 0.4Gb.
In our experience, it's hard enough to compute whole genome alignments (WGA) among assemblies from the same species to even consider wider taxonomic levels.
If you really want to do something like that you might want to construct a gene-level pangenome. This approach can be done without WGAs and can be computed from nucleotide or protein sequences. Nucleotides give you more resolution (see GET_HOMOLOGUES-EST), proteins allow you to increase evolutionary distances and combined with gene order have been shown to work across species (see for instance GENESPACE).
Collection of pangenome tools (perhaps you will find something in there): https://github.com/colindaven/awesome-pangenomes
We are testing PHG on barley, it has been used on wheat before, see https://doi.org/10.1093/g3journal/jkab390
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Thankyou for your valuable feedback!
Also I am looking for a pipeline or tool that could construct linear pangenome of a crop such as wheat. I found multiple graph-based tools. If you could suggest any appropriate linear-based tool or pipeline I will be so grateful.
Here is a review about wheat genomics from November 2024. The review covers the pangenomes created, and would be a great place to start when looking for tools to create another wheat pangenome.