Hello everyone,

I am new to pangenome graph analysis and am planning to construct a bread wheat (Triticum aestivum) pangenome graph using the PGGB pipeline for my PhD research.

I will use around 30 bread wheat cultivars, all assembled at chromosome level using PacBio HiFi reads and Hi-C data. From this pangenome, I aim to investigate structural variations (SVs), presence/absence variations (PAVs), and identify genes associated with agronomic traits.

Since bread wheat has a large (~16 Gb) and highly repetitive (~80%) genome, I expect significant computational and runtime challenges. I have read that in some studies (for example, in Arabidopsis pangenome graphs), assemblies were preprocessed by splitting into chromosomes and removing unplaced contigs before running PGGB.

My questions are:

For bread wheat, would you recommend constructing the pangenome graph per chromosome or using the whole genome?

I am concerned that some known translocations in wheat might not be captured if the graph is built separately for each chromosome.

Some of my assemblies were generated from Illumina short reads , while most are from PacBio HiFi reads (from recently published papers).

Is it appropriate to integrate assemblies produced by different sequencing technologies into the same PGGB graph? Or would that introduce biases in SV detection due to varying assembly quality and contiguity?

Any advice, experience, or reference suggestions on constructing a large, complex plant pangenome graph like wheat using PGGB would be highly appreciated.

Thank you very much for your time and guidance.

Best regards, Sony