Now with the advent of long read sequences and the whole genome sequencing of several genotypes and the pan-genome idea, more precise determination of genome rearrangements can be done. With this advancement the question “What is the best algorithm to map B. napus genomes?” becomes more critical. Is there an algorithm that accounts for SNPs between different gene copies? Is there an algorithm that accounts for genome rearrangements?

It needs more than algorithm testing to be accurate. Cloning is mandatory for validation but yet difficult in B. napus because of gene copies. I know failed attempts to clone in the past. Perhaps CRISPER technology might be a candidate. Has anyone given it a try?

It has long been known that genomes of newly formed polyploids stabilize over evolutionary time-scale. Has anyone figured how many generations it takes for the genome of the newly synthesized B. napus takes to stabilize ie go through minimal rearrangements?