Isolation of supernumerary mini-chromosomes from fungi for enrichment sequencing v1

Fungal genomes are highly dynamic and often contain supernumerary mini-chromosomes. However, our knowledge about the role of mini-chromosomes in dynamic genome rearrangements and evolution is scarce. Mini-chromosomes are usually smaller then core-chromosomes and are variable in size and numbers between individuals of a species. Mini-chromosome occurence in fungi is well documented since decades, but many genomic projects have neglected them, mainly because it was technically challenging to identify them in whole genome assemblies. Here we present a protocol for isolation of mini-chromosomes for enrichment sequencing. This allows identification of mini-chromosomes in whole genome assemblies and thus comparative genomics analyses of core- and mini-chromosomes.