A haplotype-resolved chromosomal reference genome for the European Boletus edulis

In my first paper when characterizing the inbreeding of the different lineages of B. edulis, we were quite limited by the contiguity of the reference genomes of certain lineages, especially the European one.

Since the next chapters of my PhD were focused on the European lineage and the analysis we were planning to use were heavily dependant on good reference contiguity (IBD segment detection, for example), we decided to assemble a new reference genome.

When doing so, we realized there were very few EMF with chromosomal reference genomes available, so we decided to add Hi-C sequencing to the Hi-Fi and short reads, to construct one of the first EMF haplotype-resolved chromosomal level genome.

We identified various features such as the centromeres, some of the telomeres, and the final assembly contains almost no gap.

The manuscript describing this new assembly and a preliminary population structure analysis of the European B. edulis is published in G3: Genes|Genomes|Genetics here, and you can access the code of this entire project here.