A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria

Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including <i>Armillaria</i> species. Most <i>Armillaria</i> species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in <i>Armillaria</i> genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future <i>Armillaria</i> genome projects were developed. Knowledge gained from genomic studies of <i>Armillaria</i> species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.