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 Armillaria species. Most Armillaria 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 Armillaria genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future Armillaria genome projects were developed. Knowledge gained from genomic studies of Armillaria species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.

Automated summary

Technological advancements in genome sequencing, assembly, and annotation have allowed for further understanding of Armillaria species and their impact on agriculture and forestry. This review evaluates the methods and samples used in Armillaria genome projects and provides guidelines and resources for future research. The knowledge gained from genomic studies of Armillaria can also be applied to other fungal genomics.