Genome Assembly and Annotation of a Plant Pathogen Using the Example of Botrytis cinerea

The availability of a high-quality genome assembly facilitates the analysis of fungal genomes. This chapter outlines the tools and steps involved in genome sequence assembly and annotation of a plant pathogen, Botrytis cinerea. We describe the use of Illumina short-read and Oxford Nanopore long-read sequencing data to assemble the B. cinerea genome. The steps include the pre-processing of sequencing data, genome assembly using Flye, scaffolding with NtLink, and polishing with Racon, Medaka, and NextPolish. The quality of the final assembly is evaluated using BUSCO, which serves as a benchmark for the completeness of a genome. We also provide details on the identification and masking of repetitive elements using the EarlGrey pipeline, as well as the gene prediction and annotation process with Funannotate. The methodologies and insights described can be applied to genome research in other fungal species.