Gapless genome sequence of Botrytis cinerea strain B05.10

Through a combination of sequencing technologies (Illumina, PacBio), we have assembled a gapless genome sequence of Botrytis cinerea strain B05.10, which is corroborated by an optical map. The assembly comprises 18 chromosomes, of which 10 are full-length from one telomere to the other. Two chromosomes are very small (208 and 247 kbp). RNAseq information from a wide range of developmental stages and culture conditions was included in gene prediction pipelines, which permitted to improve gene models significantly and (partly) annotate splice variants. RNASeq analysis revealed non-coding transcripts in intergenic regions. The previously unresolved structure of some secondary metabolite gene clusters was determined (e.g. the botcinic acid cluster, which is important in virulence). Several transcripts appear to have an operon structure, with a single mRNA encoding two proteins. Large scale proteomics was performed to experimentally assess the quality of current gene models and compare it with former versions of the B. cinerea genome. Genetic characterization was performed of a progeny of ~70 individuals from a cross between B05.10 and a field isolate, using Illumina resequencing. A high density linkage map was obtained on which multiple fungicide resistance factors could be mapped. One translocation was observed between the two strains used in the cross. Comparison of genetic with physical distances enabled to identify regions with low recombination rates as well as potential recombination hotspots. This novel, near-finished genome sequence is a major step forward for the community and provides a valuable resource for future research on B.cinerea. A community annotation effort will be organized with support from EBI in the framework of the Ensembl Fungi platform. Community members are invited to participate in the process by adopting chromosomes for curation and annotation.