Genome sequencing and integrative gene annotation of Malassezia sympodialis. Malassezia sympodialis genomes (strain ATCC 42132 and four clinical isolates)

The skin commensal yeast Malassezia is associated with several skin disorders. To establish a reference resource, we sought to determine the complete genome sequence of Malassezia sympodialis strain ATCC 42132 and identify its protein-coding genes. Through long-read DNA sequencing on the PacBio RS II system, we obtained a gap free genome assembly, comprising eight nuclear and one mitochondrial chromosome. We additionally sequenced and independently assembled the genomes of four M. sympodialis clinical isolates (KS004, KS024, KS269 and KS327) using the same methodology. The sequence reads indicated the existence of multiple mitochondrial genome configurations and the ATCC 42132 mitochondrial sequence deposited here represents one of those. A novel genome annotation workflow combining RNA-seq, proteomics and manual curation was developed to determine gene structures with high accuracy across the M. sympodialis ATCC 42132 genome. The resulting annotation contains 4,494 protein-coding genes, all of which were supported by RNA-seq and 86% confirmed by proteomics data. The RNA-seq data have been deposited in the ArrayExpress repository (accession E-MTAB-4589) and the proteomics data in the PRIDE repository (accession PXD003773).