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Nucleic Acids Res. 2017 Mar 17;45(5):2629-2643. doi: 10.1093/nar/gkx006.

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Author information

Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 17121 Solna, Sweden.
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden.
National Genomics Infrastructure, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden.
Department of Biology, Saint Louis University, St. Louis, MO 63103, USA.
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
School of Biomedical and Biomolecular Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet and University Hospital, 17177 Stockholm, Sweden.
Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, 17121 Solna, Sweden.
Computational and Systems Biology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672, Singapore.
Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, India.
The Institute of Mathematical Sciences/HBNI, Taramani, Chennai 600 113, India.
Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75123 Uppsala, Sweden.
CBS-Fungal Biodiversity Centre, Utrecht, 3508, The Netherlands and Institute for Biodiversity and ecosystem Dynamics (IBED), University of Amsterdam, 1012 WX Amsterdam, The Netherlands.
Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), 138648, Singapore.
Science for Life Laboratory, Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden.


Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome. We also sequenced and assembled four M. sympodialis clinical isolates, and showed their value for understanding Malassezia reproduction by confirming four alternative allele combinations at the two mating-type loci. Importantly, we demonstrated how proteomics data could be readily integrated with transcriptomics data in standard annotation tools. This increased the number of annotated protein-coding genes by 14% (from 3612 to 4113), compared to using transcriptomics evidence alone. Manual curation further increased the number of protein-coding genes by 9% (to 4493). All of these genes have RNA-seq evidence and 87% were confirmed by proteomics. The M. sympodialis genome assembly and annotation presented here is at a quality yet achieved only for a few eukaryotic organisms, and constitutes an important reference for future host-microbe interaction studies.

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