Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue 5, Pages 2629-2643Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkx006
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Funding
- Swedish Research Council
- Swedish Foundation for Strategic Research
- Karolinska Institutet (KID)
- Cancer and Allergy Association
- Stockholm County Council
- Karolinska Institutet
- National Institutes of Health [AI50113-12, AI39115-19]
- Procter Gamble Co.
- A*STAR/IMB
- Knut and Alice Wallenberg Foundation
- PRISM 12th plan project at IMSc Chennai
- JNCASR
- DBT, Govt. of India
- SERB, Govt. of India
- Swedish Research Council [2015-04622]
- Swedish Research Council [2015-04622] Funding Source: Swedish Research Council
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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 an-notation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodi-alis (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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