ArticleNucleic acids research2017
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Advances in Scalp Microbiome Research: Molecular Insights into the Metabolism-Inflammation-Barrier Axis and Dandruff Pathogenesis.Molecules (Basel, Switzerland) · 2026Review
- Malassezia responds to environmental pH signals through the conserved Rim/Pal pathway.bioRxiv : the preprint server for biology · 2024Article
- What are the 100 most cited fungal genera?Studies in mycology · 2024Article
- Proteogenomic Gene Structure Validation in the Pineapple Genome.Journal of proteome research · 2024Article
- Frequent transitions in mating-type locus chromosomal organization inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Frequent transitions in mating-type locus chromosomal organization inbioRxiv : the preprint server for biology · 2023Article
- Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia.Scientific reports · 2023Article
- Article
- Comparative analysis of Malassezia furfur mitogenomes and the development of a mitochondria-based typing approach.FEMS yeast research · 2021Article
- The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks.Fungal diversity · 2021Review
- Article
- Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.Nature communications · 2020Article
- Article
- Identification ofFrontiers in cellular and infection microbiology · 2020Article
- Approaches for Genetic Discoveries in the Skin Commensal and PathogenicFrontiers in cellular and infection microbiology · 2020Review
- The Evolution of Sexual Reproduction and the Mating-Type Locus: Links to Pathogenesis ofAnnual review of genetics · 2019Review
- Combination of Proteogenomics with PeptidemBio · 2019Article
- Advancing Functional Genetics ThroughGenetics · 2019Article
- Article
- Secreted Hydrolytic and Haemolytic Activities of Malassezia Clinical Strains.Mycopathologia · 2019Article
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Authors and funding
22 authors.
Funding
Abstract
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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