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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis
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2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 5, p. 2629-2643Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Oxford University Press , 2017. Vol. 45, no 5, p. 2629-2643
Keywords [en]
allele, animal cell, Article, atopic dermatitis, chromosome 5, controlled study, DNA base composition, DNA sequence, functional genomics, gene locus, gene mapping, human, Malassezia sympodialis, mitochondrial genome, nonhuman, nucleotide sequence, peptide analysis, phylogeny, priority journal, protein domain, proteogenomics, RNA sequence, sequence analysis, sequence homology, transcriptomics, fungal gene, fungal genome, genetics, Malassezia, molecular genetics, procedures, fungal protein, peptide, Fungal Proteins, Genes, Fungal, Genome, Fungal, Genome, Mitochondrial, Molecular Sequence Annotation, Peptides, Protein Domains, Sequence Analysis, RNA
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-216548DOI: 10.1093/nar/gkx006ISI: 000397286600039Scopus ID: 2-s2.0-85018260556OAI: oai:DiVA.org:kth-216548DiVA, id: diva2:1155672
Note

Funding details: KI, Karolinska Institutet; Funding text: Swedish Research Council [to J.Le. and A.S.]; Swedish Foundation for Strategic Research [to J.Le.];Karolinska Institutet (KID) [to Y.Z. and J.Le.]; Cancer and Allergy Association [to A.S.]; the regional agreement on medical training and clinical research (ALF) between Stockholm County Council and Karolinska Institutet [to A.S. and J.Le.]; National Institutes of Health [R01 grant AI50113-12, R37 grant AI39115-19 to S.S., B.B. and J.H.]; Procter & Gamble Co. and A∗STAR/IMB [to T.D.]; Knut and Alice Wallenberg Foundation to the Wallenberg Advanced Bioinformatics Infrastructure [to P.E.]; PRISM 12th plan project at IMSc Chennai [to R.S.]; JNCASR [to S.R.S.]; DBT and SERB, Govt. of India [to K.S.]. Funding for open access charge: Swedish Research Council [2015-04622]. Conflict of interest statement. During initial relevant work T.D. was, but is no longer supported by the Procter & Gamble Company. The rest of the authors declare that they have no relevant conflicts of interest.

QC 20171108

Available from: 2017-11-08 Created: 2017-11-08 Last updated: 2017-11-08Bibliographically approved

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Lundeberg, Joakim

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