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

Published

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Zhu, Y; Engström, PG; Tellgren-Roth, C; Baudo, CD; Kennell, JC; Sun, S; Billmyre, RB; Schröder, MS; Andersson, A; Holm, T; Sigurgeirsson, B; Wu, G; Sankaranarayanan, SR; Siddharthan, R; Sanyal, K; Lundeberg, J; Nystedt, B; Boekhout, T; Dawson, TL; Heitman, J; Scheynius, A; Lehtiö, J

Published Date

  • March 2017

Published In

Volume / Issue

  • 45 / 5

Start / End Page

  • 2629 - 2643

PubMed ID

  • 28100699

Pubmed Central ID

  • 28100699

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

International Standard Serial Number (ISSN)

  • 0305-1048

Digital Object Identifier (DOI)

  • 10.1093/nar/gkx006

Language

  • eng