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

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 Jr, Heitman J, Scheynius A, Lehtiö J.

 

 

If you are interested to know how proteomics can contribute to genome annotation, take a look of our new publication (Zhu Y et al, Nucleic Acids Res. 2017 Jan 18.)! J

By using proteomics we could annotate 501 new protein coding genes in a skin commensal yeast Malassezia sympodialis. We did that with our new workflow for genome annotation by combining evolutionary, mRNA and protein level evidence. We also publish here a gap free genome assembly of Mala S generated by long read sequencing.

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx006

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https://www.ncbi.nlm.nih.gov/pubmed/28100699

In this paper, we present a high quality reference genome annotation for M. sympodialis in terms of both completeness and accuracy, produced by a novel genome annotation workflow followed by manual curation.The workflow integrated several computational gene predictors, transcriptome sequencing and mass spectrometry based proteomics data. The annotation obtained contains 4493 protein-coding genes, 957 more than in our previous M. sympodialis annotation and it is exceptionally well supported by transcriptome and proteome data.