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

Yafeng Zhu; Pär G. Engström; Christian Tellgren-Roth; Charles Baudo; Jack Kennell; Sheng Sun; Blake Robert Billmyre; Markus S Schröder; Anna Andersson; Tina Holm; Benjamin Sigurgeirsson; Guangxi Wu; Sundar Sankaranarayanan; Rahul Siddharthan; Kaustuv Sanyal; Joakim Lundeberg; Björn Nystedt; Teun Boekhout; Thomas L., Jr. Dawson; Janne Lehtiö

doi:10.1093/nar/gkx006

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

Yafeng Zhu, Pär G. Engström, Christian Tellgren-Roth, Charles Baudo, Jack Kennell, Sheng Sun, Blake Robert Billmyre, Markus S Schröder, Anna Andersson, Tina Holm, Benjamin Sigurgeirsson, Guangxi Wu, Sundar Sankaranarayanan, Rahul Siddharthan, Kaustuv Sanyal, Joakim Lundeberg, Björn Nystedt, Teun Boekhout, Thomas L., Jr. Dawson, Janne Lehtiö

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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.

Original language	English
Pages (from-to)	gkx006
Journal	Nucleic Acids Research
Volume	45
DOIs	https://doi.org/10.1093/nar/gkx006
Publication status	Published - 01 Jan 2017

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Zhu, Y., G. Engström, P., Tellgren-Roth, C., Baudo, C., Kennell, J., Sun, S., Billmyre, B. R., Schröder, M. S., Andersson, A., Holm, T., Sigurgeirsson, B., Wu, G., Sankaranarayanan, S., Siddharthan, R., Sanyal, K., Lundeberg, J., Nystedt, B., Boekhout, T., Dawson, T. L. . J., & Lehtiö, J. (2017). Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. Nucleic Acids Research, 45, gkx006. https://doi.org/10.1093/nar/gkx006

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title = "Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis",

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.",

author = "Yafeng Zhu and {G. Engstr{\"o}m}, P{\"a}r and Christian Tellgren-Roth and Charles Baudo and Jack Kennell and Sheng Sun and Billmyre, {Blake Robert} and Schr{\"o}der, {Markus S} and Anna Andersson and Tina Holm and Benjamin Sigurgeirsson and Guangxi Wu and Sundar Sankaranarayanan and Rahul Siddharthan and Kaustuv Sanyal and Joakim Lundeberg and Bj{\"o}rn Nystedt and Teun Boekhout and Dawson, {Thomas L., Jr.} and Janne Lehti{\"o}",

year = "2017",

month = jan,

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doi = "10.1093/nar/gkx006",

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Zhu, Y, G. Engström, P, Tellgren-Roth, C, Baudo, C, Kennell, J, Sun, S, Billmyre, BR, Schröder, MS, Andersson, A, Holm, T, Sigurgeirsson, B, Wu, G, Sankaranarayanan, S, Siddharthan, R, Sanyal, K, Lundeberg, J, Nystedt, B, Boekhout, T, Dawson, TLJ & Lehtiö, J 2017, 'Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis', Nucleic Acids Research, vol. 45, pp. gkx006. https://doi.org/10.1093/nar/gkx006

TY - JOUR

T1 - Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis

AU - Zhu, Yafeng

AU - G. Engström, Pär

AU - Tellgren-Roth, Christian

AU - Baudo, Charles

AU - Kennell, Jack

AU - Sun, Sheng

AU - Billmyre, Blake Robert

AU - Schröder, Markus S

AU - Andersson, Anna

AU - Holm, Tina

AU - Sigurgeirsson, Benjamin

AU - Wu, Guangxi

AU - Sankaranarayanan, Sundar

AU - Siddharthan, Rahul

AU - Sanyal, Kaustuv

AU - Lundeberg, Joakim

AU - Nystedt, Björn

AU - Boekhout, Teun

AU - Dawson, Thomas L., Jr.

AU - Lehtiö, Janne

PY - 2017/1/1

Y1 - 2017/1/1

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkx006

DO - 10.1093/nar/gkx006

M3 - Article

SN - 0305-1048

VL - 45

SP - gkx006

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

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

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