Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication

Li Jun Ma, Ashraf S. Ibrahim, Christopher Skory, Manfred G. Grabherr, Gertraud Burger, Margi Butler, Marek Elias, Alexander Idnurm, B. Franz Lang, Teruo Sone, Ayumi Abe, Sarah E. Calvo, Luis M. Corrochano, Reinhard Engels, Jianmin Fu, Wilhelm Hansberg, Jung Mi Kim, Chinnappa D. Kodira, Michael J. Koehrsen, Bo LiuDiego Miranda-Saavedra, Sinead O'Leary, Lucila Ortiz-Castellanos, Russell Poulter, Julio Rodriguez-Romero, José Ruiz-Herrera, Yao Qing Shen, Qiandong Zeng, James Galagan, Bruce W. Birren, Christina A. Cuomo, Brian L Wickes

Research output: Contribution to journalArticle

207 Citations (Scopus)

Abstract

Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called "zygomycetes," R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99-880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs), comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin-proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14ademethylase (ERG11), could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments.

Original languageEnglish (US)
Article numbere1000549
JournalPLoS Genetics
Volume5
Issue number7
DOIs
StatePublished - Jul 2009

Fingerprint

Rhizopus oryzae
Rhizopus
genomics
Fungi
genome
fungus
Genome
fungi
azoles
gene
Mucormycosis
Azoles
DNA Transposable Elements
transposons
genes
protein
lanosterol
Respiratory Transport
genome assembly
aspartic proteinases

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. / Ma, Li Jun; Ibrahim, Ashraf S.; Skory, Christopher; Grabherr, Manfred G.; Burger, Gertraud; Butler, Margi; Elias, Marek; Idnurm, Alexander; Lang, B. Franz; Sone, Teruo; Abe, Ayumi; Calvo, Sarah E.; Corrochano, Luis M.; Engels, Reinhard; Fu, Jianmin; Hansberg, Wilhelm; Kim, Jung Mi; Kodira, Chinnappa D.; Koehrsen, Michael J.; Liu, Bo; Miranda-Saavedra, Diego; O'Leary, Sinead; Ortiz-Castellanos, Lucila; Poulter, Russell; Rodriguez-Romero, Julio; Ruiz-Herrera, José; Shen, Yao Qing; Zeng, Qiandong; Galagan, James; Birren, Bruce W.; Cuomo, Christina A.; Wickes, Brian L.

In: PLoS Genetics, Vol. 5, No. 7, e1000549, 07.2009.

Research output: Contribution to journalArticle

Ma, LJ, Ibrahim, AS, Skory, C, Grabherr, MG, Burger, G, Butler, M, Elias, M, Idnurm, A, Lang, BF, Sone, T, Abe, A, Calvo, SE, Corrochano, LM, Engels, R, Fu, J, Hansberg, W, Kim, JM, Kodira, CD, Koehrsen, MJ, Liu, B, Miranda-Saavedra, D, O'Leary, S, Ortiz-Castellanos, L, Poulter, R, Rodriguez-Romero, J, Ruiz-Herrera, J, Shen, YQ, Zeng, Q, Galagan, J, Birren, BW, Cuomo, CA & Wickes, BL 2009, 'Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication', PLoS Genetics, vol. 5, no. 7, e1000549. https://doi.org/10.1371/journal.pgen.1000549
Ma, Li Jun ; Ibrahim, Ashraf S. ; Skory, Christopher ; Grabherr, Manfred G. ; Burger, Gertraud ; Butler, Margi ; Elias, Marek ; Idnurm, Alexander ; Lang, B. Franz ; Sone, Teruo ; Abe, Ayumi ; Calvo, Sarah E. ; Corrochano, Luis M. ; Engels, Reinhard ; Fu, Jianmin ; Hansberg, Wilhelm ; Kim, Jung Mi ; Kodira, Chinnappa D. ; Koehrsen, Michael J. ; Liu, Bo ; Miranda-Saavedra, Diego ; O'Leary, Sinead ; Ortiz-Castellanos, Lucila ; Poulter, Russell ; Rodriguez-Romero, Julio ; Ruiz-Herrera, José ; Shen, Yao Qing ; Zeng, Qiandong ; Galagan, James ; Birren, Bruce W. ; Cuomo, Christina A. ; Wickes, Brian L. / Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. In: PLoS Genetics. 2009 ; Vol. 5, No. 7.
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AU - Butler, Margi

AU - Elias, Marek

AU - Idnurm, Alexander

AU - Lang, B. Franz

AU - Sone, Teruo

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AU - Corrochano, Luis M.

AU - Engels, Reinhard

AU - Fu, Jianmin

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AU - Kodira, Chinnappa D.

AU - Koehrsen, Michael J.

AU - Liu, Bo

AU - Miranda-Saavedra, Diego

AU - O'Leary, Sinead

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AU - Poulter, Russell

AU - Rodriguez-Romero, Julio

AU - Ruiz-Herrera, José

AU - Shen, Yao Qing

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