Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

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Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

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dc.contributor.author Ma, Li-Jun
dc.contributor.author Ibrahim, Ashraf S.
dc.contributor.author Skory, Christopher
dc.contributor.author Grabherr, Manfred G.
dc.contributor.author Burger, Gertraud
dc.contributor.author Butler, Margi
dc.contributor.author Elias, Marek
dc.contributor.author Idnurm, Alexander
dc.contributor.author Lang, B. Franz
dc.contributor.author Sone, Teruo
dc.contributor.author Abe, Ayumi
dc.contributor.author Corrochano, Luis M.
dc.contributor.author Fu, Jianmin
dc.contributor.author Hansberg, Wilhelm
dc.contributor.author Kim, Jung-Mi
dc.contributor.author Kodira, Chinnappa D.
dc.contributor.author Koehrsen, Michael J.
dc.contributor.author Miranda-Saavedra, Diego
dc.contributor.author O'Leary, Sinead
dc.contributor.author Ortiz-Castellanos, Lucila
dc.contributor.author Poulter, Russell
dc.contributor.author Rodriguez-Romero, Julio
dc.contributor.author Ruiz-Herrera, José
dc.contributor.author Shen, Yao-Qing
dc.contributor.author Zeng, Qiandong
dc.contributor.author Birren, Bruce W.
dc.contributor.author Cuomo, Christina A.
dc.contributor.author Wickes, Brian L.
dc.contributor.author Calvo, Sarah E
dc.contributor.author Engels, Reinhard
dc.contributor.author Galagan, James E
dc.contributor.author Liu, Bo
dc.date.accessioned 2012-02-09T20:36:50Z
dc.date.issued 2009
dc.identifier.citation Ma, Li-Jun, Ashraf S. Ibrahim, Christopher Skory, Manfred G. Grabherr, Gertraud Burger, Margi Butler, Marek Elias, et al. 2009. Genomic analysis of the basal lineage fungus rhizopus oryzae reveals a whole-genome duplication. PLoS Genetics 5(7): e1000549. en_US
dc.identifier.issn 1553-7390 en_US
dc.identifier.uri http://nrs.harvard.edu/urn-3:HUL.InstRepos:8148898
dc.description.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 14α-demethylase (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. en_US
dc.language.iso en_US en_US
dc.publisher Public Library of Science en_US
dc.relation.isversionof doi:10.1371/journal.pgen.1000549 en_US
dc.relation.hasversion http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699053/pdf/ en_US
dash.license LAA
dc.subject comparative sequence analysis en_US
dc.subject genomics en_US
dc.subject microbial evolution and genomics en_US
dc.subject fungal infections en_US
dc.subject medical microbiology en_US
dc.title Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication en_US
dc.type Journal Article en_US
dc.description.version Version of Record en_US
dc.relation.journal PLoS Genetics en_US
dash.depositing.author Calvo, Sarah E
dc.date.available 2012-02-09T20:36:50Z
dash.affiliation.other HMS^Neurology-Massachusetts General Hospital en_US
dash.affiliation.other SPH^Immunology and Infectious Diseases TPH en_US

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