Gene expansion shapes genome architecture in the human pathogen lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)

Schwartze, Volker U.; Winter, Sascha; Shelest, Ekaterina; Marcet Houben, Marina; Horn, Fabian; Wehner, Stefanie; Linde, Jörg; Valiante, Vito; Sammeth, Michael; Riege, Konstantin; Nowrousian, Minou; Kaerger, Kerstin; Jacobsen, Ilse D.; Marz, Manja; Brakhage, Axel A.; Gabaldón Estevan, Juan Antonio, 1973-; Böcker, Sebastian; Voigt, Kerstin

Gene expansion shapes genome architecture in the human pathogen lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)

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dc.contributor.author Schwartze, Volker U.
dc.contributor.author Winter, Sascha
dc.contributor.author Shelest, Ekaterina
dc.contributor.author Marcet Houben, Marina
dc.contributor.author Horn, Fabian
dc.contributor.author Wehner, Stefanie
dc.contributor.author Linde, Jörg
dc.contributor.author Valiante, Vito
dc.contributor.author Sammeth, Michael
dc.contributor.author Riege, Konstantin
dc.contributor.author Nowrousian, Minou
dc.contributor.author Kaerger, Kerstin
dc.contributor.author Jacobsen, Ilse D.
dc.contributor.author Marz, Manja
dc.contributor.author Brakhage, Axel A.
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
dc.contributor.author Böcker, Sebastian
dc.contributor.author Voigt, Kerstin
dc.date.accessioned 2025-01-14T08:12:37Z
dc.date.available 2025-01-14T08:12:37Z
dc.date.issued 2014
dc.description.abstract Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1–4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparision to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.en
dc.description.sponsorship TG group is funded in part by a grant from the Spanish Ministry of Science and Innovation (BFU2009-09168). MM group was in part supported by the German Science Foundation (DFG) MA5082/1-1 (KR). MN would like to thank Ulrich Kück for generous support, and the DFG for funding (project NO407/4-1). SB group was in part supported by DFG BO 1910/8-1 (SWi). KV and AAB acknowledge financial support of the Leibniz Institute of Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.format.mimetype application/pdf
dc.identifier.citation Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, et al. Gene expansion shapes genome architecture in the human pathogen lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PLoS Genet. 2014 Aug 14;10(8):e1004496. DOI: 10.1371/journal.pgen.1004496
dc.identifier.doi http://dx.doi.org/10.1371/journal.pgen.1004496
dc.identifier.issn 1553-7390
dc.identifier.uri http://hdl.handle.net/10230/69094
dc.language.iso eng
dc.publisher Public Library of Science (PLoS)
dc.relation.ispartof PLOS Genetics . 2014 Aug 14;10(8):e1004496
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-09168
dc.rights © 2014 Schwartze et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Fongs -- Expressió gènicaca
dc.subject.other Fongs -- Genèticaca
dc.subject.other Enzims proteolítics -- Inhibidorsca
dc.title Gene expansion shapes genome architecture in the human pathogen lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina)
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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