title: Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina).
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 comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.
authors.affiliation: University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany.
authors.forename: Volker U
authors.initials: VU
authors.lastname: Schwartze
authors.affiliation: University of Jena, Department of Bioinformatics, Jena, Germany.
authors.forename: Sascha
authors.initials: S
authors.lastname: Winter
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Systems Biology/Bioinformatics, Jena, Germany.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Shelest
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Marcet-Houben
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Systems Biology/Bioinformatics, Jena, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Horn
authors.affiliation: University of Jena, Department of Bioinformatics, Jena, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wehner
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Systems Biology/Bioinformatics, Jena, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Linde
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany.
authors.forename: Vito
authors.initials: V
authors.lastname: Valiante
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG), Functional Bioinformatics, Barcelona, Spain; Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil.
authors.forename: Michael
authors.initials: M
authors.lastname: Sammeth
authors.affiliation: University of Jena, Department of Bioinformatics, Jena, Germany.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Riege
authors.affiliation: Ruhr University Bochum, Department of General and Molecular Botany, Bochum, Germany.
authors.forename: Minou
authors.initials: M
authors.lastname: Nowrousian
authors.affiliation: University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Kaerger
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Department of Microbial Immunology, Jena, Germany.
authors.forename: Ilse D
authors.initials: ID
authors.lastname: Jacobsen
authors.affiliation: University of Jena, Department of Bioinformatics, Jena, Germany.
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.affiliation: University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany.
authors.forename: Axel A
authors.initials: AA
authors.lastname: Brakhage
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: University of Jena, Department of Bioinformatics, Jena, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Böcker
authors.affiliation: University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Voigt
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D016681:Genome, Fungal; D023281:Genomics; D006801:Humans; D009090:Mucorales / Q000235:genetics* / Q000472:pathogenicity; D009091:Mucormycosis / Q000235:genetics* / Q000382:microbiology; D037521:Virulence Factors / Q000235:genetics / Q000302:isolation & purification
chemical_list: D037521:Virulence Factors