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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{"title"=>"Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)", "type"=>"journal", "authors"=>[{"first_name"=>"Volker U.", "last_name"=>"Schwartze", "scopus_author_id"=>"54918713500"}, {"first_name"=>"Sascha", "last_name"=>"Winter", "scopus_author_id"=>"56957734500"}, {"first_name"=>"Ekaterina", "last_name"=>"Shelest", "scopus_author_id"=>"8311052900"}, {"first_name"=>"Marina", "last_name"=>"Marcet-Houben", "scopus_author_id"=>"27267797400"}, {"first_name"=>"Fabian", "last_name"=>"Horn", "scopus_author_id"=>"54388997000"}, {"first_name"=>"Stefanie", "last_name"=>"Wehner", "scopus_author_id"=>"55785547700"}, {"first_name"=>"Jörg", "last_name"=>"Linde", "scopus_author_id"=>"36637920900"}, {"first_name"=>"Vito", "last_name"=>"Valiante", "scopus_author_id"=>"23993378700"}, {"first_name"=>"Michael", "last_name"=>"Sammeth", "scopus_author_id"=>"57193078807"}, {"first_name"=>"Konstantin", "last_name"=>"Riege", "scopus_author_id"=>"56079647900"}, {"first_name"=>"Minou", "last_name"=>"Nowrousian", "scopus_author_id"=>"7004508910"}, {"first_name"=>"Kerstin", "last_name"=>"Kaerger", "scopus_author_id"=>"55937737500"}, {"first_name"=>"Ilse D.", "last_name"=>"Jacobsen", "scopus_author_id"=>"8676553500"}, {"first_name"=>"Manja", "last_name"=>"Marz", "scopus_author_id"=>"23134902300"}, {"first_name"=>"Axel A.", "last_name"=>"Brakhage", "scopus_author_id"=>"7003471386"}, {"first_name"=>"Toni", "last_name"=>"Gabaldón", "scopus_author_id"=>"35229109400"}, {"first_name"=>"Sebastian", "last_name"=>"Böcker", "scopus_author_id"=>"6603367089"}, {"first_name"=>"Kerstin", "last_name"=>"Voigt", "scopus_author_id"=>"7202591013"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "scopus"=>"2-s2.0-84929144085", "sgr"=>"84929144085", "pui"=>"607916869", "doi"=>"10.1371/journal.pgen.1004496", "pmid"=>"25121733", "issn"=>"15537404"}, "id"=>"973d0546-68b7-3df7-abc6-33e2662f0fbe", "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.", "link"=>"http://www.mendeley.com/research/gene-expansion-shapes-genome-architecture-human-pathogen-lichtheimia-corymbifera-evolutionary-genomi", "reader_count"=>48, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>12, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>12, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>25, "Medicine and Dentistry"=>4, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>25}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Taiwan"=>1, "United Kingdom"=>1, "Australia"=>1, "India"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1636567"], "description"=>"<p>For each species the thin red bar represents the proportion of proteins that have a homolog in <i>L. corymbifera</i> (upper axis). The coloured bars represent the number of proteins found in different ranges of species (lower axis): black: wide-spread proteins found in at least 23 of the 25 species, light blue: proteins found exclusively in all four Mucorales species, darker blue: proteins found only in Mucorales species, red: proteins found in early diverging fungi, yellow: proteins found in fungi, purple: proteins found in fungi and at least one of the outgroups, grey: species-specific proteins without orthologs in other species but with paralogs within the genome, white: proteins with no homologs. All nodes in the tree have a bootstrap support of 100.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139726, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_tree_including_the_25_species_used_during_phylome_reconstruction_/1139726", "title"=>"Species tree including the 25 species used during phylome reconstruction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636568"], "description"=>"<p>(A) Venn diagram of shared gene families between <i>L. corymbifera</i> and other mucoralean fungi based on GhostFam gene families. Numbers indicate percentage of <i>L. corymbifera</i> gene families. (B) Number and size of conserved clusters of <i>L. corymbifera</i> with other mucoralean genomes. (C) Proportions of conserved clusters of <i>L. corymbifera</i> shared with different mucoralean genomes. Occurrences in more than one of the genomes are indicated by a slash between the species.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139727, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conserved_regions_of_the_L_corymbifera_genome_with_other_mucoralean_genomes_/1139727", "title"=>"Conserved regions of the <i>L. corymbifera</i> genome with other mucoralean genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636569"], "description"=>"<p>The genome of <i>A. fumigatus</i> serves as measure for low incidences of singular and segmental gene duplications <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004496#pgen.1004496-Nierman1\" target=\"_blank\">[115]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004496#pgen.1004496-Galagan1\" target=\"_blank\">[116]</a>. (A) Comparison of gene families between <i>L. corymbifera</i>, <i>R. oryzae</i> and non-mucoralean fungi. Gene families are based on GhostFam homology families. Values for <i>L. corymbifera</i> and <i>R. oryzae</i> are excluded from the “mean fungi” value. (B) Regions with a minimum of 3 genes were tested for multiple occurrences within the genomes by GECKO2.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139728, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_duplication_and_duplication_of_genomic_regions_within_mucoralean_genomes_in_comparison_to_the_genome_of_A_fumigatus_which_i_inhabits_the_same_natural_habitats_and_ii_causes_similar_symptomatology_in_human_like_L_corymbifera_and_iii_serves_as_model_o/1139728", "title"=>"Gene duplication and duplication of genomic regions within mucoralean genomes in comparison to the genome of <i>A. fumigatus</i>, which (i) inhabits the same natural habitats and (ii) causes similar symptomatology in human like <i>L. corymbifera</i> and (iii) serves as model organism for causative agents of invasive mycoses [56], [75].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636570"], "description"=>"<p>(A) Tree representing an expansion of HET proteins in <i>L. corymbifera</i>. Branches enclosed in the grey shaded area represent paralogs of <i>L. corymbifera</i>. The black square represents the point where the expansion started. (B) Number and size of gene expansions in the <i>L. corymbifera</i> genome. (C) Main functional domains of gene expansions based on PFAM annotation. The numbers of genes with the different functional domains were combined if a domain was present in more than one expansion. (D) Proportion of genes within gene expansions which are arranged in tandem duplications. Each bar represents an expansion with the red part as the percentage of tandem duplicated genes (left). Clustering of tandem duplicated genes of cytochrome P450 genes in <i>L. corymbifera</i> (based on reconstruction with RaxML <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004496#pgen.1004496-Stamatakis1\" target=\"_blank\">[130]</a>). Red branches represent tandem duplicated genes. Numbers at the branch tips indicate different tandems.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139729, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expansions_and_tandem_duplications_found_in_L_corymbifera_/1139729", "title"=>"Gene expansions and tandem duplications found in <i>L. corymbifera</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636571"], "description"=>"<p>(A) Expression levels of FTR1 domain genes and their corresponding multicopper oxidases under standard conditions and iron limitation. (B) Heat map showing the regulation of iron uptake genes under iron-limited conditions.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139730, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_iron_uptake_genes_under_iron_limited_conditions_/1139730", "title"=>"Expression of iron uptake genes under iron limited conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636572"], "description"=>"<p>Iron uptake genes in the <i>L. corymbifera</i> genome.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139731, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Iron_uptake_genes_in_the_L_corymbifera_genome_/1139731", "title"=>"Iron uptake genes in the <i>L. corymbifera</i> genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636573"], "description"=>"<p>Protease families in the <i>L. corymbifera</i> genome.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139732, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protease_families_in_the_L_corymbifera_genome_/1139732", "title"=>"Protease families in the <i>L. corymbifera</i> genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636574"], "description"=>"<p>Statistics of the <i>L. corymbifera</i> genome.</p>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139733, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistics_of_the_L_corymbifera_genome_/1139733", "title"=>"Statistics of the <i>L. corymbifera</i> genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-14 11:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1636575", "https://ndownloader.figshare.com/files/1636576", "https://ndownloader.figshare.com/files/1636577", "https://ndownloader.figshare.com/files/1636578", "https://ndownloader.figshare.com/files/1636579", "https://ndownloader.figshare.com/files/1636580", "https://ndownloader.figshare.com/files/1636581", "https://ndownloader.figshare.com/files/1636582", "https://ndownloader.figshare.com/files/1636583", "https://ndownloader.figshare.com/files/1636584", "https://ndownloader.figshare.com/files/1636585", "https://ndownloader.figshare.com/files/1636586", "https://ndownloader.figshare.com/files/1636587", "https://ndownloader.figshare.com/files/1636588", "https://ndownloader.figshare.com/files/1636589", "https://ndownloader.figshare.com/files/1636590"], "description"=>"<div><p><i>Lichtheimia</i> 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 <i>L. corymbifera</i> and compared it to the genome of <i>Rhizopus oryzae</i>, 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 <i>L. corymbifera</i> genome to <i>R. oryzae</i>: (i) the presence of an highly elevated number of gene duplications which are unlike <i>R. oryzae</i> 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) <i>L. corymbifera</i> 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 <i>L. corymbifera</i>, (ii) Over 25% of the proteins are apparently specific for <i>L. corymbifera</i>. (iii) <i>L. corymbifera</i> contains only 2/3 of the proteases (known to be essential virulence factors) in comparision to <i>R. oryzae</i>. On the other hand, the number of secreted proteases, however, is roughly twice as high as in <i>R. oryzae</i>.</p></div>", "links"=>[], "tags"=>["Human Pathogen Lichtheimia corymbifera", "calcineurin pathway", "genome sequence", "11 copies", "siderophore metabolism", "Virulence factors", "transcription factors LCor 08192.1", "corymbifera genome", "Novel virulence factors", "wgd", "iron limitation", "Evolutionary Genomics Analysis", "Rhizopus oryzae", "GATA type regulators", "Genome assembly", "basal Mucorales", "genome duplication", "33.6 MB", "Ancient Terrestrial Mucorales", "CRZ", "LCor 01340.1 encoding", "Lichtheimia species", "siderophore transporter", "gene Expansion Shapes Genome Architecture", "gene duplications", "as", "Genes encoding", "LCor 00410.1"], "article_id"=>1139734, "categories"=>["Biological Sciences"], "users"=>["Volker U. Schwartze", "Sascha Winter", "Ekaterina Shelest", "Marina Marcet-Houben", "Fabian Horn", "Stefanie Wehner", "Jörg Linde", "Vito Valiante", "Michael Sammeth", "Konstantin Riege", "Minou Nowrousian", "Kerstin Kaerger", "Ilse D. Jacobsen", "Manja Marz", "Axel A. Brakhage", "Toni Gabaldón", "Sebastian Böcker", "Kerstin Voigt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004496.s001", "https://dx.doi.org/10.1371/journal.pgen.1004496.s002", "https://dx.doi.org/10.1371/journal.pgen.1004496.s003", "https://dx.doi.org/10.1371/journal.pgen.1004496.s004", "https://dx.doi.org/10.1371/journal.pgen.1004496.s005", "https://dx.doi.org/10.1371/journal.pgen.1004496.s006", "https://dx.doi.org/10.1371/journal.pgen.1004496.s007", "https://dx.doi.org/10.1371/journal.pgen.1004496.s008", "https://dx.doi.org/10.1371/journal.pgen.1004496.s009", "https://dx.doi.org/10.1371/journal.pgen.1004496.s010", "https://dx.doi.org/10.1371/journal.pgen.1004496.s011", "https://dx.doi.org/10.1371/journal.pgen.1004496.s012", "https://dx.doi.org/10.1371/journal.pgen.1004496.s013", "https://dx.doi.org/10.1371/journal.pgen.1004496.s014", "https://dx.doi.org/10.1371/journal.pgen.1004496.s015", "https://dx.doi.org/10.1371/journal.pgen.1004496.s016"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Gene_Expansion_Shapes_Genome_Architecture_in_the_Human_Pathogen_Lichtheimia_corymbifera_An_Evolutionary_Genomics_Analysis_in_the_Ancient_Terrestrial_Mucorales_Mucoromycotina_/1139734", "title"=>"Gene Expansion Shapes Genome Architecture in the Human Pathogen <i>Lichtheimia corymbifera</i>: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-08-14 11:07:14"}

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