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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Draft Genome Sequence of the Pathogenic Fungus <italic>Scedosporium apiospermum</italic></title><author><name sortKey="Vandeputte, Patrick" sort="Vandeputte, Patrick" uniqKey="Vandeputte P" first="Patrick" last="Vandeputte">Patrick Vandeputte</name></author><author><name sortKey="Ghamrawi, Sarah" sort="Ghamrawi, Sarah" uniqKey="Ghamrawi S" first="Sarah" last="Ghamrawi">Sarah Ghamrawi</name><affiliation><nlm:aff id="aff1">L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène, Angers, France</nlm:aff></affiliation></author><author><name sortKey="Rechenmann, Mathias" sort="Rechenmann, Mathias" uniqKey="Rechenmann M" first="Mathias" last="Rechenmann">Mathias Rechenmann</name><affiliation><nlm:aff id="aff3">Genostar, Montbonnot, France</nlm:aff></affiliation></author><author><name sortKey="Iltis, Agnes" sort="Iltis, Agnes" uniqKey="Iltis A" first="Agnès" last="Iltis">Agnès Iltis</name><affiliation><nlm:aff id="aff3">Genostar, Montbonnot, France</nlm:aff></affiliation></author><author><name sortKey="Giraud, Sandrine" sort="Giraud, Sandrine" uniqKey="Giraud S" first="Sandrine" last="Giraud">Sandrine Giraud</name><affiliation><nlm:aff id="aff1">L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène, Angers, France</nlm:aff></affiliation></author><author><name sortKey="Fleury, Maxime" sort="Fleury, Maxime" uniqKey="Fleury M" first="Maxime" last="Fleury">Maxime Fleury</name><affiliation><nlm:aff id="aff1">L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène, Angers, France</nlm:aff></affiliation></author><author><name sortKey="Thornton, Christopher" sort="Thornton, Christopher" uniqKey="Thornton C" first="Christopher" last="Thornton">Christopher Thornton</name><affiliation><nlm:aff id="aff4">Hybridoma, Exeter, United Kingdom</nlm:aff></affiliation></author><author><name sortKey="Delhaes, Laurence" sort="Delhaes, Laurence" uniqKey="Delhaes L" first="Laurence" last="Delhaès">Laurence Delhaès</name><affiliation><nlm:aff id="aff5">Université de Lille II, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France</nlm:aff></affiliation></author><author><name sortKey="Meyer, Wieland" sort="Meyer, Wieland" uniqKey="Meyer W" first="Wieland" last="Meyer">Wieland Meyer</name><affiliation><nlm:aff id="aff6">Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Millenium Institute for Medical Research, Westmead, New South Wales, Australia</nlm:aff></affiliation></author><author><name sortKey="Papon, Nicolas" sort="Papon, Nicolas" uniqKey="Papon N" first="Nicolas" last="Papon">Nicolas Papon</name><affiliation><nlm:aff id="aff7">Université de Tours, Biomolécules et Biotechnologie Végétales, Faculté de Pharmacie, Tours, France</nlm:aff></affiliation></author><author><name sortKey="Bouchara, Jean Philippe" sort="Bouchara, Jean Philippe" uniqKey="Bouchara J" first="Jean-Philippe" last="Bouchara">Jean-Philippe Bouchara</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25278533</idno><idno type="pmc">4183877</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183877</idno><idno type="RBID">PMC:4183877</idno><idno type="doi">10.1128/genomeA.00988-14</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001249</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001249</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Draft Genome Sequence of the Pathogenic Fungus <italic>Scedosporium apiospermum</italic></title><author><name sortKey="Vandeputte, Patrick" sort="Vandeputte, Patrick" uniqKey="Vandeputte P" first="Patrick" last="Vandeputte">Patrick Vandeputte</name></author><author><name sortKey="Ghamrawi, Sarah" sort="Ghamrawi, Sarah" uniqKey="Ghamrawi S" first="Sarah" last="Ghamrawi">Sarah Ghamrawi</name><affiliation><nlm:aff id="aff1">L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène, Angers, France</nlm:aff></affiliation></author><author><name sortKey="Rechenmann, Mathias" sort="Rechenmann, Mathias" uniqKey="Rechenmann M" first="Mathias" last="Rechenmann">Mathias Rechenmann</name><affiliation><nlm:aff id="aff3">Genostar, Montbonnot, France</nlm:aff></affiliation></author><author><name sortKey="Iltis, Agnes" sort="Iltis, Agnes" uniqKey="Iltis A" first="Agnès" last="Iltis">Agnès Iltis</name><affiliation><nlm:aff id="aff3">Genostar, Montbonnot, France</nlm:aff></affiliation></author><author><name sortKey="Giraud, Sandrine" sort="Giraud, Sandrine" uniqKey="Giraud S" first="Sandrine" last="Giraud">Sandrine Giraud</name><affiliation><nlm:aff id="aff1">L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène, Angers, France</nlm:aff></affiliation></author><author><name sortKey="Fleury, Maxime" sort="Fleury, Maxime" uniqKey="Fleury M" first="Maxime" last="Fleury">Maxime Fleury</name><affiliation><nlm:aff id="aff1">L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène, Angers, France</nlm:aff></affiliation></author><author><name sortKey="Thornton, Christopher" sort="Thornton, Christopher" uniqKey="Thornton C" first="Christopher" last="Thornton">Christopher Thornton</name><affiliation><nlm:aff id="aff4">Hybridoma, Exeter, United Kingdom</nlm:aff></affiliation></author><author><name sortKey="Delhaes, Laurence" sort="Delhaes, Laurence" uniqKey="Delhaes L" first="Laurence" last="Delhaès">Laurence Delhaès</name><affiliation><nlm:aff id="aff5">Université de Lille II, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France</nlm:aff></affiliation></author><author><name sortKey="Meyer, Wieland" sort="Meyer, Wieland" uniqKey="Meyer W" first="Wieland" last="Meyer">Wieland Meyer</name><affiliation><nlm:aff id="aff6">Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Millenium Institute for Medical Research, Westmead, New South Wales, Australia</nlm:aff></affiliation></author><author><name sortKey="Papon, Nicolas" sort="Papon, Nicolas" uniqKey="Papon N" first="Nicolas" last="Papon">Nicolas Papon</name><affiliation><nlm:aff id="aff7">Université de Tours, Biomolécules et Biotechnologie Végétales, Faculté de Pharmacie, Tours, France</nlm:aff></affiliation></author><author><name sortKey="Bouchara, Jean Philippe" sort="Bouchara, Jean Philippe" uniqKey="Bouchara J" first="Jean-Philippe" last="Bouchara">Jean-Philippe Bouchara</name></author></analytic><series><title level="j">Genome Announcements</title><idno type="eISSN">2169-8287</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The first genome of one species of the <italic>Scedosporium apiospermum</italic> complex, responsible for localized to severe disseminated infections according to the immune status of the host, will contribute to a better understanding of the pathogenicity of these fungi and also to the discovery of the mechanisms underlying their low susceptibility to current antifungals.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Guarro, J" uniqKey="Guarro J">J Guarro</name></author><author><name sortKey="Kantarcioglu, As" uniqKey="Kantarcioglu A">AS Kantarcioglu</name></author><author><name sortKey="Horre, R" uniqKey="Horre R">R Horré</name></author><author><name sortKey="Rodriguez Tudela, Jl" uniqKey="Rodriguez Tudela J">JL Rodriguez-Tudela</name></author><author><name sortKey="Cuenca Estrella, M" uniqKey="Cuenca Estrella M">M Cuenca Estrella</name></author><author><name sortKey="Berenguer, J" uniqKey="Berenguer J">J Berenguer</name></author><author><name sortKey="De Hoog, Gs" uniqKey="De Hoog G">GS de Hoog</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chaisson, Mj" uniqKey="Chaisson M">MJ Chaisson</name></author><author><name sortKey="Tesler, G" uniqKey="Tesler G">G Tesler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boetzer, M" uniqKey="Boetzer M">M Boetzer</name></author><author><name sortKey="Henkel, Cv" uniqKey="Henkel C">CV Henkel</name></author><author><name sortKey="Jansen, Hj" uniqKey="Jansen H">HJ Jansen</name></author><author><name sortKey="Butler, D" uniqKey="Butler D">D Butler</name></author><author><name sortKey="Pirovano, W" uniqKey="Pirovano W">W Pirovano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boetzer, M" uniqKey="Boetzer M">M Boetzer</name></author><author><name sortKey="Pirovano, W" uniqKey="Pirovano W">W Pirovano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stanke, M" uniqKey="Stanke M">M Stanke</name></author><author><name sortKey="Steinkamp, R" uniqKey="Steinkamp R">R Steinkamp</name></author><author><name sortKey="Waack, S" uniqKey="Waack S">S Waack</name></author><author><name sortKey="Morgenstern, B" uniqKey="Morgenstern B">B Morgenstern</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Announc</journal-id><journal-id journal-id-type="iso-abbrev">Genome Announc</journal-id><journal-id journal-id-type="hwp">ga</journal-id><journal-id journal-id-type="pmc">ga</journal-id><journal-id journal-id-type="publisher-id">GA</journal-id><journal-title-group><journal-title>Genome Announcements</journal-title></journal-title-group><issn pub-type="epub">2169-8287</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25278533</article-id><article-id pub-id-type="pmc">4183877</article-id><article-id pub-id-type="publisher-id">genomeA00988-14</article-id><article-id pub-id-type="doi">10.1128/genomeA.00988-14</article-id><article-categories><subj-group subj-group-type="heading"><subject>Eukaryotes</subject></subj-group></article-categories><title-group><article-title>Draft Genome Sequence of the Pathogenic Fungus <italic>Scedosporium apiospermum</italic></article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Vandeputte</surname><given-names>Patrick</given-names></name><xref ref-type="aff" rid="aff1 aff2"><sup>a,b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ghamrawi</surname><given-names>Sarah</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rechenmann</surname><given-names>Mathias</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Iltis</surname><given-names>Agnès</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Giraud</surname><given-names>Sandrine</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fleury</surname><given-names>Maxime</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Thornton</surname><given-names>Christopher</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Delhaès</surname><given-names>Laurence</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Meyer</surname><given-names>Wieland</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author"><name><surname>Papon</surname><given-names>Nicolas</given-names></name><xref ref-type="aff" rid="aff7"><sup>g</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bouchara</surname><given-names>Jean-Philippe</given-names></name><xref ref-type="aff" rid="aff1 aff2"><sup>a,b</sup></xref></contrib><aff id="aff1"><label>a</label>L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène, Angers, France</aff><aff id="aff2"><label>b</label>Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire, Angers, France</aff><aff id="aff3"><label>c</label>Genostar, Montbonnot, France</aff><aff id="aff4"><label>d</label>Hybridoma, Exeter, United Kingdom</aff><aff id="aff5"><label>e</label>Université de Lille II, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France</aff><aff id="aff6"><label>f</label>Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School, Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Millenium Institute for Medical Research, Westmead, New South Wales, Australia</aff><aff id="aff7"><label>g</label>Université de Tours, Biomolécules et Biotechnologie Végétales, Faculté de Pharmacie, Tours, France</aff></contrib-group><author-notes><corresp id="cor1">Address correspondence to Patrick Vandeputte, <email>pvandepu@gmail.com</email>.</corresp></author-notes><pub-date pub-type="epub"><day>2</day><month>10</month><year>2014</year></pub-date><pub-date pub-type="collection"><season>Sep-Oct</season><year>2014</year></pub-date><volume>2</volume><issue>5</issue><elocation-id>e00988-14</elocation-id><history><date date-type="received"><day>25</day><month>8</month><year>2014</year></date><date date-type="accepted"><day>26</day><month>8</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Vandeputte et al.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Vandeputte et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported license</ext-link>.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="jga005141674001.pdf"></self-uri><abstract><p>The first genome of one species of the <italic>Scedosporium apiospermum</italic> complex, responsible for localized to severe disseminated infections according to the immune status of the host, will contribute to a better understanding of the pathogenicity of these fungi and also to the discovery of the mechanisms underlying their low susceptibility to current antifungals.</p></abstract><counts><page-count count="2"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>September/October 2014</meta-value></custom-meta><custom-meta><meta-name>access-type</meta-name><meta-value>free</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec><title>GENOME ANNOUNCEMENT</title><p><italic>Scedosporium apiospermum</italic> is a soil-borne opportunistic pathogen responsible for cutaneous or subcutaneous mycetomas following traumatic inoculation of fungal elements and for respiratory tract infections. Moreover, it becomes a redoubtable pathogen in immunocompromised patients, where it may cause disseminated infections in the skin, eye, bones, joints, and deep organs, such as the heart and central nervous system (<xref rid="B1" ref-type="bibr">1</xref>). Species of the <italic>Scedosporium apiospermum</italic> complex are the second most frequent molds, after <italic>Aspergillus fumigatus</italic>, and colonize the respiratory tract of cystic fibrosis patients, causing in this clinical context respiratory infections such as bronchitis and allergic broncho-pulmonary mycoses, or disseminated life-threatening infections in cases of immunodeficiency such as corticosteroid-induced diabetes or after lung transplantation. Here we report the sequencing and annotation of the genome of one of the major species within this closely related species complex.</p><p>The genome sequence of <italic>Scedosporium apisopermum</italic> strain IHEM 14462, isolated in 1998 from a sputum sample from a cystic fibrosis patient in Tours, France, was resolved by two distinct high-throughput Illumina sequencing technologies on an HiSeq2000: a paired-end run, sequencing on average 50 bp at each extremity of approximately 120.3 million 250-bp inserts, and a mate-pairs run, sequencing on average 50 bp at each extremity of approximately 82.2 million 4-kb inserts. <italic>De novo</italic> assembly was achieved by an additional single-molecule real-time sequencing on a PacBio RSII instrument (Pacific Biosciences), thus fully sequencing 273,000 inserts with a mean size of 2.3 kb. After trimming bad-quality Illumina runs, the sequences were assembled by Genostar (Montbonnot, France) in 3,744 contigs with the CLC Genomics Workbench version 6.0.2 (<ext-link ext-link-type="uri" xlink:href="http://www.clcbio.com/products/clc-genomics-workbench">http://www.clcbio.com/products/clc-genomics-workbench</ext-link>). PacBio RSII reads were then used to generate scaffolds from the contigs using the softwares BLASR (<xref rid="B2" ref-type="bibr">2</xref>) and SSPACE Premium scaffolder version 2.3 (<xref rid="B3" ref-type="bibr">3</xref>). Subsequently, gaps were closed with GapFiller version 1.10 (<xref rid="B4" ref-type="bibr">4</xref>). Finally, 176 scaffolds were obtained with a mean size of 246,804 bp, representing a total length of 43.4 Mbp.</p><p>The genome annotation was performed by Genostar; prediction of coding DNA sequences (CDSs) was performed with Augustus version 2.5.5 (<xref rid="B5" ref-type="bibr">5</xref>), trained on an algorithm optimized for <italic>Neurospora crassa</italic>. The 10,919 putative CDSs identified were annotated by BLASTP (<xref rid="B6" ref-type="bibr">6</xref>) against the TrEmbl database (<xref rid="B7" ref-type="bibr">7</xref>). A function was inferred for a given CDS when the deduced protein sequence shared at least 80% similarity and 40% identity with a protein of known function in the TrEmbl database. A putative function was attributed to the remaining CDSs by functional domain searches through the Pfam database (<xref rid="B8" ref-type="bibr">8</xref>). Thus, a function was assigned to 8,818 out of the 10,919 CDSs (80.75%). For 813 CDSs, the functional annotation was refined by attribution of the enzyme classification numbers.</p><p>Genomic data will greatly improve our comprehension of the pathogenic mechanisms underlying scedosporiosis and will help our understanding of the low susceptibility of <italic>Scedosporium apiospermum</italic> to currently available antifungal drugs (<xref rid="B9" ref-type="bibr">9</xref>).</p><sec id="h1"><title>Nucleotide sequence accession numbers.</title><p>This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number <ext-link ext-link-type="NCBI:nucleotide" xlink:href="JOWA00000000">JOWA00000000</ext-link>. The version described in this paper is the first version, JOWA01000000.</p></sec></sec></body><back><fn-group><fn fn-type="other"><p><bold>Citation</bold> Vandeputte P, Ghamrawi S, Rechenmann M, Iltis A, Giraud S, Fleury M, Thornton C, Delhaès L, Meyer W, Papon N, Bouchara J-P. 2014. Draft genome sequence of the pathogenic fungus <italic>Scedosporium apiospermum</italic>. 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