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Title: De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

Abstract

Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While nextgeneration sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30–90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/ Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in ~4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed thatmore » S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology.« less

Authors:
 [1];  [2];  [3];  [1];  [4];  [5];  [1];  [6];  [7];  [3];  [7];  [8];  [3];  [9];  [10];  [4];  [1];  [10]
+ Show Author Affiliations
  1. Ruhr Univ., Bochum (Germany). Lehrstuhl fur Allgemeine und Molekulare Botanik
  2. Univ. of California, Riverside, CA (United States). Dept. of Plant Pathology and Microbiology
  3. Univ. of Edinburgh, Scotland (United Kingdom). Inst. of Cell Biology. Fungal Cell Biology Group
  4. Univ. Paris-Sud, Orsay (France). Inst. de Genetique et Microbiologie
  5. Univ. of Edinburgh, Scotland (United Kingdom). Biological Sciences. Inst. of Molecular Plant Sciences
  6. Christian-Albrechts-Universitat zu Kiel (Germany). Botanisches Institut und Botanischer Garten. Abteilung Botanische Genetik und Molekularbiologie
  7. Johann Wolfgang Goethe Univ., Frankfurt (Germany). Faculty for Biosciences and Cluster of Excellence Macromolecular Complexes. Inst. of Molecular Biosciences
  8. Georg-August Univ., Gottingen (Germany). Dept. of Genetics of Eukaryotic Microorganisms. Inst. of Microbiology and Genetics
  9. Georg-August Univ., Gottingen (Germany). DFG Research Center Molecular Physiology of the Brain (CMPB). Dept. of Molecular Microbiology and Genetics. Inst. of Microbiology and Genetics
  10. Oregon State Univ., Corvallis, OR (United States). Dept. of Biochemistry and Biophysics. Center for Genome Research and Biocomputing
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; German Research Foundation (DFG); American Cancer Society; Biotechnological and Biological Sciences Research Council (BBSRC)
OSTI Identifier:
1627282
Grant/Contract Number:  
AC02-05CH11231; NO 407/2-1; SFB480; PO523/3-2; SP1111; RSG-08-030-01-CCG; BB/F013574
Resource Type:
Accepted Manuscript
Journal Name:
PLoS Genetics
Additional Journal Information:
Journal Volume: 6; Journal Issue: 4; Journal ID: ISSN 1553-7404
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity

Citation Formats

Nowrousian, Minou, Stajich, Jason E., Chu, Meiling, Engh, Ines, Espagne, Eric, Halliday, Karen, Kamerewerd, Jens, Kempken, Frank, Knab, Birgit, Kuo, Hsiao-Che, Osiewacz, Heinz D., Pöggeler, Stefanie, Read, Nick D., Seiler, Stephan, Smith, Kristina M., Zickler, Denise, Kück, Ulrich, and Freitag, Michael. De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis. United States: N. p., 2010. Web. doi:10.1371/journal.pgen.1000891.
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Nowrousian, Minou, Stajich, Jason E., Chu, Meiling, Engh, Ines, Espagne, Eric, Halliday, Karen, Kamerewerd, Jens, Kempken, Frank, Knab, Birgit, Kuo, Hsiao-Che, Osiewacz, Heinz D., Pöggeler, Stefanie, Read, Nick D., Seiler, Stephan, Smith, Kristina M., Zickler, Denise, Kück, Ulrich, & Freitag, Michael. De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis. United States. https://doi.org/10.1371/journal.pgen.1000891
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Nowrousian, Minou, Stajich, Jason E., Chu, Meiling, Engh, Ines, Espagne, Eric, Halliday, Karen, Kamerewerd, Jens, Kempken, Frank, Knab, Birgit, Kuo, Hsiao-Che, Osiewacz, Heinz D., Pöggeler, Stefanie, Read, Nick D., Seiler, Stephan, Smith, Kristina M., Zickler, Denise, Kück, Ulrich, and Freitag, Michael. Thu . "De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis". United States. https://doi.org/10.1371/journal.pgen.1000891. https://www.osti.gov/servlets/purl/1627282.
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@article{osti_1627282,
title = {De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis},
author = {Nowrousian, Minou and Stajich, Jason E. and Chu, Meiling and Engh, Ines and Espagne, Eric and Halliday, Karen and Kamerewerd, Jens and Kempken, Frank and Knab, Birgit and Kuo, Hsiao-Che and Osiewacz, Heinz D. and Pöggeler, Stefanie and Read, Nick D. and Seiler, Stephan and Smith, Kristina M. and Zickler, Denise and Kück, Ulrich and Freitag, Michael},
abstractNote = {Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While nextgeneration sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30–90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/ Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in ~4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology.},
doi = {10.1371/journal.pgen.1000891},
journal = {PLoS Genetics},
number = 4,
volume = 6,
place = {United States},
year = {Thu Apr 08 00:00:00 EDT 2010},
month = {Thu Apr 08 00:00:00 EDT 2010}
}
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