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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

Journal Article · · PLoS Genetics
 [1];  [2];  [3];  [1];  [4];  [5];  [1];  [6];  [7];  [3];  [7];  [8];  [3];  [9];  [10];  [4];  [1];  [10]
  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
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Organization:
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)
Grant/Contract Number:
AC02-05CH11231; NO 407/2-1; SFB480; PO523/3-2; SP1111; RSG-08-030-01-CCG; BB/F013574
OSTI ID:
1627282
Journal Information:
PLoS Genetics, Vol. 6, Issue 4; ISSN 1553-7404
Publisher:
Public Library of ScienceCopyright Statement
Country of Publication:
United States
Language:
English

References (154)

Improved Prediction of Signal Peptides: SignalP 3.0 journal July 2004
Neurospora: the organism behind the molecular revolution. journal April 1992
AMID, an Apoptosis-inducing Factor-homologous Mitochondrion-associated Protein, Induces Caspase-independent Apoptosis journal April 2002
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses journal July 2005
Fatal Attraction: Nonself Recognition and Heterokaryon Incompatibility in Filamentous Fungi journal February 2003
Dendroscope: An interactive viewer for large phylogenetic trees journal November 2007
The WW Domain Protein PRO40 Is Required for Fungal Fertility and Associates with Woronin Bodies journal March 2007
The Pfam protein families database journal December 2007
A Eukaryotic Protein, NOP-1, Binds Retinal To Form an Archaeal Rhodopsin-like Photochemically Reactive Pigment † journal October 1999
The novel ER membrane protein PRO41 is essential for sexual development in the filamentous fungus Sordaria macrospora journal May 2007
The genome sequence of the model ascomycete fungus Podospora anserina journal January 2008
Coupling meiotic chromosome axis integrity to recombination journal March 2008
InterProScan - an integration platform for the signature-recognition methods in InterPro journal September 2001
The magnitude of fungal diversity: the 1.5 million species estimate revisited journal December 2001
Mining meiosis and gametogenesis with DNA microarrays journal April 2003
Genome-wide high throughput analysis of DNA methylation in eukaryotes journal March 2009
Highly efficient generation of signal transduction knockout mutants using a fungal strain deficient in the mammalian ku70 ortholog journal August 2006
Dothideomycete–Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum journal November 2007
Differential proteomic profiling of mitochondria from Podospora anserina, rat and human reveals distinct patterns of age-related oxidative changes journal September 2007
Quelling: post-transcriptional gene silencing guided by small RNAs in Neurospora crassa journal April 2007
White Collar-1, a Circadian Blue Light Photoreceptor, Binding to the frequency Promoter journal July 2002
Polymorphism of het-genes prevents resource plundering in Neurospora crassa journal November 1998
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
Functional and Physical Interaction of Blue- and Red-Light Sensors in Aspergillus nidulans journal February 2008
The Fungi journal September 2009
Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny journal March 2004
Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes journal December 2003
A Sordaria macrospora mutant lacking the leu1 gene shows a developmental arrest during fruiting body formation journal August 2005
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence journal March 1997
A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa journal June 2002
The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion journal August 2009
Genetic Control of Horizontal Virus Transmission in the Chestnut Blight Fungus, Cryphonectria parasitica journal September 2001
A WD40 Repeat Protein Regulates Fungal Cell Differentiation and Can Be Replaced Functionally by the Mammalian Homologue Striatin journal February 2004
Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa journal April 2009
Identification of Specificity Determinants and Generation of Alleles with Novel Specificity at the het-cHeterokaryon Incompatibility Locus of Neurospora crassa journal February 2001
Horizontal Gene Transfer of Glycosyl Hydrolases of the Rumen Fungi journal March 2000
Ancestral polymorphism and linkage disequilibrium at the het-6 region in pseudohomothallic Neurospora tetrasperma journal September 2007
Gene prediction with a hidden Markov model and a new intron submodel journal September 2003
Control of mating type heterokaryon incompatibility by the tol gene in Neurospora crassa and N . tetrasperma journal April 1992
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction journal January 2008
Role of Horizontal Gene Transfer in the Evolution of Fungi journal September 2000
MRBAYES: Bayesian inference of phylogenetic trees journal August 2001
Nonallelic Interactions Between het-c and a Polymorphic Locus, pin-c , Are Essential for Nonself Recognition and Programmed Cell Death in Neurospora crassa journal March 2006
Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation journal March 2004
Genome quality control: RIP (repeat-induced point mutation) comes to Podospora: RIP (repeat-induced point mutation ) in Podospora journal May 2001
Genetic Analysis of Phototropism of Neurospora crassa Perithecial Beaks Using White Collar and Albino Mutants journal August 1983
The Genetics and Molecular Biology of the Synaptonemal Complex journal November 2004
Genesis of a Fungal Non-Self Recognition Repertoire journal March 2007
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen journal January 2001
Elusive Origins of the Extra Genes in Aspergillus oryzae journal August 2008
Cell Differentiation during Sexual Development of the Fungus Sordaria macrospora Requires ATP Citrate Lyase Activity journal January 1999
Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain journal August 2008
A universal classification of eukaryotic transposable elements implemented in Repbase journal May 2008
Gene finding in novel genomes journal May 2004
Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora journal March 2005
Molecular analysis of aging processes in fungi journal January 1990
Meiotic double-strand breaks at the interface of chromosome movement, chromosome remodeling, and reductional division journal October 2003
White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein. journal April 1996
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae journal December 2008
The degenerate DNA transposon Pat and repeat-induced point mutation (RIP) in Podospora anserina journal August 2000
Neurospora in Temperate Forests of Western North America journal January 2004
The use of Duplication-Generating Rearrangements for Studying Heterokaryon Incompatibility Genes in Neurospora journal May 1975
A scanning electron microscopic study of the external features of perithecium development in Sordaria humana journal December 1983
Vegetative incompatibility in Neurospora: its effect on horizontal transfer of mitochondrial plasmids and senescence in natural populations journal August 1994
MrBayes 3: Bayesian phylogenetic inference under mixed models journal August 2003
The Aspergillus nidulans Phytochrome FphA Represses Sexual Development in Red Light journal October 2005
Principles governing amino acid composition of integral membrane proteins: application to topology prediction 1 1Edited by J. Thornton journal October 1998
HET-E and HET-D Belong to a New Subfamily of WD40 Proteins Involved in Vegetative Incompatibility Specificity in the Fungus Podospora anserina journal May 2002
Infernal 1.0: inference of RNA alignments journal March 2009
Mating-Type Genes From the Homothallic Fungus Sordaria macrospora Are Functionally Expressed in a Heterothallic Ascomycete journal October 1997
The B73 Maize Genome: Complexity, Diversity, and Dynamics journal November 2009
A Gene Essential for De Novo Methylation and Development in Ascobolus Reveals a Novel Type of Eukaryotic DNA Methyltransferase Structure journal October 1997
An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis journal August 2008
The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) journal December 2002
Transposons in filamentous fungi-facts and perspectives journal August 1998
Molecular and Functional Analyses of Incompatibility Genes at het-6 in a Population of Neurospora crassa journal August 2000
An analysis of the feasibility of short read sequencing journal October 2005
Profile hidden Markov models journal October 1998
Jalview Version 2--a multiple sequence alignment editor and analysis workbench journal January 2009
An electrophoretic karyotype of Neurospora crassa. journal April 1988
Combo: a whole genome comparative browser journal May 2006
Isolation of a transposable element from Neurospora crassa. journal March 1989
The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization journal September 2007
The genome sequence of the rice blast fungus Magnaporthe grisea journal April 2005
Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus journal January 2009
New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales journal July 2006
Fot1, a new family of fungal transposable elements journal March 1992
Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans journal June 2003
RIP: the evolutionary cost of genome defense journal September 2004
HETEROKARYON INCOMPATIBILITY GENES IN NEUROSPORA CRASSA DETECTED USING DUPLICATION-PRODUCING CHROMOSOME REARRANGEMENTS journal May 1975
Heterokaryon incompatibility blocks virus transfer among natural isolates of black Aspergilli journal September 1997
Multiple layers of temporal and spatial control regulate accumulation of the fruiting body-specific protein APP in Sordaria macrospora and Neurospora crassa journal July 2007
Genomic evidence for mating abilities in the asexual pathogen Aspergillus fumigatus journal December 2002
A Methylated Neurospora 5S rRNA Pseudogene Contains a Transposable Element Inactivated by Repeat-Induced Point Mutation journal August 1998
Over-expression of an S-adenosylmethionine-dependent methyltransferase leads to an extended lifespan of Podospora anserina without impairments in vital functions journal October 2008
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools journal December 1997
Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi journal January 2008
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data text January 2009
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data journal January 2009
White Collar-1, a DNA Binding Transcription Factor and a Light Sensor journal July 2002
Karyotype polymorphism correlates with intraspecific infertility in the homothallic ascomycete Sordaria macrospora journal March 2000
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research journal August 2005
Microscopic and Ultrastructural Examination of Vegetative Incompatibility in Partial Diploids Heterozygous athetLoci inNeurospora crassa journal February 1998
Heterocaryosis in Neurospora Crassa journal May 1944
Transposons in biotechnologically relevant strains of Aspergillus niger and Penicillium chrysogenum journal December 2007
Guest, a transposable element belonging to the Tc1/mariner superfamily is an ancient invader of Neurospora genomes journal January 2004
Repeats in genomic DNA: mining and meaning journal June 1998
Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes journal January 2007
VIB-1 Is Required for Expression of Genes Necessary for Programmed Cell Death in Neurospora crassa journal September 2006
Metabolic Pathway Gene Clusters in Filamentous Fungi journal February 1997
The pro1+ Gene From Sordaria macrospora Encodes a C6 Zinc Finger Transcription Factor Required for Fruiting Body Development journal May 1999
On the High Value of Low Standards journal December 2002
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes journal September 2003
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal February 2008
Natural Products of Filamentous Fungi: Enzymes, Genes, and Their Regulation journal July 2007
A Cytosine Methyltransferase Homologue Is Essential for Sexual Development in Aspergillus nidulans journal June 2008
The hAT family: a versatile transposon group common to plants, fungi, animals, and man journal April 2001
The Bioperl Toolkit: Perl Modules for the Life Sciences journal October 2002
Life with 6000 Genes journal October 1996
Versatile EGFP reporter plasmids for cellular localization of recombinant gene products in filamentous fungi journal January 2003
GeneWise and Genomewise journal May 2004
Vegetative Incompatibility in the het-6 Region of Neurospora crassa Is Mediated by Two Linked Genes journal July 2000
The S-adenosylmethionine dependent O-methyltransferase PaMTH1: a longevity assurance factor protecting Podospora anserina against oxidative stress journal March 2009
Molecular Genetics of Heterokaryon Incompatibility in Filamentous Ascomycetes journal September 2000
Emergence of a new disease as a result of interspecific virulence gene transfer journal July 2006
Repeat-induced point mutation (RIP) in Magnaporthe grisea: implications for its sexual cycle in the natural field context: Repeat-induced point mutation in Magnaporthe grisea journal September 2002
The transcriptional program of meiosis and sporulation in fission yeast journal August 2002
Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism journal March 2004
The genome sequence of the filamentous fungus Neurospora crassa journal April 2003
Regulation of melanin biosynthesis via the dihydroxynaphthalene pathway is dependent on sexual development in the ascomycete Sordaria macrospora journal October 2007
Identification and characterization of PaMTH1, a putative O -methyltransferase accumulating during senescence of Podospora anserina cultures journal March 2000
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus journal April 2008
Seeing the Light: News in Neurospora Blue Light Signal Transduction book January 1999
Neurospora. I. Preliminary Observations of the Chromosomes of Neurospora crassa journal December 1945
Detection of hyphal fusion in filamentous fungi using differently fluorescence-labeled histones journal October 2007
Absence of differences in polysomal RNAs from vegetative monokaryotic and dikaryotic cells of the fungus Schizophyllum commune journal September 1982
Genome sequencing in microfabricated high-density picolitre reactors journal July 2005
Next-generation DNA sequencing journal October 2008
Spo76p Is a Conserved Chromosome Morphogenesis Protein that Links the Mitotic and Meiotic Programs journal July 1999
Transformation of Sordaria macrospora to hygromycin B resistance: characterization of transformants by electrophoretic karyotyping and tetrad analysis journal December 1995
A novel polyketide biosynthesis gene cluster is involved in fruiting body morphogenesis in the filamentous fungi Sordaria macrospora and Neurospora crassa journal March 2009
Polyketide and Nonribosomal Peptide Antibiotics: Modularity and Versatility journal March 2004
Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets journal January 2007
Comparative gene expression analysis of fruiting body development in two filamentous fungi journal April 2006
Nonself recognition is mediated by HET-C heterocomplex formation during vegetative incompatibility journal September 2002
TFAM 1.0: an online tRNA function classifier journal May 2007
Molecular Characterization of tol, a Mediator of Mating-Type-Associated Vegetative Incompatibility in Neurospora crassa journal February 1999
From early homologue recognition to synaptonemal complex formation journal March 2006
Observing Meiosis in Filamentous Fungi: Sordaria and Neurospora book January 2009
Fungal Senescence journal December 1992
A Nonself Recognition Gene Complex in Neurospora crassa journal June 2006
New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales journal July 2006
Meiotic Silencing by Unpaired DNA journal December 2001
An efficient procedure to isolate fungal genes from an indexed cosmid library journal April 1997

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