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 next-generation 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 approximately 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.
authors.affiliation: Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany.
authors.forename: Minou
authors.initials: M
authors.lastname: Nowrousian
authors.forename: Jason E
authors.initials: JE
authors.lastname: Stajich
authors.forename: Meiling
authors.initials: M
authors.lastname: Chu
authors.forename: Ines
authors.initials: I
authors.lastname: Engh
authors.forename: Eric
authors.initials: E
authors.lastname: Espagne
authors.forename: Karen
authors.initials: K
authors.lastname: Halliday
authors.forename: Jens
authors.initials: J
authors.lastname: Kamerewerd
authors.forename: Frank
authors.initials: F
authors.lastname: Kempken
authors.forename: Birgit
authors.initials: B
authors.lastname: Knab
authors.forename: Hsiao-Che
authors.initials: HC
authors.lastname: Kuo
authors.forename: Heinz D
authors.initials: HD
authors.lastname: Osiewacz
authors.forename: Stefanie
authors.initials: S
authors.lastname: Pöggeler
authors.forename: Nick D
authors.initials: ND
authors.lastname: Read
authors.forename: Stephan
authors.initials: S
authors.lastname: Seiler
authors.forename: Kristina M
authors.initials: KM
authors.lastname: Smith
authors.forename: Denise
authors.initials: D
authors.lastname: Zickler
authors.forename: Ulrich
authors.initials: U
authors.lastname: Kück
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
mesh_terms: D001483:Base Sequence; D020869:Gene Expression Profiling; D016678:Genome; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D008954:Models, Biological; D008969:Molecular Sequence Data; D009492:Neurospora crassa / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D020037:Sordariales / Q000235:genetics*
references.citation: Aging Cell. 2008 Oct;7(5):651-62
references.pmid: 18616635
references.citation: Mol Cell Biol. 2001 Feb;21(4):1045-57
references.pmid: 11158292
references.citation: FEMS Microbiol Lett. 2007 Oct;275(1):62-70
references.pmid: 17681008
references.citation: Bioinformatics. 2006 Jul 15;22(14):1782-3
references.pmid: 16709588
references.citation: Trends Genet. 2004 Sep;20(9):417-23
references.pmid: 15313550
references.citation: J Mol Biol. 1998 Oct 23;283(2):489-506
references.pmid: 9769220
references.citation: Genome Biol. 2008;9(5):R77
references.pmid: 18460219
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W350-3
references.pmid: 17591612
references.citation: Curr Genet. 2000 Mar;37(3):200-8
references.pmid: 10794178
references.citation: Genetics. 1975 May;80(1):107-24
references.pmid: 124287
references.citation: Methods Mol Biol. 2009;558:91-114
references.pmid: 19685321
references.citation: Genetics. 2006 Aug;173(4):1991-2004
references.pmid: 16751666
references.citation: Genetics. 2006 Mar;172(3):1545-55
references.pmid: 16554411
references.citation: Plant Cell. 2007 Nov;19(11):3347-68
references.pmid: 18024570
references.citation: Mycologia. 2004 Jan-Feb;96(1):66-74
references.pmid: 21148830
references.citation: Curr Genet. 2009 Apr;55(2):185-98
references.pmid: 19277664
references.citation: Proc Natl Acad Sci U S A. 1989 Mar;86(6):1929-33
references.pmid: 2538822
references.citation: Mol Genet Genomics. 2005 Apr;273(2):137-49
references.pmid: 15778868
references.citation: Annu Rev Cell Dev Biol. 2004;20:525-58
references.pmid: 15473851
references.citation: Nature. 2009 Jan 22;457(7228):471-4
references.pmid: 19043401
references.citation: Reproduction. 2003 Apr;125(4):447-56
references.pmid: 12683916
references.citation: Genetics. 2000 Jul;155(3):1095-104
references.pmid: 10880472
references.citation: Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15670-5
references.pmid: 14676319
references.citation: Science. 2007 Sep 7;317(5843):1400-2
references.pmid: 17823352
references.citation: Mutat Res. 1990 Jan;237(1):1-8
references.pmid: 2181297
references.citation: BMC Microbiol. 2005 Nov 03;5:64
references.pmid: 16266439
references.citation: Mol Cell Biol. 1999 Jan;19(1):450-60
references.pmid: 9858569
references.citation: Genome Res. 2009 Feb;19(2):294-305
references.pmid: 19015323
references.citation: Eukaryot Cell. 2007 May;6(5):831-43
references.pmid: 17351077
references.citation: Plant Physiol. 1983 Aug;72(4):996-1000
references.pmid: 16663152
references.citation: Science. 2009 Nov 20;326(5956):1112-5
references.pmid: 19965430
references.citation: EMBO J. 1996 Apr 1;15(7):1650-7
references.pmid: 8612589
references.citation: Genome. 1992 Apr;35(2):347-53
references.pmid: 1535606
references.citation: Methods. 2009 Mar;47(3):142-50
references.pmid: 18950712
references.citation: Cell. 2001 Dec 28;107(7):905-16
references.pmid: 11779466
references.citation: Mol Genet Genomics. 2005 Oct;274(3):307-15
references.pmid: 16133166
references.citation: Genetics. 2002 May;161(1):71-81
references.pmid: 12019224
references.citation: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references.pmid: 9023104
references.citation: J Mol Biol. 2004 Jul 16;340(4):783-95
references.pmid: 15223320
references.citation: PLoS Genet. 2008 Apr 11;4(4):e1000046
references.pmid: 18404212
references.citation: Nucleic Acids Res. 2005 Nov 07;33(19):e171
references.pmid: 16275781
references.citation: Fungal Genet Biol. 2004 Jan;41(1):52-61
references.pmid: 14643259
references.citation: PLoS One. 2007 Mar 14;2(3):e283
references.pmid: 17356694
references.citation: Genome Res. 2004 May;14(5):988-95
references.pmid: 15123596
references.citation: Nat Prod Rep. 2007 Apr;24(2):393-416
references.pmid: 17390002
references.citation: J Bacteriol. 2002 Dec;184(23):6403-5; discusion 6405
references.pmid: 12426324
references.citation: Fungal Genet Biol. 1998 Feb;23(1):45-56
references.pmid: 9514694
references.citation: Curr Biol. 2009 Sep 29;19(18):R840-5
references.pmid: 19788875
references.citation: Curr Genet. 2007 Nov;52(5-6):259-66
references.pmid: 17929020
references.citation: BMC Genomics. 2005 Dec 08;6:177
references.pmid: 16336669
references.citation: Eukaryot Cell. 2004 Feb;3(1):232-40
references.pmid: 14871953
references.citation: Genes Dev. 2003 Nov 1;17(21):2675-87
references.pmid: 14563680
references.citation: Curr Genet. 1997 Sep;32(3):209-17
references.pmid: 9339346
references.citation: Cell. 1997 Oct 17;91(2):281-90
references.pmid: 9346245
references.citation: Bioinformatics. 2001 Aug;17(8):754-5
references.pmid: 11524383
references.citation: Curr Genet. 1995 Dec;29(1):88-95
references.pmid: 8595663
references.citation: Genome Res. 2002 Oct;12(10):1611-8
references.pmid: 12368254
references.citation: Genome Biol. 2008 Jan 24;9(1):R18
references.pmid: 18218086
references.citation: Mol Genet Genomics. 2008 Oct;280(4):319-25
references.pmid: 18677513
references.citation: Nat Biotechnol. 2008 Oct;26(10):1135-45
references.pmid: 18846087
references.citation: PLoS One. 2009 Apr 21;4(4):e5286
references.pmid: 19461939
references.citation: Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25
references.pmid: 14534192
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4
references.pmid: 15980510
references.citation: BMC Bioinformatics. 2007 Nov 22;8:460
references.pmid: 18034891
references.citation: Mol Microbiol. 2002 Sep;45(5):1355-64
references.pmid: 12207702
references.citation: Genetics. 1999 Feb;151(2):545-55
references.pmid: 9927450
references.citation: Curr Genet. 2002 Dec;42(3):153-60
references.pmid: 12491009
references.citation: Eukaryot Cell. 2003 Feb;2(1):1-8
references.pmid: 12582117
references.citation: EMBO J. 2002 Sep 16;21(18):4841-50
references.pmid: 12234924
references.citation: Curr Genet. 1994 Aug;26(2):113-9
references.pmid: 8001163
references.citation: Microbiol Mol Biol Rev. 2004 Mar;68(1):1-108
references.pmid: 15007097
references.citation: Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4507-12
references.pmid: 15070748
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Z Vererbungsl. 1958;89(5):729-46
references.pmid: 13648694
references.citation: Curr Biol. 2008 Feb 26;18(4):255-9
references.pmid: 18291652
references.citation: Fungal Genet Biol. 2007 Dec;44(12):1399-414
references.pmid: 17881255
references.citation: Cell. 1999 Jul 23;98(2):261-71
references.pmid: 10428037
references.citation: Nature. 2010 Jan 21;463(7279):311-7
references.pmid: 20010809
references.citation: Nature. 2005 Apr 21;434(7036):980-6
references.pmid: 15846337
references.citation: Nat Genet. 2006 Aug;38(8):953-6
references.pmid: 16832356
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Mol Microbiol. 2007 May;64(4):923-37
references.pmid: 17501918
references.citation: Bioessays. 1998 Aug;20(8):652-9
references.pmid: 9841641
references.citation: Mol Microbiol. 2001 May;40(3):586-95
references.pmid: 11359565
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8
references.pmid: 18039703
references.citation: Annu Rev Phytopathol. 2000 Sep;38:325-363
references.pmid: 11701846
references.citation: Nature. 2005 Sep 15;437(7057):376-80
references.pmid: 16056220
references.citation: BMC Bioinformatics. 2006 Feb 09;7:62
references.pmid: 16469098
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Genes Dev. 2008 Mar 15;22(6):796-809
references.pmid: 18347098
references.citation: Genetics. 1975 May;80(1):87-105
references.pmid: 124288
references.citation: Methods Mol Biol. 2007;395:221-36
references.pmid: 17993677
references.citation: Bioinformatics. 2009 May 1;25(9):1189-91
references.pmid: 19151095
references.citation: Genetics. 2001 Sep;159(1):107-18
references.pmid: 11560890
references.citation: Fungal Genet Biol. 2003 Jun;39(1):31-7
references.pmid: 12742061
references.citation: FEMS Microbiol Lett. 2006 Apr;257(2):328-35
references.pmid: 16553871
references.citation: Bioinformatics. 1998;14(9):755-63
references.pmid: 9918945
references.citation: Annu Rev Genet. 1992;26:351-72
references.pmid: 1482117
references.citation: Curr Genet. 2003 Apr;43(1):54-61
references.pmid: 12684845
references.citation: Genetics. 1998 Aug;149(4):1787-97
references.pmid: 9691037
references.citation: Bioinformatics. 2008 Mar 1;24(5):597-605
references.pmid: 18187439
references.citation: Nat Genet. 2002 Sep;32(1):143-7
references.pmid: 12161753
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Science. 2002 Aug 2;297(5582):815-9
references.pmid: 12098706
references.citation: J Bacteriol. 2002 Dec;184(23):6406-9; discussion 6409
references.pmid: 12426325
references.citation: Genetics. 1944 May;29(3):291-308
references.pmid: 17247122
references.citation: Genetics. 1992 Apr;130(4):687-701
references.pmid: 1582553
references.citation: Nat Rev Genet. 2008 May;9(5):411-2; author reply 414
references.pmid: 18421312
references.citation: Mycologia. 2006 Jul-Aug;98(4):550-9
references.pmid: 17139848
references.citation: J Mol Biol. 2001 Jan 19;305(3):567-80
references.pmid: 11152613
references.citation: Science. 1996 Oct 25;274(5287):546, 563-7
references.pmid: 8849441
references.citation: Bioinformatics. 2001 Sep;17(9):847-8
references.pmid: 11590104
references.citation: Fungal Genet Biol. 2000 Aug;30(3):197-205
references.pmid: 11035941
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Adv Biochem Eng Biotechnol. 2008;111:99-147
references.pmid: 18253709
references.citation: Curr Biol. 2005 Oct 25;15(20):1833-8
references.pmid: 16243030
references.citation: Eukaryot Cell. 2006 Dec;5(12):2161-73
references.pmid: 17012538
references.citation: Genetics. 1997 Oct;147(2):567-80
references.pmid: 9335594
references.citation: Genetics. 1999 May;152(1):191-9
references.pmid: 10224253
references.citation: Genome Biol. 2009;10(9):R94
references.pmid: 19747388
references.citation: Biochemistry. 1999 Oct 26;38(43):14138-45
references.pmid: 10571987
references.citation: PLoS Genet. 2009 Aug;5(8):e1000618
references.pmid: 19714214
references.citation: PLoS One. 2007 Aug 06;3(8):e2879
references.pmid: 18663385
references.citation: Fungal Genet Biol. 2007 Sep;44(9):896-904
references.pmid: 17576083
references.citation: Mol Cell Biol. 1988 Apr;8(4):1469-73
references.pmid: 2967910
references.citation: Chromosoma. 2006 Jun;115(3):158-74
references.pmid: 16570189
references.citation: Adv Genet. 1999;41:35-54
references.pmid: 10494616
references.citation: Chromosoma. 2001 Apr;110(1):1-9
references.pmid: 11398971
references.citation: PLoS One. 2008 Aug 22;3(8):e3036
references.pmid: 18725939
references.citation: Bioinformatics. 2009 May 15;25(10):1335-7
references.pmid: 19307242
references.citation: Fungal Genet Biol. 2004 Mar;41(3):285-92
references.pmid: 14761789
references.citation: Curr Opin Struct Biol. 1998 Jun;8(3):333-7
references.pmid: 9666329
references.citation: Aging (Albany NY). 2009 Mar 03;1(3):328-34
references.pmid: 20157520
references.citation: Fungal Genet Biol. 2007 Jul;44(7):602-14
references.pmid: 17092746
references.citation: Science. 2004 Mar 19;303(5665):1805-10
references.pmid: 15031493
references.citation: Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8802-7
references.pmid: 12072568
references.citation: Mol Gen Genet. 2000 Jul;263(6):1061-9
references.pmid: 10954093
references.citation: Science. 2002 Aug 2;297(5582):840-3
references.pmid: 12098705
references.citation: PLoS One. 2008 Jun 25;3(6):e2531
references.pmid: 18575630
references.citation: Mol Gen Genet. 1992 Mar;232(1):12-6
references.pmid: 1313143
references.citation: Gene. 2006 Aug 15;378:1-10
references.pmid: 16814491
references.citation: Mol Biol Evol. 2000 Mar;17(3):352-61
references.pmid: 10723736
references.citation: BMC Evol Biol. 2007 Sep 26;7:174
references.pmid: 17897469
references.citation: Curr Opin Microbiol. 2007 Apr;10(2):199-203
references.pmid: 17395524
references.citation: Fungal Genet Biol. 1997 Feb;21(1):17-29
references.pmid: 9126615
references.citation: Nature. 2003 Apr 24;422(6934):859-68
references.pmid: 12712197
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: Microbiol Mol Biol Rev. 2000 Sep;64(3):489-502
references.pmid: 10974123
references.citation: Comput Appl Biosci. 1996 Aug;12(4):357-8
references.pmid: 8902363
references.citation: J Biol Chem. 2002 Jul 12;277(28):25617-23
references.pmid: 11980907
references.citation: Org Biomol Chem. 2007 Jul 7;5(13):2010-26
references.pmid: 17581644
references.citation: BMC Bioinformatics. 2004 May 14;5:59
references.pmid: 15144565
references.citation: Exp Gerontol. 2007 Sep;42(9):887-98
references.pmid: 17689904