Fine De Novo Sequencing of a Fungal Genome Using only SOLiD Short Read Data: Verification on Aspergillus oryzae RIB40

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Umemura, Myco ^a   Koyama, Yoshinori ^b   Takeda, Itaru ^b,c   Hagiwara, Hiroko ^b   Ikegami, Tsutomu ^b   Koike, Hideaki ^b   Machida, Masayuki ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NONRIBOSOMAL PEPTIDE SYNTHETASE; POLYKETIDE SYNTHASE;

ARTICLE; ASPERGILLUS ORYZAE; CONTROLLED STUDY; DATA FILTERING; DATA PROCESSING; DE NOVO SEQUENCING; FEASIBILITY STUDY; FUNGAL GENOME; GENE; GENE CLUSTER; GENE DELETION; GENE INSERTION; GENE LIBRARY; GENE RECONSTRUCTION; GENE SEQUENCE; GENETIC PROCEDURES; GENOME ANALYSIS; GENOME ASSEMBLY; GENOME SIZE; INSERT SIZE; K MER SIZE; NONHUMAN; NONRIBOSOMAL PEPTIDE SYNTHETASE GENE; NUCLEOTIDE SEQUENCE; POLYKETIDE SYNTHASE GENE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SHORT READ SEQUENCE; VALIDATION PROCESS;

ASPERGILLUS ORYZAE; BASE PAIRING; BASE SEQUENCE; GENE LIBRARY; GENES, FUNGAL; GENOME, FUNGAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MULTIGENE FAMILY; MUTATION; NUCLEOTIDES; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84877120155     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063673     Document Type: Article

References (43)

1. Marroni F, Pinosio S, Morgante M, (2012) The quest for rare variants: pooled multiplexed next generation sequencing in plants. Front Plant Sci 3: 133.
2. Lee SW, Markham PF, Markham JF, Petermann I, Noormohammadi AH, et al. (2011) First complete genome sequence of infectious laryngotracheitis virus. BMC Genomics 12: 197.
3. Cunningham C, Gatherer D, Hilfrich B, Baluchova K, Dargan DJ, et al. (2010) Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. J Gen Virol 91(Pt 3): 605-615.
4. Ghosh W, George A, Agarwal A, Raj P, Alam M, et al. (2011) Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis. J Bacteriol 193(19): 5553-5554.
5. Perez Chaparro PJ, McCulloch JA, Cerdeira LT, Al-Dilaimi A, Canto de Sa LL, et al. (2011) Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads. J Microbiol Methods 87(2): 208-212.
6. den Bakker HC, Cummings CA, Ferreira V, Vatta P, Orsi RH, et al. (2010) Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics 11: 688.
7. Silva A, Schneider MP, Cerdeira L, Barbosa MS, Ramos RT, et al. (2011) Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis. J Bacteriol 193(1): 323-324.
8. Farrer RA, Kemen E, Jones JD, Studholme DJ, (2009) De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett 291(1): 103-111.
9. Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, et al. (2010) Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330(6010): 1543-1546.
10. Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, et al. (2010) De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet 6(4): e1000891.
11. Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol 10(9): R94.
12. Haridas S, Breuill C, Bohlmann J, Hsiang T, (2011) A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes. J Microbiol Methods 86(3): 368-375.
13. Cerdeira LT, Carneiro AR, Ramos RT, de Almeida SS, D'Afonseca V, et al. (2011) Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. J Microbiol Methods 86(2): 218-223.
14. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108(4): 1513-1518.
15. Li R, Fan W, Tian G, Zhu H, He L, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463(7279): 311-317.
16. Palmer JM, Keller NP, (2010) Secondary metabolism in fungi: does chromosomal location matter? Curr Opin Microbiol 13(4): 431-436.
17. Yin W, Keller NP, (2011) Transcriptional regulatory elements in fungal secondary metabolism. J Microbiol 49(3): 329-339.
18. Sanchez JF, Somoza AD, Keller NP, Wang CC, (2012) Advances in Aspergillus secondary metabolite research in the post-genomic era. Nat Prod Rep 29(3): 351-371.
19. Staunton J, Weissman KJ, (2001) Polyketide biosynthesis: a millennium review. Nat Prod Rep 18(4): 380-416.
20. Schwarzer D, Finking R, Marahiel MA, (2003) Nonribosomal peptides: from genes to products. Nat Prod Rep 20(3): 275-287.
21. Yu J, Chang PK, Ehrlich KC, Cary JW, Bhatnagar D, et al. (2004) Clustered pathway genes in aflatoxin biosynthesis. Appl Environ Microbiol 70(3): 1253-1262.
22. Terabayashi Y, Sano M, Yamane N, Marui J, Tamano K, et al. (2010) Identification and characterization of genes responsible for biosynthesis of kojic acid, an industrially important compound from Aspergillus oryzae. Fungal Genet Biol 47(12): 953-961.
23. Machida M, Asai K, Sano M, Tanaka T, Kumagai T, et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438(7071): 1157-1161.
24. Umemura M, Koike H, Yamane N, Koyama Y, Satou Y, et al. (2012) Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species. DNA Res 19(5): 375-382.
25. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5): 821-829.
26. Kielbasa SM, Wan R, Sato K, Horton P, Frith MC, (2011) Adaptive seeds tame genomic sequence comparison. Genome Res 21(3): 487-493.
27. Frith MC, Wan R, Horton P, (2010) Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res 38(7): e100.
28. Frith MC, Hamada M, Horton P, (2010) Parameters for accurate genome alignment. BMC Bioinformatics 11: 80.
29. Earl D, Bradnam K, St John J, Darling A, Lin D, et al. (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 21(12): 2224-2241.
30. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215(3): 403-410.
31. States DJ, Gish W, (1994) Combined use of sequence similarity and codon bias for coding region identification. J Comput Biol 1(1): 39-50.
32. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, et al. (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 5(5): e1000386.
33. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5(2): R12.
34. Cane DE, Walsh CT, (1999) The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases. Chem Biol 6(12): R319-325.
35. Kiyota T, Hamada R, Sakamoto K, Iwashita K, Yamada O, et al. (2011) Aflatoxin non-productivity of Aspergillus oryzae caused by loss of function in the aflJ gene product. J Biosci Bioeng 111(5): 512-517.
36. Tominaga M, Lee YH, Hayashi R, Suzuki Y, Yamada O, et al. (2006) Molecular analysis of an inactive aflatoxin biosynthesis gene cluster in Aspergillus oryzae RIB strains. Appl Environ Microbiol 72(1): 484-490.
37. Kusumoto K, Nogata Y, Ohta H, (2000) Directed deletions in the aflatoxin biosynthesis gene homolog cluster of Aspergillus oryzae. Curr Genet 37(2): 104-111.
38. Watson AJ, Fuller LJ, Jeenes DJ, Archer DB, (1999) Homologs of aflatoxin biosynthesis genes and sequence of aflR in Aspergillus oryzae and Aspergillus sojae. Appl Environ Microbiol 65(1): 307-310.
39. Georgianna DR, Fedorova ND, Burroughs JL, Dolezal AL, Bok JW, et al. (2010) Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters. Molecular Plant Pathology 11(2): 213-226.
40. Georgianna DR, Payne GA, (2009) Genetic regulation of aflatoxin biosynthesis: from gene to genome. Fungal Genet Biol 46(2): 113-125.
41. Brown DW, Yu JH, Kelkar HS, Fernandes M, Nesbitt TC, et al. (1996) Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans. Proc Natl Acad Sci U S A 93(4): 1418-1422.
42. Lin Y, Li J, Shen H, Zhang L, Papasian CJ, et al. (2011) Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 27(15): 2031-2037.
43. Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, et al. (2009) ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol 10(10): R103.