LTR retrotransposons in fungi

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Muszewska, Anna ^a   Hoffman Sommer, Marta ^a   Grynberg, Marcin ^a  

^a INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC PROTEINASE; INTEGRASE; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE;

ARTICLE; FUNGAL GENOME; FUNGUS; GENE SEQUENCE; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROTEIN ANALYSIS; RETROPOSON; TRANSPOSON;

BASE SEQUENCE; CLUSTER ANALYSIS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; FUNGI; GENOME, FUNGAL; INTEGRASES; LIKELIHOOD FUNCTIONS; PEPTIDE HYDROLASES; PROTEIN STRUCTURE, TERTIARY; RETROELEMENTS; RIBONUCLEASE H; RNA-DIRECTED DNA POLYMERASE; TERMINAL REPEAT SEQUENCES;

EUKARYOTA; FUNGI;

EID: 84855291327     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029425     Document Type: Article

References (88)

1. Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z, et al. (2009) Evolution of genome size and complexity in Pinus. PLoS One 4: e4332.
2. Rachidi N, Barre P, Blondin B, (1999) Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261: 841-850.
3. Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M, (2009) Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet 25: 63-66.
4. Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK, (2007) Evaluating the protein coding potential of exonized transposable element sequences. Biol Direct 2: 31.
5. Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, et al. (2008) Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci U S A 105: 4220-4225.
6. Craig NL, (2002) Mobile DNA II Washington, D.C. ASM Press pp xviii, 1204 p., [1232] p. of plates p.
7. Kapitonov VV, Jurka J, (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23: 521-529.
8. Pritham EJ, Putliwala T, Feschotte C, (2007) Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390: 3-17.
9. Wicker T, Keller B, (2007) Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res 17: 1072-1081.
10. Capy P, Langin T, Higuet D, Maurer P, Bazin C, (1997) Do the integrases of LTR-retrotransposons and class II element transposases have a common ancestor? Genetica 100: 63-72.
11. Kordis D, (2005) A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene 347: 161-173.
12. Llorens C, Fares MA, Moya A, (2008) Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. BMC Evol Biol 8: 276.
13. Daboussi MJ, Capy P, (2003) Transposable elements in filamentous fungi. Annu Rev Microbiol 57: 275-299.
14. Gao X, Hou Y, Ebina H, Levin HL, Voytas DF, (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res 18: 359-369.
15. Gorinsek B, Gubensek F, Kordis D, (2004) Evolutionary genomics of chromoviruses in eukaryotes. Mol Biol Evol 21: 781-798.
16. Kejnovsky E, Kubat Z, Macas J, Hobza R, Mracek J, et al. (2006) Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat. Mol Genet Genomics 276: 254-263.
17. Chicas A, Cogoni C, Macino G, (2004) RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa. Nucleic Acids Res 32: 4237-4243.
18. Galagan JE, Selker EU, (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20: 417-423.
19. Wang X, Hsueh YP, Li W, Floyd A, Skalsky R, et al. (2010) Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi. Genes Dev 24: 2566-2582.
20. Windhofer F, Catcheside DE, Kempken F, (2000) Methylation of the foreign transposon Restless in vegetative mycelia of Neurospora crassa. Curr Genet 37: 194-199.
21. Cameron JR, Loh EY, Davis RW, (1979) Evidence for transposition of dispersed repetitive DNA families in yeast. Cell 16: 739-751.
22. Dobinson KF, Hamer JE, (1993) The ebb and flow of a fungal genome. Trends Microbiol 1: 348-352.
23. Nakayashiki H, Kiyotomi K, Tosa Y, Mayama S, (1999) Transposition of the retrotransposon MAGGY in heterologous species of filamentous fungi. Genetics 153: 693-703.
24. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, et al. (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434: 980-986.
25. Lynch M, Conery JS, (2003) The origins of genome complexity. Science 302: 1401-1404.
26. Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, et al. (2009) A functional role for transposases in a large eukaryotic genome. Science 324: 935-938.
27. Clutterbuck JA, (2010) Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes. Fungal Genet Biol 48: 306-326.
28. Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, et al. (2008) The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol 9: R77.
29. Kamper J, Kahmann R, Bolker M, Ma LJ, Brefort T, et al. (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444: 97-101.
30. Novikova OS, (2010) [Diversity and evolution of LTR retrotransposons in the genome of Phanerochaete chrysosporium (Fungi: Basidiomycota)]. Genetika 46: 725-733.
31. Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, et al. (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A 106: 1954-1959.
32. Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, et al. (2009) Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet 5: e1000549.
33. Schmid-Berger N, Schmid B, Barth G, (1994) Ylt1, a highly repetitive retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica. J Bacteriol 176: 2477-2482.
34. Malik HS, (2005) Ribonuclease H evolution in retrotransposable elements. Cytogenet Genome Res 110: 392-401.
35. Llorens C, Futami R, Renaud G, Moya A, (2009) Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases. Biol Direct 4: 3.
36. Cuomo CA, Guldener U, Xu JR, Trail F, Turgeon BG, et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400-1402.
37. Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, et al. (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 12: R40.
38. Hughes SE, Hawley RS, (2009) Heterochromatin: a rapidly evolving species barrier. PLoS Biol 7: e1000233.
39. Neuveglise C, Feldmann H, Bon E, Gaillardin C, Casaregola S, (2002) Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Res 12: 930-943.
40. Ellinghaus D, Kurtz S, Willhoeft U, (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9: 18.
41. Xu Z, Wang H, (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35: W265-268.
42. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
43. Huang Y, Niu B, Gao Y, Fu L, Li W, (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680-682.
44. Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
45. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T, (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973.
46. Abascal F, Zardoya R, Posada D, (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
47. Guindon S, Delsuc F, Dufayard JF, Gascuel O, (2009) Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 537: 113-137.
48. Letunic I, Bork P, (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128.
49. Olson SA, (2002) EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 3: 87-91.
50. Eddy SR, (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23: 205-211.
51. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-222.
52. Dutta S,(2007) Using the tools and resources of the RCSB protein data bank. Curr Protoc Bioinformatics Chapter 1 pp. Unit1 9.
53. Frickey T, Lupas A, (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20: 3702-3704.
54. Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22: 695-700.
55. Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, et al. (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A 107: 11889-11894.
56. Martin F, Aerts A, Ahren D, Brun A, Danchin EG, et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-92.
57. Plett JM, Martin F, (2011) Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. Trends Genet 27: 14-22.
58. Chaturvedi V, Chaturvedi S, (2011) Cryptococcus gattii: a resurgent fungal pathogen. Trends Microbiol.
59. Cleveland TE, Yu J, Fedorova N, Bhatnagar D, Payne GA, et al. (2009) Potential of Aspergillus flavus genomics for applications in biotechnology. Trends Biotechnol 27: 151-157.
60. Baker SE, (2006) Aspergillus niger genomics: past, present and into the future. Med Mycol 44 (Suppl 1): S17-21.
61. Balajee SA, (2009) Aspergillus terreus complex. Med Mycol 47 (Suppl 1): S42-46.
62. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, et al. (2009) Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 19: 1722-1731.
63. Pantou MP, Kouvelis VN, Typas MA, (2008) The complete mitochondrial genome of Fusarium oxysporum: insights into fungal mitochondrial evolution. Gene 419: 7-15.
64. Dorn B, Forrer HR, Jenny E, Wettstein FE, Bucheli TD, et al. (2011) Fusarium species complex and mycotoxins in grain maize from maize hybrid trials and from grower's fields. J Appl Microbiol 111: 693-706.
65. Pelizza S, Stenglein S, Cabello M, Dinolfo M, Lange C, (2011) First Record of Fusarium verticillioides as an Entomopathogenic Fungus of Grasshoppers. J Insect Sci 11: 70.
66. Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, et al. (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5: e1000618.
67. Paoletti M, Saupe SJ, (2008) The genome sequence of Podospora anserina, a classic model fungus. Genome Biol 9: 223.
68. Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, et al. (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7: e1002230.
69. Reissinger A, Winter S, Steckelbroeck S, Hartung W, Sikora RA, (2003) Infection of barley roots by Chaetomium globosum: evidence for a protective role of the exodermis. Mycol Res 107: 1094-1102.
70. Yu J, Yang S, Zhao Y, Li R, (2006) A case of subcutaneous phaeohyphomycosis caused by Chaetomium globosum and the sequences analysis of C. globosum. Med Mycol 44: 541-545.
71. Oliver RP, Solomon PS, (2010) New developments in pathogenicity and virulence of necrotrophs. Curr Opin Plant Biol.
72. Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, et al. (2008) Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet 4: e1000046.
73. Rokas A, (2009) The effect of domestication on the fungal proteome. Trends Genet 25: 60-63.
74. Turgeon BG, Baker SE, (2007) Genetic and genomic dissection of the Cochliobolus heterostrophus Tox1 locus controlling biosynthesis of the polyketide virulence factor T-toxin. Adv Genet 57: 219-261.
75. Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, et al. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26: 553-560.
76. Goodwin SB, M'Barek SB, Dhillon B, Wittenberg AH, Crane CF, et al. (2011) Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet 7: e1002070.
77. Tian C, Beeson WT, Iavarone AT, Sun J, Marletta MA, et al. (2009) Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proc Natl Acad Sci U S A 106: 22157-22162.
78. Desnos-Ollivier M, Ragon M, Robert V, Raoux D, Gantier JC, et al. (2008) Debaryomyces hansenii (Candida famata), a rare human fungal pathogen often misidentified as Pichia guilliermondii (Candida guilliermondii). J Clin Microbiol 46: 3237-3242.
79. Blandin G, Ozier-Kalogeropoulos O, Wincker P, Artiguenave F, Dujon B, (2000) Genomic exploration of the hemiascomycetous yeasts: 16. Candida tropicalis. FEBS Lett 487: 91-94.
80. Favel A, Michel-Nguyen A, Peyron F, Martin C, Thomachot L, et al. (2003) Colony morphology switching of Candida lusitaniae and acquisition of multidrug resistance during treatment of a renal infection in a newborn: case report and review of the literature. Diagn Microbiol Infect Dis 47: 331-339.
81. Lockhart SR, Messer SA, Pfaller MA, Diekema DJ, (2008) Lodderomyces elongisporus masquerading as Candida parapsilosis as a cause of bloodstream infections. J Clin Microbiol 46: 374-376.
82. Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25: 319-326.
83. Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, et al. (2010) Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res 20: 1451-1458.
84. Bruckner S, Mosch HU, (2011) Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae. FEMS Microbiol Rev.
85. Replansky T, Koufopanou V, Greig D, Bell G, (2008) Saccharomyces sensu stricto as a model system for evolution and ecology. Trends Ecol Evol 23: 494-501.
86. Yukawa M, Maki T, (1931) Schizosaccharomyces japonicus nov. spec. La Bul. Sci. Falkultato Terkultura. Kjusu Imp Univ, Fukuoka, Japan 4: 218-226.
87. Northam BE, Norris FW, (1951) Growth requirements of Schizosaccharomyces octosporus, a yeast exacting towards adenine. J Gen Microbiol 5: 502-507.
88. Lannoo MJ, Petersen C, Lovich RE, Nanjappa P, Phillips C, et al. (2011) Do frogs get their kicks on Route 66? Continental U.S. transect reveals spatial and temporal patterns of Batrachochytrium dendrobatidis infection. PLoS One 6: e22211.