Truncated and RIP-degenerated copies of the LTR retrotransposon Pholy are clustered in a pericentromeric region of the Leptosphaeria maculans genome

Fungal Genetics and Biology

Volumn 42, Issue 1, 2005, Pages 30-41

  Attard, Agnès ^a   Gout, Lilian ^a   Ross, Simon ^a   Parlange, Francis ^a   Cattolico, Laurence ^b   Balesdent, Marie Hélène ^a   Rouxel, Thierry ^a  

^a CEMAGREF   (France)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

Author keywords

Avirulence; AvrLm1; Brassica napus; Centromere; copia Ty1; Phoma lingam

Indexed keywords

ARTICLE; ASCOMYCETES; CENTROMERE; CHROMOSOME; FUNGUS ISOLATION; GENE CLUSTER; GENE FREQUENCY; GENE SEQUENCE; GENOME ANALYSIS; INTERSPERSED REPEAT; LEPTOSPHAERIA MACULANS; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; RETROPOSON; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ASCOMYCOTA; CENTROMERE; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; GENES, FUNGAL; INTERSPERSED REPETITIVE SEQUENCES; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; POINT MUTATION; RETROELEMENTS; SEQUENCE DELETION; SEQUENCE HOMOLOGY, AMINO ACID; TERMINAL REPEAT SEQUENCES;

BRASSICA; BRASSICA NAPUS; LEPTOSPHAERIA; LEPTOSPHAERIA MACULANS; PHAEOSPHAERIA NODORUM; PHOMA; STAGONOSPORA;

EID: 10444281982     PISSN: 10871845     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fgb.2004.09.004     Document Type: Article

References (45)

1. Attard, A., 2001. Marquage et caractérisation moléculaire de l'environnement génomique du gène d'avirulence AvrLm1 chez le champignon phytopathogène Leptosphaeria maculans. Ph.D. Thesis, INAPG, Paris
2. A. Attard, L. Gout, M. Gourgues, M.L. Kühn, J. Schmit, S. Laroche, D. Ansan-Melayah, A. Billault, L. Cattolico, M.H. Balesdent, and T. Rouxel Analysis of molecular markers genetically linked to the Leptosphaeria maculans avirulence gene AvrLm1 in field populations indicates a highly conserved event leading to virulence on Rlm1 genotypes Mol. Plant Microbe Interact. 2002 672 682
3. M.H. Balesdent, A. Attard, M.L. Kühn, and T. Rouxel New avirulence genes in the phytopathogenic fungus Leptosphaeria maculans Phytopathology 92 2002 1122 1133
4. M.H. Balesdent, M. Jedryczka, L. Jain, E. Mendes-Pereira, J. Bertrandy, and T. Rouxel Conidia as a substrate for internal transcribed spacer-based PCR identification of members of the Leptosphaeria maculans species complex Phytopathology 88 1998 1210 1217
5. M. Bibbins, N.J. Cummings, and I.F. Connerton DAB1: a degenerate retrotransposon-like element from Neurospora crassa Mol. Gen. Genet. 258 1998 431 436
6. E.B. Cambareri, B.C. Jensen, E. Schabtach, and E.U. Selker Repeat-induced G-C to A-T mutations in Neurospora Science 244 1989 1571 1575
7. E.B. Cambareri, R. Aisner, and J. Carbon Structure of the chromosome VII centromere region in Neurospora crassa: degenerate transposons and simple repeats Mol. Cell. Biol. 18 1998 5464 5477
8. F. Corpet Multiple sequence alignment with hierarchical clustering Nucleic Acids Res. 16 1988 10881 10890
9. M.-J. Daboussi, and P. Capy Transposable elements in filamentous fungi Annu. Rev. Microbiol. 57 2003 275 299
10. K.M. Devos, J.K.M. Brown, and J.L. Bennetzen Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis Genome Res. 12 2002 1075 1079
11. E.E. Eichler, and D. Sankoff Structural dynamics of eukaryotic chromosome evolution Science 301 2003 793 797
12. S.W. Emmons, B. Rosenzweig, and D. Hirsh Arrangement of repeated sequences in the DNA of the nematode Caenorhabditis elegans J. Mol. Biol. 144 1980 481 500
13. B. Ewing, and P. Green Base-calling of automated sequencer traces using Phred. II. Error probabilities Genome Res. 8 1998 186 194
14. J.E. Galagan, S.E. Calvo, K.A. Borkovich, E.U. Selker, N.D. Read, D. Jaffe, W. FitzHugh, L.J. Ma, S. Smirnov, S. Purcell, B. Rehman, T. Elkins, R. Engels, S. Wang, C.B. Nielsen, J. Butler, M. Endrizzi, D. Qui, P. Ianakiev, D. Bell-Pedersen, M.A. Nelson, M. Werner-Washburne, C.P. Selitrennikoff, J.A. Kinsey, E.L. Braun, A. Zelter, U. Schulte, G.O. Kothe, G. Jedd, W. Mewes, C. Staben, E. Marcotte, D. Greenberg, A. Roy, K. Foley, J. Naylor, N. Stange-Thomann, R. Barrett, S. Gnerre, M. Kamal, M. Kamvysselis, E. Mauceli, C. Bielke, S. Rudd, D. Frishman, S. Krystofova, C. Rasmussen, R.L. Metzenberg, D.D. Perkins, S. Kroken, C. Cogoni, G. Macino, D. Catcheside, W. Li, R.J. Pratt, S.A. Osmani, C.P.C. DeSouza, L. Glass, M.J. Orbach, J.A. Berglund, R. Voelker, O. Yarden, M. Plamann, S. Seiler, J. Dunlap, A. Radford, R. Aramayo, D.O. Natvig, L.A. Alex, G. Mannhaupt, D.J. Ebbole, M. Freitag, I. Paulsen, M.S. Sachs, E.S. Lander, C. Nusbaum, and B. Birren The genome sequence of the filamentous fungus Neurospora crassa Nature 422 2003 859 868
15. F. Graïa, O. Lespinet, B. Rimbault, M. Dequard-Chablat, E. Coppin, and M. Picard Genome quality control: RIP (repeat-induced point mutation) comes to Podospora Mol. Microbiol. 40 2001 586 595
16. W.S. Grayburn, and E.U. Selker A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication Mol. Cell. Biol. 9 1989 4416 4421
17. A. Houben, and I. Schubert DNA and proteins of plant centromeres Curr. Opin. Plant Biol. 6 2003 554 560
18. A. Hua-Van, F. Hericourt, P. Capy, M.J. Daboussi, and T. Langin Three highly divergent subfamilies of the impala transposable element coexist in the genome of the fungus Fusarium oxysporum Mol. Gen. Genet. 259 1998 354 362
19. M.J. Hynes The Neurospora crassa genome opens up the world of filamentous fungi Genome Biol. 4 2003 217.1 217.4
20. K. Ikeda, H. Nakayashiki, T. Kataoka, H. Tamba, Y. Hashimoto, Y. Tosa, and S. Mayama Repeat-induced point mutation (RIP) in Magnaporthe grisea: implications for its sexual cycle in the natural field context Mol. Microbiol. 45 2002 1355 1364
21. A. Idnurm, and B.J. Howlett Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans Fungal Genet. Biol. 39 2003 31 37
22. International Human Genome Sequencing Consortium, 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921
23. J. Jurka Repeats in genomic DNA: mining and meaning Curr. Opin. Struct. Biol. 8 1998 333 337
24. F. Kempken, and U. Kück Transposons in filamentous fungi-facts and perspectives BioEssays 20 1998 652 659
25. J.A. Kinsey, P.W. Garrett-Engele, E.B. Cambareri, and E.U. Selker The Neurospora transposon Tad is sensitive to repeat-induced point mutation Genetics 138 1994 657 664
26. S. Leclair, D. Ansan-Melayah, T. Rouxel, and M.-H. Balesdent Meiotic behaviour of the minichromosome in the phytopathogenic ascomycete Leptosphaeria maculans Curr. Genet. 30 1996 541 548
27. W. Makalowski Genomic scrap yard: how genomes utilize all that junk Gene 259 2000 61 67
28. H.S. Malik, and S. Henikoff Conflict begets complexity: the evolution of centromeres Curr. Opin. Genet. Dev. 12 2002 711 718
29. G. Mannhaupt, C. Montrone, D. Haase, H.W. Mewes, V. Aign, J.D. Hoheisel, B. Fartmann, G. Nyakatura, F. Kempken, J. Maier, and U. Schulte What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence Nucleic Acids Res. 31 2003 1944 1954
30. B.S. Margolin, P.W. Garrett-Engele, J.N. Stevens, D.Y. Fritz, C. Garrett-Engele, R.L. Metzenberg, and E.U. Selker A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation Genetics 149 1998 1787 1797
31. H. Nakayashiki, N. Nishimoto, K. Ikeda, Y. Tosa, and S. Mayama Degenerate MAGGY elements in a subgroup of Pyricularia grisea: a possible example of successful capture of a genetic invader by a fungal genome Mol. Gen. Genet. 261 1999 958 966
32. C. Neuvéglise, J. Sarfati, J.P. Latge, and S. Paris Afut1, a retrotransposon-like element from Aspergillus fumigatus Nucleic Acids Res. 24 1996 1428 1434
33. C. Neuvéglise, H. Feldmann, E. Bon, C. Gaillardin, and S. Casaregola Genomic evolution of the Long Terminal Repeat retrotransposons in Hemiascomycetous yeasts Genome Res. 12 2002 930 943
34. Nicholas, K.B., Nicholas, H.B., Deerfield, D.W., 1997. GeneDoc: analysis and visualization of genetic variation. EMBNEW.NEWS 4, 14
35. M.L. Nielsen, T.D. Hermansen, and A. Aleksenko A family of DNA repeats in Aspergillus nidulans has assimilated degenerated retrotransposon Mol. Genet. Genomics 256 2001 883 887
36. D.D. Perkins, B.S. Margolin, E.U. Selker, and S.D. Haedo Occurrence of Repeat Induced Point mutation in long segmental duplications of Neurospora Genetics 147 1997 125 136
37. K.M. Plummer, and B.J. Howlett Major chromosomal length polymorphisms are evident after meiosis in the phytopathogenic fungus Leptosphaeria maculans Curr. Genet. 24 1993 107 113
38. P. Silar, C. Barreau, R. Debuchy, S. Kicka, B. Turcq, A. Sainsard-Chaet, C. Sellem, A. Billault, L. Cattolico, S. Duprat, and J. Weissenbach Characterisation of the centromeric organisation of the region bordering the centromer of chromosome V of Podospora anserina by direct sequencing Fungal Genet. Biol. 39 2003 250 263
39. A.F. Smit The origin of interspersed repeats in the human genome Curr. Opin. Genet. Dev. 6 1996 743 748
40. J.L. Taylor, and I.E. Borgmann An unusual repetitive element from highly virulent isolates of Leptosphaeria maculans and evidence of its transfer to a weakly virulent isolate Mol. Plant Microbe Interact. 7 1994 181 188
41. J.L. Taylor, M.S.C. Pedras, and I.E. Borgmann Horizontal transfer in the phytopathogenic fungal genus Leptosphaeria and host range expansion Trends Microbiol. 3 1995 202 206
42. The Rice Chromosome 10 Sequencing Consortium, 2003. In-depth view of structure, activity and evolution of rice chromosome 10. Science 300, 1566-1569
43. C. Vitte, and O. Panaud Formation of solo-LTRs through unequal homologous recombination counterbalances amplification of LTR retrotransposons in rice Oryza sativa L Mol. Biol. Evol. 20 2003 528 540
44. M.K. Watters, and D.R. Stadler Spontaneous mutation during the sexual cycle of Neurospora crassa Genetics 139 1995 137 145
45. M.K. Watters, T.A. Randall, B.S. Margolin, E.U. Selker, and D.R. Stadler Action of Repeat-Induced Point mutation on both strands of a duplex and on tandem duplications of various sizes in Neurospora Genetics 153 1999 705 714