BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea

Fungal Genetics and Biology

Volumn 41, Issue 7, 2004, Pages 657-666

  Thon, Michael R ^a   Martin, Stanton L ^a   Goff, Stephen ^b   Wing, Rod A ^c   Dean, Ralph A ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b SYNGENTA BIOTECHNOLOGY INC   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; DNA TRANSPOSITION; FUNGAL GENETICS; GENE CLUSTER; GENE IDENTIFICATION; GENE LIBRARY; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENOME; MAGNAPORTHE GRISEA; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; RICE BLAST; TRANSPOSON; VALIDATION PROCESS;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, FUNGAL; DNA TRANSPOSABLE ELEMENTS; DNA, FUNGAL; GENE LIBRARY; GENOME, FUNGAL; MAGNAPORTHE; PHYSICAL CHROMOSOME MAPPING; POINT MUTATION; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

FUNGI; ILEX COOKII; MAGNAPORTHE; MAGNAPORTHE GRISEA;

EID: 2942591971     PISSN: 10871845     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fgb.2004.02.003     Document Type: Article

References (45)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402
2. Bartolomé C., Maside X., Charlesworth B. On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol. Biol. Evol. 19:2002;926-937
3. Borromeo E.S., Nelson R.J., Bonman J.M., Leung H. Genetic Differentiation among isolates of Pyricularia infecting rice and weed hosts. Phytopathology. 83:1993;393-399
4. Cambareri E.B., Jensen B.C., Schabtach E., Selker E.U. Repeat-induced G-C to A-T mutations in Neurospora. Science. 244:1989;1571-1575
5. Chalvet F., Grimaldi C., Kaper F., Langin T., Daboussi M.J. Hop, an active Mutator -like element in the genome of the fungus Fusarium oxysporum. Mol. Biol. Evol. 20:2003;1362-1375
6. Chao C.T., Ellingboe A.H. Selection for mating competence in Magnaporthe grisea pathogenic to rice. Can. J. Bot. 69:1991;2130-2134
7. Charlesworth B., Sniegowski P.D., Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature. 271:1994;215-220
8. Couch B.C., Kohn L.M. A multilocus gene genealogy concordant with host preference indicates segregation of a new species, Magnaporthe oryzae, from M. grisea. Mycologia. 94:2002;683-693
9. Daboussi M.J., Capy P. Transposable elements in filamentous fungi. Annu. Rev. Microbiol. 57:2003;275-299
10. Daboussi M.J., Daviere J.M., Graziani S., Langin T. Evolution of the FotI transposon in the genus Fusarium: discontinuous distribution and epigenetic inactivation. Mol. Biol. Evol. 19:2002;510-520
11. Dobinson K.F., Harris R.E., Hamer J.E. Grasshopper, a long terminal repeat (LTR) retroelement in the phytopathogenic fungus Magnaporthe grisea. Mol. Plant-Microbe. Interact. 6:1993;114-126
12. El Amrani A., Marie L., Ainouche A., Nicolas J., Couee I. Genome-wide distribution and potential regulatory functions of AtATE, a novel family of miniature inverted-repeat transposable elements in Arabidopsis thaliana. Mol. Genet. Genomics. 267:2002;459-471
13. Ewing B., Hillier L., Wendl M.C., Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:1998;175-178
14. ′ end of an inverted repeat transposon Mol. Gen. Genet. 251:1996;675-681
15. Farman M.L., Tosa Y., Nitta N., Leong S.A. MAGGY, a retrotransposon in the genome of the rice blast fungus Magnaporthe grisea. Mol. Gen. Genet. 251:1996;665-674
16. Graia F., Lespinet O., Rimbault B., Dequard-Chablat M., Coppin E., Picard M. Genome quality control: RIP (repeat-induced point mutation) comes to Podospora. Mol. Microbiol. 40:2001;586-595
17. Hamer J.E., Farrall L., Orbach M.J., Valent B., Chumley F.G. Host species-specific conservation of a family of repeated DNA sequences in the genome of a fungal plant pathogen. Proc. Natl. Acad. Sci. USA. 86:1989;9981-9985
18. Hua-Van A., Daviere J.M., Kaper F., Langin T., Daboussi M.J. Genome organization in Fusarium oxysporum: clusters of class II transposons. Curr. Genet. 37:2000;339-347
19. Ikeda K., Nakayashiki H., Kataoka T., Tamba H., Hashimoto Y., Tosa Y., Mayama S. Repeat-induced point mutation (RIP) in Magnaporthe grisea: implications for its sexual cycle in the natural field context. Mol. Microbiol. 45:2002;1355-1364
20. Irelan J.T., Selker E.U. Gene silencing in filamentous fungi: RIP, MIP and quelling. J. Genet. 75:1996;313-324
21. Kachroo P., Leong S.A., Chattoo B.B. Pot2, an inverted repeat transposon from the rice blast fungus Magnaporthe grisea. Mol. Gen. Genet. 245:1994;339-348
22. Kachroo P., Leong S.A., Chattoo B.B. Mg-SINE - a short interspersed nuclear-element from the rice blast fungus, Magnaporthe grisea. Proc. Natl. Acad. Sci. USA. 92:1995;11125-11129
23. Kang S. Organization and distribution pattern of MGLR-3, a novel retrotransposon in the rice blast fungus Magnaporthe grisea. Fungal Genet. Biol. 32:2001;11-19
24. Kang S.C., Sweigard J.A., Valent B. The PWL host specificity gene family in the blast fungus Magnaporthe grisea. Mol. Plant-Microbe Interact. 8:1995;939-948
25. Kang S., Lebrun M.H., Farrall L., Valent B. Gain of virulence caused by insertion of a Pot3 transposon in a Magnaporthe grisea avirulence gene. Mol. Plant-Microbe. Interact. 14:2001;671-674
26. Kidwell M.G., Lisch D. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA. 94:1997;7704-7711
27. Lau G.W., Chao C.T., Ellingboe A.H. Interaction of genes controlling avirulence/virulence of Magnaporthe grisea on rice cultivar Katy. Phytopathology. 83:1993;375-382
28. Mao L., Wood T., Yu Y., Budiman M.A., Tomkins J., Woo S.-s., Sasinowski M., Presting G., Frisch D., Goff S., Dean R.A., Wing R.A. Rice transposable elements: a survey of 73, 000 sequence-tagged-connectors. Genome Res. 10:2000;982-990
29. Martin S.L., Blackmon B.P., Rajagopalan R., Houfek T.D., Sceeles R.G., Denn S.O., Mitchell T.K., Brown D.E., Wing R.A., Dean R.A. MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea. Nucleic Acids Res. 30:2002;121-124
30. Nakayashiki H., Kiyotomi K., Tosa Y., Mayama S. Transposition of the retrotransposon MAGGY in heterologous species of filamentous fungi. Genetics. 153:1999;693-703
31. Nakayashiki H., Nishimoto N., Ikeda K., Tosa Y., Mayama S. 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. Nakayashiki H., Matsuo H., Chuma I., Ikeda K., Betsuyaku S., Kusaba M., Tosa Y., Mayama S. Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea contains an extra domain between the nucleocapsid and protease domains. Nucleic Acids Res. 29:2001;4106-4113
33. Nishimura M., Nakamura S., Hayashi N., Asakawa S., Shimizu N., Kaku H., Hasebe A., Kawasaki S. Construction of a BAC library of the rice blast fungus Magnaporthe grisea and finding specific genome regions in which its transposons tend to cluster. Biosci. Biotechnol. Biochem. 62:1998;1515-1521
34. Nishimura M., Nakamura S., Hayashi N., Masuya M., Asakawa S., Shimizu N., Kaku H., Hasebe A., Kawasaki S. Analysis of transposable-element clustering patterns in Magnaporthe grisea genome using BAC library. Tharreau D. Advances in Rice Blast Research. 2000;316-322 Kluwer Academic Publishers, The Netherlands
35. Nitta N., Farman M.L., Leong S.A. Genome organization of Magnaporthe grisea: integration of genetic maps, clustering of transposable elements and identification of genome duplications and rearrangements. Theor. Appl. Genet. 95:1997;20-32
36. ′ sequences: A review Gene. 205:1997;229-243
37. Ou S.H. Rice Diseases. 1987;Commonwealth Mycological Institute, Surrey
38. Pearson W.R. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 2000;185-219
39. Raina S., Mahalingam R., Chen F.Q., Fedoroff N. A collection of sequenced and mapped Ds transposon insertion sites in Arabidopsis thaliana. Plant Mol. Biol. 50:2002;93-110
40. Shull V., Hamer J.E. Genetic differentiation in the rice blast fungus revealed by the distribution of the Fosbury retrotransposon. Fungal Genet. Biol. 20:1996;59-69
41. Singleton T.L., Levin H.L. A long terminal repeat retrotransposon of fission yeast has strong preferences for specific sites of insertion. Eukaryot. Cell. 1:2002;44-55
42. Skinner D.Z., Budde A.D., Farman M.L., Smith J.R., Leung H., Leong S.A. Genome organization of Magnaporthe grisea - genetic map, electrophoretic karyotype, and occurrence of repeated DNAs. Theor. Appl. Genet. 87:1993;545-557
43. Sone T., Suto M., Tomita F. Host species specific repetitive DNA sequence in the genome of Magnaporthe grisea, the rice blast fungus. Biosci. Biotechnol. Biochem. 57:1993;1228-1230
44. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680
45. Zhu H., Choi S.D., Johnston A.K., Wing R.A., Dean R.A. A large-insert (130. kbp) bacterial artificial chromosome library of the rice blast fungus Magnaporthe grisea: genome analysis, contig assembly, and gene cloning Fungal Genet. Biol. 21:1997;337-347