Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals

Fungal Genetics and Biology

Volumn 43, Issue 9, 2006, Pages 655-666

  Bakkeren, Guus ^a   Jiang, Guoqiao ^b   Warren, René L ^c   Butterfield, Yaron ^c   Shin, Heesun ^c   Chiu, Readman ^c   Linning, Rob ^a   Schein, Jacqueline ^c   Lee, Nancy ^b   Hu, Guanggan ^b   Kupfer, Doris M ^d   Tang, Yuhong ^d   Roe, Bruce A ^d   Jones, Steven ^c   Marra, Marco ^c   Kronstad, James W ^b  

^a SUMMERLAND RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c BRITISH COLUMBIA CANCER AGENCY   (Canada)

^d UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

BAC mapping; MAT locus; Retrotransposons; rRNA unit; Sex chromosome; Ustilago hordei

Indexed keywords

FUNGAL DNA; REPETITIVE DNA;

ARTICLE; BASIDIOMYCETES; CEREAL; CONTROLLED STUDY; FUNGAL GENE; GENE CLUSTER; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC LINKAGE; GENETIC RECOMBINATION; GENOME ANALYSIS; MATING SYSTEM; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROPOSON; SEQUENCE HOMOLOGY; SEXUAL BEHAVIOR; USTILAGO; USTILAGO HORDEI; USTILAGO MAYDIS;

CEREALS; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENES, MATING TYPE, FUNGAL; GENOME, FUNGAL; LINKAGE (GENETICS); PHEROMONES; PHYSICAL CHROMOSOME MAPPING; PLANT DISEASES; RETROELEMENTS; SEX DETERMINATION (GENETICS); TANDEM REPEAT SEQUENCES; USTILAGO;

USTILAGO; USTILAGO HORDEI; USTILAGO MAYDIS;

EID: 33746851583     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2006.04.002     Document Type: Article

References (49)

1. Abdennadher M., and Mills D. Telomere-associated RFLPs and electrophoretic karyotyping reveal lineage relationships among race-specific strains of Ustilago hordei. Curr. Genet. 38 (2000) 141-147
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST, a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Anderson C.M., Willits D.A., Kosted P.J., Ford E.J., Martinez-Espinoza A.D., and Sherwood J.E. Molecular analysis of the pheromone and pheromone receptor genes of Ustilago hordei. Gene 240 (1999) 89-97
4. Anderson O.D., Rausch C., Moullet O., and Lagudah E.S. The wheat D-genome HMW-glutenin locus, BAC sequencing, gene distribution, and retrotransposon clusters. Funct. Integr. Genomics 3 (2003) 56-68
5. Arkhipova I., and Meselson M. Deleterious transposable elements and the extinction of asexuals. Bioessays 27 (2005) 76-85
6. Bakkeren G., Gibbard B., Yee A., Froeliger E., Leong S., and Kronstad J. The a and b loci of Ustilago maydis hybridize with DNA sequences from other smut fungi. Mol. Plant Microbe Interact. 5 (1992) 347-355
7. Bakkeren G., and Kronstad J.W. Conservation of the b mating-type gene complex among bipolar and tetrapolar smut fungi. Plant Cell 5 (1993) 123-136
8. Bakkeren G., and Kronstad J.W. Linkage of mating-type loci distinguishes bipolar from tetrapolar mating in basidiomycetous smut fungi. Proc. Natl. Acad. Sci. USA 91 (1994) 7085-7089
9. Bakkeren G., and Kronstad J.W. The pheromone cell signaling components of the Ustilago a mating-type loci determine intercompatibility between species. Genetics 143 (1996) 1601-1613
10. Bolker M., Urban M., and Kahmann R. The a mating type locus of Ustilago maydis specifies cell signaling components. Cell 68 (1992) 441-450
11. Borkovich K.A., Alex L.A., Yarden O., Freitag M., Turner G.E., Read N.D., Seiler S., Bell-Pedersen D., Paietta J., Plesofsky N., et al. Lessons from the genome sequence of Neurospora crassa, tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev. 68 (2004) 1-108
12. Charlesworth B., and Langley C.H. The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23 (1989) 251-287
13. Erlandsson R., Wilson J.F., and Paabo S. Sex chromosomal transposable element accumulation and male-driven substitutional evolution in humans. Mol. Biol. Evol. 17 (2000) 804-812
14. Feldbrugge M., Kamper J., Steinberg G., and Kahmann R. Regulation of mating and pathogenic development in Ustilago maydis. Curr. Opin. Microbiol. 7 (2004) 666-672
15. Fisher G.W., and Holton C.S. Biology and Control of the Smut Fungi (1957), Ronald Press, New York
16. Fraser J.A., Diezmann S., Subaran R.L., Allen A., Lengeler K.B., Dietrich F.S., and Heitman J. Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. PLoS Biol. 2 (2004) e384
17. Fraser J.A., and Heitman J. Chromosomal sex-determining regions in animals, plants and fungi. Curr. Opin. Genet. Dev. 15 (2005) 645-651
18. Fuhrmann D.R., Krzywinski M.I., Chiu R., Saeedi P., Schein J.E., Bosdet I.E., Chinwalla A., Hillier L.W., Waterston R.H., McPherson J.D., et al. Software for automated analysis of DNA fingerprinting gels. Genome Res. 13 (2003) 940-953
19. Galagan J.E., Calvo S.E., Cuomo C., Ma L.J., Wortman J.R., Batzoglou S., Lee S.I., Basturkmen M., Spevak C.C., Clutterbuck J., et al. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438 (2005) 1105-1115
20. Gaudet D.A., and Kiesling R.L. Variation in aggressiveness among and within races of Ustilago hordei on barley. Phytopathology 81 (1991) 1385-1390
21. Gaudet D.A., Gusse J., and Laroche A. Origins and inheritance of chromosome-length polymorphisms in the barley covered smut fungus, Ustilago hordei. Curr. Genet. 33 (1998) 216-224
22. Green P. Ancient conserved regions in gene sequences. Curr. Opin. Struct. Biol. 4 (1994) 404-412
23. Hood M.E. Dimorphic mating-type chromosomes in the fungus Microbotryum violaceum. Genetics 160 (2002) 457-461
24. Hood M.E. Repetitive DNA in the automictic fungus Microbotryum violaceum. Genetica 124 (2005) 1-10
25. Hu G.G., Linning R., and Bakkeren G. Sporidial mating and infection process of the smut fungus, Ustilago hordei, in susceptible barley. Can. J. Bot. 80 (2002) 1103-1114
26. Hull C.M., and Johnson A.D. Identification of a mating type-like locus in the asexual pathogenic yeast Candida albicans. Science 285 (1999) 1271-1275
27. Kahmann R., and Kamper J. Ustilago maydis, how its biology relates to pathogenic development. New Phytol. 164 (2004) 31-42
28. Kronstad J.W., and Staben C. Mating type in filamentous fungi. Annu. Rev. Genet. 31 (1997) 245-276
29. Lahn B.T., and Page D.C. Four evolutionary strata on the human X chromosome. Science 286 (1999) 964-967
30. Lee N., Bakkeren G., Wong K., Sherwood J.E., and Kronstad J.W. The mating-type and pathogenicity locus of the fungus Ustilago hordei spans a 500-kb region. Proc. Natl. Acad. Sci. USA 96 (1999) 15026-15031
31. Lengeler K.B., and Kothe E. Mated, a putative peptide transporter of Schizophyllum commune expressed in dikaryons. Curr. Genet. 36 (1999) 159-164
32. Lengeler K.B., Fox D.S., Fraser J.A., Allen A., Forrester K., Dietrich F.S., and Heitman J. Mating-type locus of Cryptococcus neoformans, A step in the evolution of sex chromosomes. Eukaryotic Cell 1 (2002) 704-718
33. Linning R., Lin D., Lee N., Abdennadher M., Gaudet D., Thomas P., Mills D., Kronstad J.W., and Bakkeren G. Marker-based cloning of the region containing the UhAvr1 avirulence gene from the basidiomycete barley pathogen Ustilago hordei. Genetics 166 (2004) 99-111
34. Loftus B.J., Fung E., Roncaglia P., Rowley D., Amedeo P., Bruno D., Vamathevan J., Miranda M., Anderson I.J., Fraser J.A., et al. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307 (2005) 1321-1324
35. Ma B., Tromp J., and Li M. PatternHunter, faster and more sensitive homology search. Bioinformatics 18 (2002) 440-445
36. Majoros W.H., Pertea M., Antonescu C., and Salzberg S.L. GlimmerM, Exonomy and Unveil, three ab initio eukaryotic genefinders. Nucleic Acids Res. 31 (2003) 3601-3604
37. Marra M.A., Kucaba T.A., Dietrich N.L., Green E.D., Brownstein B., Wilson R.K., McDonald K.M., Hillier L.W., McPherson J.D., and Waterston R.H. High throughput fingerprint analysis of large-insert clones. Genome Res. 7 (1997) 1072-1084
38. Marra M., Kucaba T., Sekhon M., Hillier L., Martienssen R., Chinwalla A., Crockett J., Fedele J., Grover H., Gund C., et al. A map for sequence analysis of the Arabidopsis thaliana genome. Nat. Genet. 22 (1999) 265-270
39. McCluskey K., and Mills D. Identification and characterization of chromosome length polymorphisms among strains representing fourteen races of Ustilago hordei. Mol. Plant Microbe Interact. 3 (1990) 366-373
40. McCluskey K., Agnan J., and Mills D. Characterization of genome plasticity in Ustilago hordei. Curr. Genet. 26 (1994) 486-493
41. McPherson J.D., Marra M., Hillier L., Waterston R.H., Chinwalla A., Wallis J., Sekhon M., Wylie K., Mardis E.R., Wilson R.K., et al. A physical map of the human genome. Nature 409 (2001) 934-941
42. Ramakrishna W., Dubcovsky J., Park Y.J., Busso C., Emberton J., SanMiguel P., and Bennetzen J.L. Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162 (2002) 1389-1400
43. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A., and Barrell B. Artemis, sequence visualization and annotation. Bioinformatics 16 (2000) 944-945
44. Salamov A.A., and Solovyev V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10 (2000) 516-522
45. Schein J.E., Tangen K.L., Chiu R., Shin H., Lengeler K.B., MacDonald W.K., Bosdet I., Heitman J., Jones S.J., Marra M.A., et al. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 12 (2002) 1445-1453
46. Schirawski J., Heinze B., Wagenknecht M., and Kahmann R. Mating type loci of Sporisorium reilianum, novel pattern with three a and multiple b specificities. Euk. Cell 4 (2005) 1317-1327
47. Stoll M., Begerow D., and Oberwinkler F. Molecular phylogeny of Ustilago, Sporisorium, and related taxa based on combined analyses of rDNA sequences. Mycol. Res. 109 (2005) 342-356
48. Thompson J.D., Higgins D.G., and Gibson T.J. ClustalW, improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
49. Urban M., Kahmann R., and Bolker M. The biallelic a mating type locus of Ustilago maydis, remnants of an additional pheromone gene indicate evolution from a multiallelic ancestor. Mol. Gen. Genet. 250 (1996) 414-420