Identification and occurrence of the LTR-Copia-like retrotransposon, PSCR and other Copia-like elements in the genome of Phytophthora sojae

Current Genetics

Volumn 55, Issue 5, 2009, Pages 521-536

  Basnayake, Shiromi ^a   Maclean, Donald J ^a   Whisson, Stephen C ^b   Drenth, Andre ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

Homologs; Linkage maps; O mycetes; Phytophthora infestans; Phytophthora ramorum; Transposable elements

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMINO ACID SEQUENCE; CODON USAGE; CONTROLLED STUDY; COPIA LIKE RETROTRANSPOSON; EVOLUTIONARY HOMOLOGY; FUNGAL GENOME; FUNGAL VIRULENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC HETEROGENEITY; GENETIC IDENTIFICATION; GENETIC LINKAGE; GENETIC VARIABILITY; INTROGRESSION; LONG TERMINAL REPEAT; NONHUMAN; OPEN READING FRAME; PHYLOGENETIC TREE; PHYTOPHTHORA; PHYTOPHTHORA INFESTANS; PHYTOPHTHORA RAMORUM; PHYTOPHTHORA SOJAE; PRIORITY JOURNAL; RETROPOSON; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES COMPARISON; SPECIES DIFFERENCE;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA PRIMERS; DNA, RECOMBINANT; EXPRESSED SEQUENCE TAGS; FUNGAL PROTEINS; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYTOPHTHORA; RETROELEMENTS; SEQUENCE HOMOLOGY, AMINO ACID;

GLYCINE MAX; OOMYCETES; PHYTOPHTHORA; PHYTOPHTHORA INFESTANS; PHYTOPHTHORA RAMORUM; PHYTOPHTHORA SOJAE;

EID: 70349991283     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-009-0263-9     Document Type: Review

References (45)

1. Bhattacharyya MK, Gonzales RA, Kraft M, Buzzell RI (1997) A Copia-like retrotransposon Tgmr closely linked to the Rps1-k allele that confers race-specific resistance of soybean to Phytophthora sojae. Plant Mol Biol 34:255-264
2. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497-3500
3. Clare J, Farabaugh P (1985) Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression. Proc Natl Acad Sci USA 82:2829-2833
4. Doolittle RF, Feng DF, Johnson MS, McClure MA (1989) Origins and the evolutionary relationships of retroviruses. Q Rev Biol 64:1-30
5. Dorrance AE, Schmitthenner AF (2000) New sources of resistance to Phytophthora sojae in the soybean plant introductions. Plant Dis 84:1303-1308
6. Drenth A, Whisson SC, Maclean DJ, Irwin JAG, Obst NR, Ryley MJ (1996) The evolution of races of Phytophthora sojae in Australia. Phytopathology 86:163-169
7. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1-Copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 20:3639-3644
8. Flavell AJ, Pearce SR, Heslop-Harrison JS, Kumar A (1997) The evolution of Ty1-Copia group retrotransposons in eukaryote genomes. Genetica 100:185-195
9. Förster H, Tyler BM, Coffey MD (1994) Phytophthora sojae races have arisen by clonal evolution and rare outcrosses. Mol Plant Microbe Interact 7:780-791
10. Grandbastien MA (1998) Activation of plant retrotransposons under stress conditions. Trends Plant Sci 3:181-187
11. Grandbastien MA, Spielmann A, Caboche M (1989) Tnt1: A mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337:376-380
12. Huitema E, Vleeshouwers VGAA, Francis DM, Kamoun S (2003) Active defence responses associated with non-host resistance of Arabidopsis thaliana to the oömycete pathogen Phytophthora infestans. Mol Plant Pathol 4:487-500
13. Jiang RHY, Govers F (2006) Nonneutral GC3 and retroelement codon mimicry in Phytophthora. J Mol Evol 63:458-472
14. Jiang RHY, Dawe AL, Weide R, van Staveren M, Peters S, Nuss DL, Govers F (2005) Elicitin genes in Phytophthora infestans are clustered and interspersed with various transposon-like elements. Mol Genet Genomics 273:20-32
15. Judelson HS (2002) Sequence variation and genomic amplification of a family of Gypsy-like elements in the oömycete genus Phytophthora. Mol Biol Evol 19:1313-1322
16. Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy AH, Schulman AH (2004) Large retrotransposon derivatives: Abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166:1437-1450
17. Katoh IT, Yasunaga T, Ikawa Y, Yoshinaga Y (1987) Inhibition of retroviral protease activity by an aspartyl proteinase inhibitor. Nature 329:654-656
18. Kikuchi Y, Ando Y, Shiba T (1986) Unusual priming mechanism of RNA-directed DNA synthesis in Copia retrovirus-like particles of Drosophila. Nature 323:824-826
19. Leong SA, Farman ML, Smith J, Budde A, Tosa Y, Nitta N (1994) Molecular genetic approach to the study of cultivar specificity in the rice blast fungus. In: Zeigler RS, Leong SA, Teng PS (eds) Rice blast disease. CAB International, Wallingford, pp 87-110
20. May KJ, Whisson SC, Zwart RS, Searle IR, Irwin JAG, Maclean DJ, Carrol BJ, Drenth A (2002) Inheritance and mapping of eleven avirulence genes in Phytophthora sojae. Fungal Genet Biol 37:1-12
21. McHale MT, Roberts IN, Noble SM, Beaumont C, Whitehead MP, Seth D, Oliver RP (1992) CfT-1: An LTR-retrotransposon in Cladosporium fulvum, a fungal pathogen of tomato. Mol Gen Genet 233:337-347
22. Mount SM, Rubin GM (1985) Complete nucleotide sequence of the Drosophila transposable element Copia: Homology between Copia and retroviral proteins. Mol Cell Biol 5:1630-1638
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. Nuchprayoon I, Meyers S, Scott L, Suzow J, Hiebert S, Friedman A (1994) Pebp2/Cbf, the murine homolog of the human myeloid Aml1 and Pebp2-Beta/ Cbf-Beta Proto-Oncoproteins, regulates the murine myeloperoxidase and neutrophil elastase genes in immature myeloid cells. Mol Cell Biol 14:5558-5568
25. Pelsy F, Merdinoglu D (2002) Complete sequence of Tvv1, a family of Ty1 Copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking. Theor Appl Genet 105:614-621
26. Qutob D, Hraber PT, Sobral BWS, Gijzen M (2000) Comparative analysis of expressed sequences in Phytophthora sojae. Plant Physiol 123:243-253
27. Rawson JM (2000) Transposable elements in the phytopathogenic fungus Stagonospora nodorum. Ph.D. thesis, School of Biosciences, The University of Birmingham, Edgbaston
28. Ryley MJ, Obst NR, Irwin JAG, Drenth A (1998) Changes in the racial composition Phytophthora sojae in Australia between 1979 and 1996. Plant Dis 82:1048-1054
29. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
30. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768
31. Shaw DS (1988) The Phytophthora Species. In: Sidhu GS (ed) Advances in plant pathology: Genetics of plant pathogenic fungi, vol 6. Academic, London, pp 27-51
32. Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503-517
33. Springer MS, Tusneem NA, Davidson EH, Britten RJ (1995) Phylogeny, rates of evolution, and patterns of codon usage among Sea-Urchin retroviral-like elements, with implications for the recognition of horizontal transfer. Mol Biol Evol 12:219-230
34. Tooley PW, Garfinkel DJ (1996) Presence of Ty1-Copia group retrotransposon sequences in the potato late blight pathogen Phytophthora infestans. Mol Plant Microbe Interact 9:305-309
35. Tooley PW, Carras MM, Falkenstein KF (1996) Relationships among group IV Phytophthora species inferred by restriction analysis of the ITS2 region. J Phytopathol 144:363-369
36. Tripathy S, Pandey VN, Fang B, Salas F, Tyler BM (2006) VMD: A community annotation database for microbial genomes. Nucleic Acids Res 34:379-381
37. Tyler BM, Förster H, Coffey MD (1995) Inheritance of avirulence factors and RFLP markers in outcrosses of the oömycete Phytophthora sojae. Mol Plant Microbe Interact 8:515-523
38. Varmus H, Brown P (1989) Retroviruses. In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington DC, pp 53-108
39. Vershinin AV, Ellis THN (1999) Heterogeneity of the internal structure of PDR1, a family of Ty1/Copia-like retrotransposons. Mol Gen Genet 262:703-713
40. Whisson SC, Drenth A, Maclean DJ, Irwin JAG (1994) Evidence for outcrossing in Phytophthora sojae and linkage of a DNA marker to two avirulence genes. Curr Genet 27:77-82
41. Whisson SC, Drenth A, Maclean DJ, Irwin JAG (1995) Phytophthora sojae avirulence genes, RAPD and RFLP markers used to construct a detailed genetic linkage map. Mol Plant Microbe Interact 8:988-995
42. Whisson SC, Basnayake S, Maclean DJ, Irwin JAG, Drenth A (2004) Phytophthora sojae avirulence genes Avr4 and Avr6 are located in a 24 kb, recombination-rich region of genomic DNA. Fungal Genet Biol 41:62-74
43. Wilhelm M, Wilhelm FX (2001) Reverse transcription of retroviruses and LTR retrotransposons. Cell Mol Life Sci 58:1246-1262
44. Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based on their reverse transcriptase sequences. EMBO J 9:3353-3362
45. Zhang X, Scheuring C, Tripathy S, Xu Z, Wu C, Ko A, Ken Tian S, Arredondo F, Lee MK, Santos FA, Jiang RHY, Zhang HB, Tyler BM (2006) An Integrated BAC and genome sequence physical map of Phytophthora sojae. Mol Plant Microbe Interact 19:1302-1310