Nonneutral GC3 and retroelement codon mimicry in Phytophthora

Journal of Molecular Evolution

Volumn 63, Issue 4, 2006, Pages 458-472

  Jiang, Rays H Y ^a   Govers, Francine ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Codon bias; GC3; Phytophthora; Retrotransposon

Indexed keywords

ARTICLE; CODON; GENE EXPRESSION; GENE MUTATION; PHYTOPHTHORA; RETROPOSON;

BASE COMPOSITION; CODON; GENE DOSAGE; GENES, PLANT; MOLECULAR MIMICRY; MUTATION; OPEN READING FRAMES; PHYLOGENY; PHYTOPHTHORA; RETROELEMENTS;

ANIMALIA; EUKARYOTA; FUNGI; PHYTOPHTHORA; STRAMENOPILES;

EID: 33750239979     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0211-3     Document Type: Article

References (47)

1. Ah Fong AM, Judelson HS (2004) The hAT -like DNA transposon DodoPi resides in a cluster of retro- and DNA transposons in the stramenopile Phytophthora infestans. Mol Genet Genomics 271:577-585
2. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Alvarez-Valin F, Lamolle G, Bernardi G (2002) Isochores, GC3 and mutation biases in the human genome. Gene 300:161-168
4. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou SG, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WWY, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:79-86
5. Baldauf SL (2003) The deep roots of eukaryotes. Science 300:1703-1706
6. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977
7. Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251-269
8. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953-958
9. Bowman S, Lawson D, Basham D, Brown D, Chillingworth T, Churcher CM, Craig A, Davies RM, Devlin K, Feltwell T, Gentles S, Gwilliam R, Hamlin N, Harris D, Holroyd S, Hornsby T, Horrocks P, Jagels K, Jassal B, Kyes S, McLean J, Moule S, Mungall K, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutter S, Skelton J, Squares R, Squares S, Sulston JE, Whitehead S, Woodward JR, Newbold C, Barrell BG (1999) The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400:532-538
10. Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci USA 101:3480-3485
11. Cooke DE, Drenth A, Duncan JM, Wagels G, Brasier CM (2000) A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet Biol 30:17-32
12. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu JR, Pan H, Read ND, Lee YH, Carbone I, Brown D, Oh YY, Donofrio N, Jeong JS, Soanes DM, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun MH, Bohnert H, Coughlan S, Butler J, Calvo S, Ma LJ, Nicol R, Purcell S, Nusbaum C, Galagan JE, Birren BW (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434:980-986
13. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA 96:4482-4487
14. Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, Van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Babu MM, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43-57
15. Erwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide American Phytopathological Society, St. Paul, MN
16. Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, vanVugt R, Palmer N, Adams MD, Gocayne J, Weidman J, Utterback T, Watthey L, McDonald L, Artiach P, Bowman C, Garland S, Fujii C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580-586
17. Gajendran K, Gonzales MD, Farmer A, Archuleta E, Win J, Waugh ME, Kamoun S (2006) Phytophthora functional genomics database (PFGD): functional genomics of Phytophthora-plant interactions. Nucleic Acids Res 34:D465-D470
18. Hraber PT, Weller JW (2001) On the species of origin: diagnosing the source of symbiotic transcripts. Genome Biol 2:37
19. Ishikawa J, Hotta K (1999) FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G + C content. FEMS Microbiol Lett 174:251-253
20. 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
21. Judelson HS (2002) Sequence variation and genomic amplification of a family of gypsy-like elements in the oomycete genus Phytophthora. Mol Biol Evol 19:1313-1322
22. Kamoun S, Hraber P, Sobral B, Nuss D, Govers F (1999) Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences. Fungal Genet Biol 28:94-106
23. Kanaya S, Yamada Y, Kudo Y, Ikemura T (1999) Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238:143-155
24. Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303:1626-1632
25. Kidwell MG, Lisch DR (2001) Perspective: transposable elements, parasitic DNA, and genome evolution. Evolut Int J Org Evolut 55:1-24
26. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245
27. Labrador M, Corces VG (1997) Transposable element-host interactions: regulation of insertion and excision. Annu Rev Genet 31:381-404
28. Latijnhouwers M, de Wit PJGM, Govers F (2003) Oomycetes and fungi: similar weaponry to attack plants. Trends Microbiol 11:462-469
29. Lerat E, Capy P, Biemont C (2002) Codon usage by transposable elements and their host genes in five species. J Mol Evol 54:625-637
30. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302:1401-1404
31. Margulis L, Schwarts KV (2000) Five kingdoms: an illustrated guide to the phyla of life on earth. W.H. Freeman, New York
32. McLeod A, Smart CD, Fry WE (2004) Core promoter structure in the oomycete Phytophthora infestans. Eukaryot Cell 3:91-99
33. Nekrutenko A, Li W-H (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet 17:619-621
34. Qutob D, Hraber PT, Sobral BWS, Gijzen M (2000) Comparative analysis of expressed sequences in Phytophthora sojae. Plant Physiol 123:243-253
35. Randall TA, Dwyer RA, Huitema E, Beyer K, Cvitanich C, Kelkar H, Fong AM, Gates K, Roberts S, Yatzkan E, Gaffney T, Law M, Testa A, Torto-Alalibo T, Zhang M, Zheng L, Mueller E, Windass J, Binder A, Birch PR, Gisi U, Govers F, Gow NA, Mauch F, van West P, Waugh ME, Yu J, Boller T, Kamoun S, Lam ST, Judelson HS (2005) Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Mol Plant Microbe Interact 18:229-243
36. Rizzo DM, Garbelotto M, Hansen EM (2005) Phytophthora ramorum: integrative research and management of an emerging pathogen in California and Oregon forests. Annu Rev Phytopathol 43:309-335
37. Sandhu D, Gill KS (2002) Gene-containing regions of wheat and the other grass genomes. Plant Physiol 128:803-811
38. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nature Genet 20:43-45
39. Scala S, Carels N, Falciatore A, Chiusano ML, Bowler C (2002) Genome properties of the diatom Phaeodactylum tricornutum. Plant Physiol 129:993-1002
40. Sharp PM, Li WH (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24:28-38
41. Sharp PM, Stenico M, Peden JF, Lloyd AT (1993) Codon usage: Mutational bias, translational selection, or both? Biochem Soc Trans 21:835-841
42. Soanes DM, Skinner W, Keon J, Hargreaves J, Talbot NJ (2002) Genomics of phytopathogenic fungi and the development of bioinformatic resources. Mol Plant Microbe Interact 15:421-427
43. Sueoka N (1995) Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol 40:318-325
44. Sueoka N (1999) Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A = T and G = C. J Mol Evol 49:49-62
45. Sueoka N, Kawanishi Y (2000) DNA G + C content of the third codon position and codon usage biases of human genes. Gene 261:53-62
46. Topp CN, Zhong CX, Dawe RK (2004) Centromere-encoded RNAs are integral components of the maize kinetochore. Proc Natl Acad Sci USA 101:15986-15991
47. Zsiros J, Jebbink MF, Lukashov VV, Voute PA, Berkhout B (1999) Biased nucleotide composition of the genome of HERV-K related endogenous retroviruses and its evolutionary implications. J Mol Evol 48:102-111