SSU rRNA reveals major trends in oomycete evolution

Fungal Diversity

Volumn 49, Issue , 2011, Pages 93-100

  Lara, Enrique ^a   Belbahri, Lassaad ^a  

^a UNIVERSITY OF NEUCHÂTEL   (Switzerland)

Author keywords

Albugo; Evolution; Oomycetes; Phylogeny; Phytophthora; Plant diseases; Pythium

Indexed keywords

ALBUGO; ANIMALIA; EUKARYOTA; OOMYCETES; PHYTOPHTHORA; PYTHIUM; STRAMENOPILES;

EID: 80051703735     PISSN: 15602745     EISSN: 18789129     Source Type: Journal    
DOI: 10.1007/s13225-011-0098-9     Document Type: Article

References (47)

1. AJ Alverson RK Jansen EC Theriot 2007 Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms Mol Phylogenet Evol 45 193 210 17553708 10.1016/j.ympev.2007.03.024 1:CAS:528:DC%2BD2sXhtVCmt7%2FE (Pubitemid 47381581)
2. Bass D, Cavalier-Smith T (2004) Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int J Syst Evol Microbiol 54:2393-2404 (Pubitemid 39585435)
3. Beakes GW (1981) Ultrastructural aspects of oospore differentiation. In: Hohl HR, Turian G (eds) The fungal spore: morphogenetic controls. Academic Press, London and New York, pp 71-94
4. Beakes GW, Sekimoto S (2009) The evolutionary phylogeny of Oomycetes-insights gained from studies of holocarpic parasites of algae and invertebrates. In: Lamour K, Kamoun S (eds) Oomycete genetics and genomics: diversity, interactions, and research tools. Wiley-Blackwell, London, pp 1-24
5. A Ben Ali R De Baere G Van der Auwera R De Wachter Y Van de Peer 2001 Phylogenetic relationships among algae based on complete large-subunit rRNA sequences Int J Syst Evol Microbiol 51 737 749 11411693 10.1099/00207713-51-3- 737 1:CAS:528:DC%2BD3MXks1Kitb0%3D (Pubitemid 32499274)
6. A Ben Ali R De Baere R De Wachter Y Van de Peer 2002 Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA Protist 153 123 132 12125754 10.1078/1434-4610-00091 1:CAS:528:DC%2BD38XmsVyisLk%3D (Pubitemid 34674224)
7. Berney C, Fahrni J, Pawlowski J (2004) How many novel eukaryotic kingdoms? Pitfalls and limitations of environmental DNA surveys. BMC Biology 2:1-13
8. Bessey EA (1942) Some problems in fungus phylogeny. Mycologia 34:355-379
9. J Brate D Klaveness T Rygh KS Jakobsen K Shalchian-Tabrizi 2010 Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations BMC Microbiology 10 168 20534135 10.1186/1471-2180-10-168
10. J Brate R Logares C Berney DK Ree D Klaveness KS Jakobsen K Shalchian-Tabrizi 2010 Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA ISME J 4 1144 1153 20393574 10.1038/ismej.2010.39 1:CAS:528:DC%2BC3cXhtVKgsr7L
11. T Cavalier-Smith EEY Chao 2006 Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista) J Mol Evol 62 388 420 16557340 10.1007/s00239-004-0353-8 1:CAS:528:DC%2BD28Xjt1CmtLg%3D
12. P Chomczynski N Sacchi 1987 Single-step method of RNA isolation by acid guanidium thiocyanate phenol chloroform extraction Anal Biochem 162 156 159 2440339 10.1016/0003-2697(87)90021-2 1:CAS:528:DyaL2sXitFSns7Y%3D (Pubitemid 17064313)
13. Cooke DEL, Drenth A, Duncan JM, Wagels G, Brasier CM (2000) A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet Microbiol 30:17-32 (Pubitemid 30666584)
14. A Duran M Gryzenhout A Drenth B Slippers R Ahumada BD Wingfield MJ Wingfield 2010 AFLP analysis reveals a clonal population of Phytophthora pinifolia in Chile Fungal Biol 114 746 752 20943184 10.1016/j.funbio.2010.06.008
15. CMM Gachon M Strittmatter DG Muller J Kleinteich FC Kupper 2009 Detection of differential host susceptibility to the marine oomycete pathogen Eurychasma dicksonii by real-time PCR: not all algae are equal Appl Environ Microbiol 75 322 328 19011072 10.1128/AEM.01885-08 1:CAS:528:DC%2BD1MXktlejs7Y%3D
16. SL Glockling GW Beakes 2006 An ultrastructural study of development and reproduction in the nematode parasite Myzocytiopsis vermicola Mycologia 98 1 15 16800299 10.3852/mycologia.98.1.1 (Pubitemid 43937663)
17. Göker M, Voglmayr H, Riethmuller A, Oberwinkler F (2007) How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews. Fungal Genet Biol 44:105-122
18. TA Hall 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symp Ser 41 95 98 1:CAS:528:DC%2BD3cXhtVyjs7Y%3D
19. HH Ho HS Chang SY Hsieh 1991 Halophytophthora kandeliae, a new marine fungus from Taiwan Mycologia 83 419 424 10.2307/3760352
20. Holzmann M, Habura A, Hannah G, Bowser SS, Pawlowski J (2003) Freshwater foraminiferans revealed by analysis of environmental DNA samples. J Eukaryot Microbiol 50:135-139 (Pubitemid 36524602)
21. DSS Hudspeth SA Nadler MES Hudspeth 2000 A COX2 molecular phylogeny of the peronosporomycetes Mycologia 92 674 684 10.2307/3761425 1:CAS:528: DC%2BD3cXlslCqurs%3D
22. G Jobb A von Haeseler K Strimmer 2004 TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics BMC Evol Biol 4 18 15222900 10.1186/1471-2148-4-18 (Pubitemid 40205271)
23. S Kamoun 2001 Nonhost resistance to Phytophthora: novel prospects for a classical problem Curr Opin Plant Biol 4 295 300 11418338 10.1016/S1369-5266(00) 00176-X 1:CAS:528:DC%2BD3MXksVykt7Y%3D (Pubitemid 32620711)
24. Kamoun S (2009). The secretome of plant-associated fungi and oomycetes. In 'Plant Relationships, 2nd Edition, The Mycota V' H. Deising (Ed.), Springer-Verlag Berlin Heidelberg
25. Karling JS (1942) The simple holocarpic biflagellate phycomycetes. Columbia University Press, New York
26. Lara E, Moreira D, López García P (2010) The environmental clade LKM11 and Rozella form the deepest branching clade of Fungi. Protist 161:116-121
27. Lara E, Mitchell EAD, Moreira D, López García P (2011) Highly diverse and seasonally dynamic protist community in a pristine peat bog. Protist 162:14-32
28. R Logares K Shalchian-Tabrizi A Boltovskoy K Rengefors 2007 Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions Mol Phylogenet Evol 45 887 903 17928239 10.1016/j.ympev.2007.08.005 1:CAS:528:DC%2BD2sXhtlajsr%2FI (Pubitemid 350102818)
29. Ludwig-Köhn H, Jahnke KD, Bahnweg G (1982) Sterol composition and sterol metabolism of Haliphthoros milfordensis and Atkinsiella dubia, fungal parasites of marine crustaceans. Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism 713:463-469
30. Massana R, Castresana J, Balague V, Guillou L, Romari K, Groisillier A, Valentin K, Pedro-Alio C (2004). Phylogenetic and ecological analysis of novel marine stramenopiles. App Environ Microbiol 70:3528-3534 (Pubitemid 38745900)
31. L Medlin HJ Elwood S Stickel ML Sogin 1988 The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions Gene 71 491 499 3224833 10.1016/0378-1119(88)90066-2 1:CAS:528:DyaL1MXovFyruw%3D%3D (Pubitemid 19010867)
32. L Mendoza JC Newton 2005 Immunology and immunotherapy of the infections caused by Pythium insidiosum Med Mycol 43 477 486 16320491 10.1080/ 13693780500279882 1:CAS:528:DC%2BD2MXhtV2htLrN (Pubitemid 41700940)
33. D Moreira P Lopez-Garcia K Vickerman 2004 An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea Int J Syst Evol Microbiol 54 1861 1875 15388756 10.1099/ijs.0.63081-0 1:CAS:528: DC%2BD2cXptVOltbo%3D (Pubitemid 39360009)
34. Petersen AB, Rosendahl S (2000) Phylogeny of the Peronosporomycetes (Oomycota) based on partial sequences of the large ribosomal subunit (LSU rDNA). Mycol Res 104:1295-1303 (Pubitemid 32102791)
35. AJ Phillips VL Anderson EJ Robertson CJ Secombes P van West 2008 New insights into animal pathogenic oomycetes Trends Microbiol 16 13 19 18096392 10.1016/j.tim.2007.10.013 1:CAS:528:DC%2BD1cXlvVKgsg%3D%3D
36. A Riethmuller H Voglmayr M Goker M Weiss F Oberwinkler 2002 Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences Mycologia 94 834 849 21156557 10.2307/3761698 (Pubitemid 36171580)
37. DM Rizzo M Garbelotto EA Hansen 2005 Phytophthora ramorum: Integrative research and management of an emerging pathogen in California and Oregon forests Annu Rev Phytopathol 43 309 335 16078887 10.1146/annurev.phyto.42.040803.140418 (Pubitemid 41318875)
38. F Rodriguez JL Oliver A Marin JR Medina 1990 The general stochastic-model of nucleotide substitution J Theor Biol 142 485 501 2338834 10.1016/S0022-5193(05)80104-3 1:CAS:528:DyaK3cXktlKksbY%3D
39. K Shalchian-Tabrizi J Brate R Logares D Klaveness C Berney KS Jakobsen 2008 Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny Environ Microbiol 10 2635 2644 18643928 10.1111/j.1462-2920.2008.01685.x 1:CAS:528:DC%2BD1cXht1CmurbF
40. Sparrow FK (1976) The present status of classification in biflagellate fungi. In: Gareth-Jones EB (ed) Recent advances in aquatic mycology. Elek Science, London, pp 213-222
41. Stamatakis, A., Hoover, P. and Rougemont, J., (2008). A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 57(5):758-771
42. M Thines S Kamoun 2010 Oomycete-plant coevolution: recent advances and future prospects Curr Opin Plant Biol 13 427 433 20447858 10.1016/j.pbi.2010.04. 001
43. S Uzuhashi M Tojo M Kakishima 2010 Phylogeny of the genus Pythium and description of new genera Mycoscience 51 337 365 10.1007/s10267-010-0046-7
44. AJ Van der Pläats-Niterink 1981 Monograph of the genus Pythium Studies in Mycology 21 1 242
45. P van West I de Bruijn KL Minor AJ Phillips EJ Robertson S Wawra J Bain VL Anderson CJ Secombes 2010 The putative RxLR effector protein SpHtp1 from the fish pathogenic oomycete Saprolegnia parasitica is translocated into fish cells FEMS Microbiol Lett 310 127 137 20659163 10.1111/j.1574-6968.2010.02055.x
46. Wolinska J, Giessler S, Koerner H (2009) Molecular identification and hidden diversity of novel daphnia parasites from European Lakes. Appl Environ Microbiol 75:7051-7059
47. WC Zattau T McInnis 1987 Life-Cycle and mode of infection of Leptolegnia chapmanii (oomycetes) parasitizing Aedes aegypti J Invertebr Pathol 50 134 145 3624894 10.1016/0022-2011(87)90113-3 1:STN:280:DyaL2szgvFyrsw%3D%3D