SSU rRNA reveals major trends in oomycete evolution

Alverson AJ, Jansen RK, Theriot EC (2007) Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Mol Phylogenet Evol 45:193–210 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 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 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 Ben Ali A, De Baere R, Van der Auwera G, De Wachter R, Van de Peer Y (2001) Phylogenetic relationships among algae based on complete large-subunit rRNA sequences. Int J Syst Evol Microbiol 51:737–749 Ben Ali A, De Baere R, De Wachter R, Van de Peer Y (2002) Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA. Protist 153:123–132 Berney C, Fahrni J, Pawlowski J (2004) How many novel eukaryotic kingdoms? Pitfalls and limitations of environmental DNA surveys. BMC Biology 2:1–13 Bessey EA (1942) Some problems in fungus phylogeny. Mycologia 34:355–379 Brate J, Klaveness D, Rygh T, Jakobsen KS, Shalchian-Tabrizi K (2010a) Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations. BMC Microbiol 10:168 Brate J, Logares R, Berney C, Ree DK, Klaveness D, Jakobsen KS, Shalchian-Tabrizi K (2010b) Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME J 4:1144–1153 Cavalier-Smith T, Chao EEY (2006) Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). J Mol Evol 62:388–420 Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidium thiocyanate phenol chloroform extraction. Anal Biochem 162:156–159 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 Duran A, Gryzenhout M, Drenth A, Slippers B, Ahumada R, Wingfield BD, Wingfield MJ (2010) AFLP analysis reveals a clonal population of Phytophthora pinifolia in Chile. Fungal Biol 114:746–752 Gachon CMM, Strittmatter M, Muller DG, Kleinteich J, Kupper FC (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 Glockling SL, Beakes GW (2006) An ultrastructural study of development and reproduction in the nematode parasite Myzocytiopsis vermicola. Mycologia 98:1–15 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 Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98 Ho HH, Chang HS, Hsieh SY (1991) Halophytophthora kandeliae, a new marine fungus from Taiwan. Mycologia 83:419–424 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 Hudspeth DSS, Nadler SA, Hudspeth MES (2000) A COX2 molecular phylogeny of the peronosporomycetes. Mycologia 92:674–684 Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4:18 Kamoun S (2001) Nonhost resistance to Phytophthora: novel prospects for a classical problem. Curr Opin Plant Biol 4:295–300 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 Karling JS (1942) The simple holocarpic biflagellate phycomycetes. Columbia University Press, New York 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 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 Logares R, Shalchian-Tabrizi K, Boltovskoy A, Rengefors K (2007) Extensive dinoflagellate phylogenies indicate infrequent marine-freshwater transitions. Mol Phylogenet Evol 45:887–903 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 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 Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions. Gene 71:491–499 Mendoza L, Newton JC (2005) Immunology and immunotherapy of the infections caused by Pythium insidiosum. Med Mycol 43:477–486 Moreira D, Lopez-Garcia P, Vickerman K (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 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 Phillips AJ, Anderson VL, Robertson EJ, Secombes CJ, van West P (2008) New insights into animal pathogenic oomycetes. Trends Microbiol 16:13–19 Riethmuller A, Voglmayr H, Goker M, Weiss M, Oberwinkler F (2002) Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences. Mycologia 94:834–849 Rizzo DM, Garbelotto M, Hansen EA (2005) Phytophthora ramorum: Integrative research and management of an emerging pathogen in California and Oregon forests. Annu Rev Phytopathol 43:309–335 Rodriguez F, Oliver JL, Marin A, Medina JR (1990) The general stochastic-model of nucleotide substitution. J Theor Biol 142:485–501 Shalchian-Tabrizi K, Brate J, Logares R, Klaveness D, Berney C, Jakobsen KS (2008) Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environ Microbiol 10:2635–2644 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 Stamatakis, A., Hoover, P. and Rougemont, J., (2008). A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 57(5):758–771 Thines M, Kamoun S (2010) Oomycete-plant coevolution: recent advances and future prospects. Curr Opin Plant Biol 13:427–433 Uzuhashi S, Tojo M, Kakishima M (2010) Phylogeny of the genus Pythium and description of new genera. Mycoscience 51:337–365 Van der Pläats-Niterink AJ (1981) Monograph of the genus Pythium. Studies in Mycology 21:1–242 van West P, de Bruijn I, Minor KL, Phillips AJ, Robertson EJ, Wawra S, Bain J, Anderson VL, Secombes CJ (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 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 Zattau WC, McInnis T (1987) Life-Cycle and mode of infection of Leptolegnia chapmanii (oomycetes) parasitizing Aedes aegypti. J Invertebr Pathol 50:134–145