1. Martens C, Vandepoele K, Van de Peer Y: Whole-genome analysis reveals
molecular innovations and evolutionary transitions in chromalveolate
species. Proc Natl Acad Sci USA 2008, 105:3427-3432.
2. Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta JR,
Bowser SS, Brugerolle G, Fensome RA, Fredericq S, et al: The new higher
level classification of eukaryotes with emphasis on the taxonomy of
protists. J Eukaryot Microbiol 2005, 52:399-451.
3. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF: A kingdom-level
phylogeny of eukaryotes based on combined protein data. Science 2000,
290:972-977.
4. Thines M, Kamoun S: Oomycete-plant coevolution: recent advances and
future prospects. Curr Opin Plant Biol 2010, 13:427-433.
5. McHale LK, Truco MJ, Kozik A, Wroblewski T, Ochoa OE, Lahre KA, Knapp SJ,
Michelmore RW: The genomic architecture of disease resistance in
lettuce. Theor Appl Genet 2009, 118:565-580.
6. Borhan MH, Gunn N, Cooper A, Gulden S, Tor M, Rimmer SR, Holub EB:
WRR4 encodes a TIR-NB-LRR protein that confers broad-spectrum white
rust resistance in Arabidopsis thaliana to four physiological races of
Albugo candida. Mol Plant Microbe Interact 2008, 21:757-768.
7. van Ooijen G, van den Burg HA, Cornelissen BJ, Takken FL: Structure and
function of resistance proteins in solanaceous plants. Annu Rev
Phytopathol 2007, 45:43-72.
8. Shan W, Cao M, Leung D, Tyler BM: The Avr1b locus of Phytophthora
sojae encodes an elicitor and a regulator required for avirulence on
soybean plants carrying resistance gene Rps1b. Mol Plant Microbe Interact
2004, 17:394-403.
9. Armstrong MR, Whisson SC, Pritchard L, Bos JI, Venter E, Avrova AO,
Rehmany AP, Bohme U, Brooks K, Cherevach I, et al: An ancestral
oomycete locus contains late blight avirulence gene Avr3a, encoding a
protein that is recognized in the host cytoplasm. Proc Natl Acad Sci USA
2005, 102:7766-7771.
10. Allen RL, Bittner-Eddy PD, Grenville-Briggs LJ, Meitz JC, Rehmany AP,
Rose LE, Beynon JL: Host-parasite coevolutionary conflict between
Arabidopsis and downy mildew. Science 2004, 306:1957-1960.
11. Rehmany AP, Gordon A, Rose LE, Allen RL, Armstrong MR, Whisson SC,
Kamoun S, Tyler BM, Birch PR, Beynon JL: Differential recognition of highly
divergent downy mildew avirulence gene alleles by RPP1 resistance
genes from two Arabidopsis lines. The Plant cell 2005, 17:1839-1850.
12. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD,
Baxter L, Bensasson D, Beynon JL, et al: Phytophthora genome sequences
uncover evolutionary origins and mechanisms of pathogenesis. Science
2006, 313:1261-1266.
13. Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM,
Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, et al: Genome sequence
and analysis of the Irish potato famine pathogen Phytophthora
infestans. Nature 2009, 461:393-398.
14. Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-
Fong A, Anderson R, Badejoko W, et al: Signatures of adaptation to
obligate biotrophy in the Hyaloperonospora arabidopsidis genome.
Science 2010, 330:1549-1551.
15. Levesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E,
Raffaele S, Robideau GP, Thines M, Win J, et al: Genome sequence of the
necrotrophic plant pathogen Pythium ultimum reveals original
pathogenicity mechanisms and effector repertoire. Genome biology 2010,
11:R73.
16. Kim KS, Judelson HS: Sporangium-specific gene expression in the
oomycete phytopathogen Phytophthora infestans. Eukaryotic cell 2003,
2:1376-1385.
17. Torto-Alalibo TA, Tripathy S, Smith BM, Arredondo FD, Zhou L, Li H,
Chibucos MC, Qutob D, Gijzen M, Mao C, et al: Expressed sequence tags
from phytophthora sojae reveal genes specific to development and
infection. Mol Plant Microbe Interact 2007, 20:781-793.
18. Kale SD, Gu B, Capelluto DG, Dou D, Feldman E, Rumore A, Arredondo FD,
Hanlon R, Fudal I, Rouxel T, et al: External lipid PI3P mediates entry of
eukaryotic pathogen effectors into plant and animal host cells. Cell 2010,
142:284-295.
19. Birch PR, Boevink PC, Gilroy EM, Hein I, Pritchard L, Whisson SC: Oomycete
RXLR effectors: delivery, functional redundancy and durable disease
resistance. Current opinion in plant biology 2008, 11:373-379.
20. Whisson SC, Boevink PC, Moleleki L, Avrova AO, Morales JG, Gilroy EM,
Armstrong MR, Grouffaud S, van West P, Chapman S, et al: A translocation
signal for delivery of oomycete effector proteins into host plant cells.
Nature 2007, 450:115-118.
21. Jiang RH, Tripathy S, Govers F, Tyler BM: RXLR effector reservoir in two
Phytophthora species is dominated by a single rapidly evolving superfamily
with more than 700 members. Proc Natl Acad Sci USA 2008, 105:4874-4879.
22. Torto TA, Li S, Styer A, Huitema E, Testa A, Gow NA, van West P, Kamoun S:
EST mining and functional expression assays identify extracellular
effector proteins from the plant pathogen Phytophthora. Genome
research 2003, 13:1675-1685.
23. Qutob D, Kamoun S, Gijzen M: Expression of a Phytophthora sojae
necrosis-inducing protein occurs during transition from biotrophy to
necrotrophy. The Plant journal 2002, 32:361-373.
24. Vleeshouwers VG, Rietman H, Krenek P, Champouret N, Young C, Oh SK,
Wang M, Bouwmeester K, Vosman B, Visser RG, et al: Effector genomics
accelerates discovery and functional profiling of potato disease
resistance and phytophthora infestans avirulence genes. PLoS One 2008,
3:e2875.
25. Choi YJ, Shin HD, Ploch S, Thines M: Evidence for uncharted biodiversity
in the Albugo candida complex, with the description of a new species.
Mycol Res 2008, 112:1327-1334.
26. Voglmayr H, Riethmuller A: Phylogenetic relationships of Albugo species
(white blister rusts) based on LSU rDNA sequence and oospore data.
Mycol Res 2006, 110:75-85.
27. Heller A, Thines M: Evidence for the importance of enzymatic digestion
of epidermal walls during subepidermal sporulation and pustule
opening in white blister rusts (Albuginaceae). Mycol Res 2009,
113:657-667.
28. Holub EB, Brose E, Tor M, Clay C, Crute IR, Beynon JL: Phenotypic and
genotypic variation in the interaction between Arabidopsis thaliana and
Albugo candida. Mol Plant Microbe Interact 1995, 8:916-928.
29. Borhan HM, Brose E, Beynon JL, Holub EB: White rust (Albugo candida)
resistance loci on three Arabidopsis chromosomes are closely linked to
downy mildew (Peronospora parasitica) resistance loci. Mol Plant Pathol
2001, 2:87-95.
30. Adhikari TB, Liu JQ, Mathur S, Wu CX, Rimmer SR: Genetic and molecular
analyses in crosses of race 2 and race 7 of Albugo candida.
Phytopathology 2003, 93:959-965.
31. Cooper AJ, Latunde-Dada AO, Woods-Tor A, Lynn J, Lucas JA, Crute IR,
Holub EB: Basic compatibility of Albugo candida in Arabidopsis thaliana
and Brassica juncea causes broad-spectrum suppression of innate
immunity. Molecular plant-microbe interactions: MPMI 2008, 21:745-756.
32. Choi YJ, Hyeon-Shin D, Hong SB, Thines M: Morphological and molecular
discrimination among Albugo candida materials infecting Capsella
bursa-pastoris world-wide. Fungal Diversity 2007, 27:11-34.
33. Kole C, Williams PH, Rimmer SR, Osborn TC: Linkage mapping of genes
controlling resistance to white rust (Albugo candida) in Brassica rapa
(syn. campestris) and comparative mapping to Brassica napus and
Arabidopsis thaliana. Genome 2002, 45:22-27.
34. Somers J, Rakow G, Rimmer R: Brassica napus DNA markers linked to
white rust resistance in Brassica juncea. Theor Appl Genet 2002,
104:1121-1124.
35. Panjabi-Massand P, Yadava SK, Sharma P, Kaur A, Kumar A, Arumugam N,
Sodhi YS, Mukhopadhyay A, Gupta V, Pradhan AK, Pental D: Molecular
mapping reveals two independent loci conferring resistance to Albugo
candida in the east European germplasm of oilseed mustard Brassica
juncea. Theor Appl Genet 2010, 121:137-145.
36. Pound GS, Williams PH: Biological races of Albugo Candida.
Phytopathology 1963, 53:1146-1149.
37. Thines NJ, Choi YJ, Kemen E, Ploch S, Holub EB, Shin HD, Jones JD: A new
species of Albugo parasitic to Arabidopsis thaliana reveals new
evolutionary patterns in white blister rusts (Albuginaceae). Persoonia
2009, 22:123-128.
38. Borhan MH, Holub EB, Beynon JL, Rozwadowski K, Rimmer SR: The
arabidopsis TIR-NB-LRR gene RAC1 confers resistance to Albugo candida
(white rust) and is dependent on EDS1 but not PAD4. Mol Plant Microbe
Interact 2004, 17:711-719.
39. Borhan MH, Holub EB, Kindrachuk C, Omidi M, Bozorgmanesh-Frad G,
Rimmer SR: WRR4, a broad-spectrum TIR-NB-LRR gene from Arabidopsis
thaliana that confers white rust resistance in transgenic oilseed brassica
crops. Molecular plant pathology 2010, 11:283-291.
40. Rimmer SR, Mathur S, Wu CR: Virulence of isolates of Albugo candida
from western Canada to Brassica species. Can J Plant Pathol 2000,
22:229-235.
41. Voglmayr H, Greilhuber J: Genome size determination in peronosporales
(Oomycota) by Feulgen image analysis. Fungal Genet Biol 1998,
25:181-195.
42. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C,
Salzberg SL: Versatile and open software for comparing large genomes.
Genome Biol 2004, 5:R12.
43. Repeat Modeler. [http://www.repeatmasker.org/RepeatModeler.html].
44. Smit A, Hubley R, Green P: Repeat Masker 2010.
45. Parra G, Bradnam K, Korf I: CEGMA: a pipeline to accurately annotate core
genes in eukaryotic genomes. Bioinformatics 2007, 23:1061-1067.
46. Kent WJ: BLAT–the BLAST-like alignment tool. Genome Res 2002,
12:656-664.
47. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J,
Birren B, Bruce DC, Buhay C, et al: Genomics. Genome project standards in a
new era of sequencing. Science 2009, 326:236-237.
48. Majoros WH, Pertea M, Salzberg SL: TigrScan and GlimmerHMM: two open
source ab initio eukaryotic gene-finders. Bioinformatics 2004,
20:2878-2879.
49. Blanco E, Parra G, Guigo R: Using geneid to identify genes. Curr Protoc
Bioinformatics 2007, Chapter 4:Unit 4 3.
50. Parra G, Blanco E, Guigo R: GeneID in Drosophila. Genome research 2000,
10:511-515.
51. Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR,
Wortman JR: Automated eukaryotic gene structure annotation using
EVidenceModeler and the Program to Assemble Spliced Alignments.
Genome Biol 2008, 9:R7.
52. Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memoryefficient
alignment of short DNA sequences to the human genome.
Genome Biol 2009, 10:R25.
53. Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions
with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
54. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ,
Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by
RNA-Seq reveals unannotated transcripts and isoform switching during
cell differentiation. Nat Biotechnol 2010, 28:511-515.
55. Raffaele S, Win J, Cano LM, Kamoun S: Analyses of genome architecture
and gene expression reveal novel candidate virulence factors in the
secretome of Phytophthora infestans. BMC Genomics 2010, 11:637.
56. François Villalba Mateos MR, Marie-Thérèse Esquerré-Tugayé: Cloning and
Characterization of a cDNA Encoding an Elicitor of Phytophthora
parasitica var. nicotianae That Shows Cellulose-Binding and Lectin-Like
Activities. Mol Plant Microbe Interact 1997, 10:1045-1053.
57. Gaulin E, Drame N, Lafitte C, Torto-Alalibo T, Martinez Y, Ameline-
Torregrosa C, Khatib M, Mazarguil H, Villalba-Mateos F, Kamoun S, et al:
Cellulose binding domains of a Phytophthora cell wall protein are novel
pathogen-associated molecular patterns. The Plant cell 2006,
18:1766-1777.
58. Jiang RH, Tyler BM, Whisson SC, Hardham AR, Govers F: Ancient origin of
elicitin gene clusters in Phytophthora genomes. Molecular biology and
evolution 2006, 23:338-351.
59. Kamoun S, Klucher KM, Coffey MD, Tyler BM: A gene encoding a hostspecific
elicitor protein of Phytophthora parasitica. Mol Plant Microbe
Interact 1993, 6:573-581.
60. Yu LM: Elicitins from Phytophthora and basic resistance in tobacco. Proc
Natl Acad Sci USA 1995, 92:4088-4094.
61. Kamoun S, van West P, de Jong AJ, de Groot KE, Vleeshouwers VG,
Govers F: A gene encoding a protein elicitor of Phytophthora infestans is
down-regulated during infection of potato. Mol Plant Microbe Interact
1997, 10:13-20.
62. Gijzen M, Nurnberger T: Nep1-like proteins from plant pathogens:
recruitment and diversification of the NPP1 domain across taxa.
Phytochemistry 2006, 67:1800-1807.
63. Dou D, Kale SD, Wang X, Chen Y, Wang Q, Jiang RH, Arredondo FD,
Anderson RG, Thakur PB, McDowell JM, et al: Conserved C-terminal motifs
required for avirulence and suppression of cell death by Phytophthora
sojae effector Avr1b. Plant Cell 2008, 20:1118-1133.
64. Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S,
Andre Levesque C, Tisserat N, Buell CR: Analysis of the Pythium ultimum
transcriptome using Sanger and Pyrosequencing approaches. BMC
genomics 2008, 9:542.
65. Gaulin E, Madoui MA, Bottin A, Jacquet C, Mathe C, Couloux A, Wincker P,
Dumas B: Transcriptome of Aphanomyces euteiches: new oomycete
putative pathogenicity factors and metabolic pathways. PLoS One 2008,
3:e1723.
66. Schornack S, van Damme M, Bozkurt TO, Cano LM, Smoker M, Thines M,
Gaulin E, Kamoun S, Huitema E: Ancient class of translocated oomycete
effectors targets the host nucleus. Proc Natl Acad Sci USA 2010.
67. Bailey TL, Elkan C: Fitting a mixture model by expectation maximization
to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994,
2:28-36.
68. Collinson I: The structure of the bacterial protein translocation complex
SecYEG. Biochem Soc Trans 2005, 33:1225-1230.
69. Robinson C, Bolhuis A: Tat-dependent protein targeting in prokaryotes
and chloroplasts. Biochim Biophys Acta 2004, 1694:135-147.
70. Joshi MV, Mann SG, Antelmann H, Widdick DA, Fyans JK, Chandra G,
Hutchings MI, Toth I, Hecker M, Loria R, Palmer T: The twin arginine
protein transport pathway exports multiple virulence proteins in the
plant pathogen Streptomyces scabies. Mol Microbiol 2010, 77:252-271.
71. Yen MR, Tseng YH, Nguyen EH, Wu LF, Saier MH Jr: Sequence and
phylogenetic analyses of the twin-arginine targeting (Tat) protein export
system. Arch Microbiol 2002, 177:441-450.
72. Thines M, Voglmayr H: An introduction to the white blister rusts
(Albuginaceae). In Oomycete genetics and genomics. Edited by: Lamour K,
Kamoun S Hoboken. New Jersey: Wiley-Blackwell; 2009:77-92.
73. Kamoun S: Molecular genetics of pathogenic oomycetes. Eukaryot Cell
2003, 2:191-199.
74. Martin F: Meiotic instability of Pythium sylvaticum as demonstrated by
inheritance of nuclear markers and karyotype analysis. Genetics 1995,
139:1233-1246.
75. Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stuber K, Ver
Loren van Themaat E, Brown JK, Butcher SA, Gurr SJ, et al: Genome
expansion and gene loss in powdery mildew fungi reveal tradeoffs in
extreme parasitism. Science 2010, 330:1543-1546.
76. Rozwadowski K, Yang W, Kagale S: Homologous recombination-mediated
cloning and manipulation of genomic DNA regions using Gateway and
recombineering systems. BMC Biotechnol 2008, 8:88.
77. Lindbo JA: High-efficiency protein expression in plants from
agroinfection-compatible Tobacco mosaic virus expression vectors. BMC
Biotechnol 2007, 7:52.
78. Ewing B, Green P: Base-calling of automated sequencer traces using
phred. II. Error probabilities. Genome research 1998, 8:186-194.
79. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated
sequencer traces using phred. I. Accuracy assessment. Genome research
1998, 8:175-185.
80. Chou HH, Holmes MH: DNA sequence quality trimming and vector
removal. Bioinformatics 2001, 17:1093-1104.
81. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y,
White J, Cheung F, Parvizi B, et al: TIGR Gene Indices clustering tools
(TGICL): a software system for fast clustering of large EST datasets.
Bioinformatics 2003, 19:651-652.
82. Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology
Open Software Suite. Trends in genetics 2000, 16:276-277.