RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 12, 2008, Pages 4874-4879

  Jiang, Rays H Y ^a,b   Tripathy, Sucheta ^a   Govers, Francine ^a   Tyler, Brett M ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Avirulence genes; Comparative genomics; Gene family evolution; Oomycete; Pathogenicity

Indexed keywords

FUNGAL PROTEIN; PROTEIN AVR; ALGAL PROTEIN;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; GENE SEQUENCE; GENOMICS; HOST CELL; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OOMYCETES; PHYTOPHTHORA; PHYTOPHTHORA RAMORUM; PHYTOPHTHORA SOJAE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; AMINO ACID SEQUENCE; CHEMISTRY; GENE REARRANGEMENT; GENETIC POLYMORPHISM; GENETICS; GENOME; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PATHOGENICITY; PROTEIN MOTIF; SYNTENY; VIRULENCE;

CERVIDAE; PHYTOPHTHORA; PHYTOPHTHORA RAMORUM; PHYTOPHTHORA SOJAE;

ALGAL PROTEINS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; GENOME; MOLECULAR SEQUENCE DATA; PHYTOPHTHORA; POLYMORPHISM, GENETIC; SYNTENY; VIRULENCE;

EID: 42449116668     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0709303105     Document Type: Article

References (36)

1. Collmer A, Lindeberg M, Petnicki-Ocwieja T, Schneider DJ, Alfano JR (2002) Genomic mining type III secretion system effectors in Pseudomonas syringae yields new picks for all TTSS prospectors. Trends Microbiol 10:462-469.
2. Hiller NL, et al. (2004) A host-targeting signal in virulence proteins reveals a secretome in malarial infection. Science 306:1934-1937.
3. Marti M, Good RT, Rug M, Knuepfer E, Cowman AF (2004) Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science 306:1930-1933.
4. Erwin DC, Ribeiro OK (1996) Phytophthora Diseases Worldwide (Am Phytopathol Soc, St. Paul, MN).
5. 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.
6. Baldauf SL (2003) The deep roots of eukaryotes. Science 300:1703-1706.
7. Kamoun S (2006) A catalogue of the effector secretome of plant pathogenic oomycetes. Annu Rev Phytopathol 44:41-60.
8. Flor HH (1942) Inheritance of pathogenicity in a cross between physiologic races 22 and 24 of Melampsora lini. Phytopathology 32:653-669.
9. Shan W, Cao M, Leung D, Tyler BM (2004) 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 17:394-403.
10. Rehmany AP, et al. (2005) Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines. Plant Cell 17:1839-1850.
11. Armstrong MR, et al. (2005) 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 102:7766-7771.
12. Allen RL, et al. (2004) Host-parasite coevolutionary conflict between Arabidopsis and downy mildew. Science 306:1957-1960.
13. Whisson SC, et al. (2007) A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450:115-118.
14. Tyler BM, et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313:1261-1266.
15. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755-763.
16. Win J, et al. (2007) Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell 19:2349-2369.
17. Bhattacharjee S, et al. (2006) The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathog 2:e50.
18. Pieterse CMJ, et al. (1994) Structure and genomic organization of the ipiB and ipiO gene clusters of Phytophthora infestans. Gene 138:67-77.
19. Stahl EA, Bishop JG (2000) Plant pathogen arms races at the molecular level. Curr Opi Plant Biol 3:299-304.
20. Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
21. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556.
22. Zhang X, et al. (2006) An integrated BAC, genome sequence physical map of Phytophthora sojae. Mol Plant-Microbe Interact 19:1302-1310.
23. Ellis JG, Dodds PN, Lawrence GJ (2007) The role of secreted proteins in diseases of plants caused by rust, powdery mildew and smut fungi. Curr Opi Microbiol 10:326-331.
24. Prince VE, Pickett FB (2002) Splitting pairs: The diverging fates of duplicated genes. Nat Rev Genet 3:827-837.
25. Jiang RHY, Tyler BM, Govers F (2006) Comparative analysis of Phytophthora genes encoding secreted proteins reveals conserved synteny and lineage-specific gene duplications and deletions. Mol Plant-Microbe Interact 19:1311-1321.
26. Reams AB, Neidle EL (2004) Selection for gene clustering by tandem duplication. Annu Rev Microbiol 58:119-142.
27. Lahaye T, Bonas U (2001) Molecular secrets of bacterial type III effector proteins. Trends Plants Sci 6:479-485.
28. Schornack S, Meyer A, Romer P, Jordan T, Lahaye T (2006) Gene-for-gene-mediated recognition of nuclear-targeted AvrBs3-like bacterial effector proteins. J Plant Physiol 163:256-272.
29. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
30. Bailey TL, Gribskov M (1997) Score distributions for simultaneous matching to multiple motifs. J Comput Biol 4:45-59.
31. Bailey TL, Gribskov M (1998) Combining evidence using p-values: Application to sequence homology searches. Bioinformatics 14:48-54.
32. Tripathy S, Pandey VN, Fang B, Salas F, Tyler BM (2006) VMD: a community annotation database for oomycetes and microbial genomes. Nucleic Acids Res 34:D379-D381.
33. Yang Z, Wong WS, Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107-1118.
34. Dehal PS, Boore JL (2006) A phylogenomic gene cluster resource: The Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics 7:201.
35. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
36. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.