Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Cantu, Dario ^a   Govindarajulu, Manjula ^a   Kozik, Alex ^a   Wang, Meinan ^b   Chen, Xianming ^b,c   Kojima, Kenji K ^d   Jurka, Jerzy ^d   Michelmore, Richard W ^a   Dubcovsky, Jorge ^a,e,f  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c U S DEPARTMENT OF AGRICULTURE   (United States)

^d Genetic Information Research Institute   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^f GORDON AND BETTY MOORE FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ARTICLE; FUNGAL GENOME; FUNGAL PLANT DISEASE; FUNGUS; GENBANK; GENE SEQUENCE; GENETIC DATABASE; MOLECULAR GENETICS; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PUCCINIA STRIIFORMIS; SEQUENCE HOMOLOGY; SYNTENY; TRANSPOSON; WHEAT STRIPE RUST; BASIDIOMYCETES; BIOSYNTHESIS; CONTIG MAPPING; DNA SEQUENCE; FUNGAL GENE; GENETICS; METHODOLOGY; MICROBIOLOGY; NUCLEOTIDE REPEAT; PLANT DISEASE; SECRETION; WHEAT;

PUCCINIA GRAMINIS F. SP. TRITICI; PUCCINIA STRIIFORMIS F. SP. TRITICI; TRITICUM AESTIVUM; UREDINALES;

ERGOSTEROL; FUNGAL DNA; FUNGAL PROTEIN;

BASIDIOMYCOTA; CONTIG MAPPING; DNA TRANSPOSABLE ELEMENTS; DNA, FUNGAL; ERGOSTEROL; FUNGAL PROTEINS; GENES, FUNGAL; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; PLANT DISEASES; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SYNTENY; TRITICUM;

EID: 80052327127     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024230     Document Type: Article

References (31)

1. Chen XM, (2005) Epidemiology and control of stripe rust [Puccinia striiformis f. sp. tritici] on wheat. Can J Plant Pathol 27: 314-337.
2. Hovmøller MS, Walter S, Justesen AF, (2010) Escalating threat of wheat rusts. Science 23: 369.
3. Wellings C, (2010) Global status of stripe rust. Borlaug Global Rust Initiative 2010 Technical Workshop. St Petersburg.
4. Millus EA, Kristensen K, Hovmøller MS, (2009) Evidence for increased aggressiveness in a recent widespread strain of Puccinia striiformis f. sp tritici causing stripe rust of wheat. Pyhtopathol 99: 89-94.
5. Duplessis S, Cuomo CA, Lin Y-C, Aerts A, Tisserant E, et al. (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci USA 10.1073/pnas.1019315108.
6. Yin C, Chen X, Wang X, Han Q, Kang Z, et al. (2009) Generation and analysis of expression sequence tags from haustoria of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. BMC Genomics 10: 626.
7. Zhang Y, Qu Z, Zheng W, Liu B, Wang Y, et al. (2008) Stage-specific gene expression during urediniospore germination in Puccinia striiformis f. sp tritici. BMC Genomics 9: 203.
8. Ling P, Wang MN, Chen XM, Campbell KG, (2007) Construction and characterization of a full-length cDNA library for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici). BMC Genomics 8: 145.
9. Cantu D, Pearce S, Distelfeld A, Christiansen M, Uauy C, et al. (Submitted) Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence. BMC Genomics.
10. Langmead B, Trapnell C, Pop M, Salzberg S, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.
11. Parra G, Bradnam K, Korf I, (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23: 1061-1067.
12. Jurka J, Kapitonov V, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
13. Wang DY-C, Kumar S, Hedges SB, (1999) Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc R Soc Lond B 266: 163-171.
14. Yuan Y, Wessler S, (2011) The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci U S A 108 7884-7889.
15. Yin C, Jurgenson JE, Hulbert SH Development of a host-Induced RNAi system in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. Mol Plant Microbe Interact 24: 554-561.
16. Kamoun S, (2006) A Catalogue of the effector secretome of plant pathogenic oomycetes. Annual Rev Phytopathol 44: 41-60.
17. Torto TA, Li S, Styer A, Huitema E, Testa A, et al. (2003) EST Mining and Functional Expression Assays Identify extracellular effector proteins from the plant pathogen Phytophthora. Genome Res 13: 1675-1685.
18. Dyrløv Bendtsen J, Nielsen H, von Heijne G, Brunak S, (2004) Improved Prediction of Signal Peptides: SignalP 3.0. J Mol Biol 340: 783-795.
19. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL, (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305: 567-580.
20. Emanuelsson O, Brunak S, von Heijne G, Nielsen H, (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protocols 2: 953-971.
21. Kemen E, Kemen A, Rafiqi M, Hempel U, Mendgen K, et al. (2005) Identification of a protein from rust fungi transferred from haustoria into infected plant cells. Mol Plant Microbe Interact 18: 1130-1139.
22. Godfrey D, Bohlenius H, Pedersen C, Zhang Z, Emmersen J, et al. (2010) Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif. BMC Genomics 11: 317.
23. Kale SD, Gu B, Capelluto DGS, Dou D, Feldman E, et al. (2010) External lipid PI3P mediates entry of eukaryotic pathogen effectors into plant and animal host cells. Cell 142: 284-295.
24. Dubcovsky J, Ramakrishna W, SanMiguel P, Busso CS, Yan L, et al. (2001) Comparative sequence analysis of colinear barley and rice BACs. Plant Physiol 125: 1342-1353.
25. Chen XM, Penman L, Wan AM, Cheng P, (2010) Virulent races of Puccinia striiformis f. sp. tritici in 2006 and 2007 and development of wheat stripe rust and distributions, dynamics, and evolutionary relationships of races from 2000 to 2007 in the United States Can J Plant Pathol In press.
26. Chen XM, Line RF, Leung H, (1993) Relationship between virulence variation and DNA polymorphism in Puccinia striiformis. Phytopathol 83: 1489-1497.
27. Clarke L, Carbon J, (1976) A colony bank containing synthetic ColE 1 hybrid plasmids representative of the entire Escherichia coli genome. Cell 9: 91-99.
28. Kohany O, Gentles AJ, Hankus L, Jurka J, (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474.
29. Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
30. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
31. Cohen SX, Moulin M, Hashemolhosseini S, Kilian K, Wegner M, et al. (2003) Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition. EMBO J 22: 1835-1845.