Open Access Highly Accessed Research article

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

Dario Cantu1, Vanesa Segovia2, Daniel MacLean3, Rosemary Bayles4, Xianming Chen56, Sophien Kamoun3, Jorge Dubcovsky789, Diane GO Saunders3* and Cristobal Uauy24*

Author Affiliations

1 Department of Viticulture & Enology, University of California Davis, Davis, USA

2 John Innes Centre, Norwich Research Park, Norwich, UK

3 The Sainsbury Laboratory, Norwich Research Park, Norwich, UK

4 National Institute of Agricultural Botany, Cambridge, UK

5 Department of Plant Pathology, Washington State University, Pullman, USA

6 USDA-ARS, Pullman, USA

7 Department of Plant Sciences, University of California Davis, Davis, USA

8 Howard Hughes Medical Institute, Chevy Chase, MD, USA

9 Gordon & Betty Moore Foundation, Palo Alto, CA, USA

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BMC Genomics 2013, 14:270  doi:10.1186/1471-2164-14-270

Published: 22 April 2013

Additional files

Additional file 1:

Summary of raw and trimmed reads and assemblies of PST-21, 43, 130, 87/7, and 08/21 genomic DNA.

Format: XLSX Size: 17KB Download file

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Additional file 2:

Quality assessment of genome assembly using CEGMA for five PST isolates. Of the 248 core eukaryotic genes (CEGs) 88.7% could be identified in the three PST US isolate genomes (PST-130, PST-43 and PST-21). The CEGMA pipeline distinguishes between CEGs found in complete (A) copies or as partial fragments (B) and separates the CEGs based on levels of conservation across higher eukaryotes, with group 4 being the most conserved. The levels of complete gene coverage were high for all US isolates, indicating few core eukaryotic genes were split across contigs. For the two UK isolates (PST-08/21 and PST-87/7) complete gene coverage was reduced compared to partial gene coverage, indicating higher levels of fragmentation for these genomes.

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Additional file 3:

Variant calls in the pairwise comparisons between all PST isolates used in this study.

Format: XLSX Size: 13KB Download file

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Additional file 4:

Summary of the reciprocal mapping of sequence reads for the 5 genomes using each in turn as a reference.

Format: XLSX Size: 19KB Download file

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Additional file 5:

Assessing the genetic diversity both within and between PST isolates. A. Summary of the main steps used to identify genetic variants between PST isolates. B. Diagram to illustrate how we defined heterokaryotic (het) and homokaryotic (hom) variants between isolates. C. Illustration to show how synthetic genes were generated from homokaryotic SNPs identified in Illumina reads of isolate B mapped to the reference isolate A.

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Additional file 6:

Number of SNPs identified in each gene of the 5 PST genomes.

Format: XLSX Size: 12.8MB Download file

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Additional file 7:

Pairwise dN values calculated using Yn00 for each gene of the 5 PST genomes, comparing all isolates.

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Additional file 8:

Pairwise dN/dS values calculated using Yn00 for each gene of the 5 PST genomes, comparing all isolates.

Format: XLSX Size: 4.8MB Download file

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Additional file 9:

(PST21_04206 displays sequence polymorphisms and positive selection between UK isolates and US PST-43 when compared to the synthetic gene from PST-130. A. Sequence alignment of PST21_04206 and the synthetic genes that incorporate the SNP information from the other four isolates sequenced, illustrating sequence polymorphisms between isolates. Polymorphic residues are indicated below the sequence by red stars. B. Positive selection analysis on the PST21_04206 synthetic gene set demonstrated positive selection when US PST-43, UK PST-87/7 and PST-08/21 when compared against the US PST-130 sequence.

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Additional file 10:

Depth, fold, and breath mapping coverage values for individual gene sequences that were identified as absent in any isolate.

Format: XLSX Size: 294KB Download file

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Additional file 11:

Summary of RNAseq reads from PST-08/21 infected tissue and haustorial libraries 1 and 2.

Format: XLSX Size: 35KB Download file

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Additional file 12:

Raw and DESeq normalized Illumina counts of reads mapped onto each of the transcripts of the 5 PST genomes with the fold enrichments in the haustoria libraries and the associated P-values calculated using the DESeq statistical analysis.

Format: XLSX Size: 3MB Download file

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Additional file 13:

Complete list of tribes with full annotation data and matching features. The file contains (i) the list of proteins included in the tribe analysis with full annotation including effector properties, and (ii) the list of tribes with the number of proteins matching effector properties they contain.

Format: XLSX Size: 1.9MB Download file

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Additional file 14:

Summary of the relative gene expression values measured using quantitative RT-PCR for 22 selected effector candidates.

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Additional file 15:

Primers used in the quantitative RT-PCR experiments.

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