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Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

Cantu, D., M. Govindarajulu, A. Kozik, M. Wang, X. Chen, K. Kojima, J. Jurka, R.W. Michelmore, and J. Dubcovsky. 2011. Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust. PLoS ONE 6(8): e24230.

http://dx.plos.org/10.1371/journal.pone.0024230

We obtained nearly 80 million high quality paired-end reads (50x coverage) that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank and this website (see links below). The assemblies of the PST-130 genomic DNA and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions.

Puccinia striiformis f. sp. tritici contigs: PST130_contigs_v2.2.fas (zipped)

Contigs with masked repeats and transposable elements: PST130_contigs_MASKED_v2.2.fas(zipped)

You can blast your nucleotide or protein sequences against the NCBI's Whole Genome Sequence (WGS) database for Puccinia striiformis f. sp. tritici, which include our contigs:

  1. First go to the NCBI's WGS blast page, here
  2. In the "Enter Query Section" paste your sequence(s) in fasta format, or one or more valid NCBI accession numbers or upload a file with your fasta sequence(s). For example, you could try with accession EG374463, which is not part of the WGS Puccinia database.
  3. Under the "Choose Search Set" heading, click on the database drop-down list, and select "Puccinia WGS (3 entries)", then choose one or more of the species in the box below.
  4. In "Program Selection" select the blast variant: megablast is faster and will find very similar sequences, while blastn is slower but will find less similar hits.
  5. To blast a protein query against the translated WGS database, look for the tab above the "Enter Query Sequence" heading, then click on tblastn. For example, you could test accession AAY67662

Supplementary Materials

This section mirrors the supplementary materials of the paper published in PLoS ONE

1_Contig_coverage.xlsx: GenBank WGS accession number and fold-coverage (coverage / median coverage) of each PST-130 contig. Genomic and mitochondrial contigs are listed in separate sheets (same as supplementary material 1).

2_geneid_predicted.fasta (zipped): Amino acid sequences of 22,815 peptides predicted ab initio using geneid with parameters trained for PGTGgenes (same as supplementary material 2).

3_geneid_predicted_annotation.xlsx: 20,423 predicted PST-130 proteins with pfam accession numbers and names (http://pfam.sanger.ac.uk/), GO descriptions (http://www.blast2go.org/) and the most similar PGTG protein accessions and annotations (BLASTP, E-value ≤ 10-5), (same as supplementary material 3).

4_geneid_effector_prediction.xlsx: 1,088 PST-130 proteins with predicted signal peptide. Additional columns describe the grouping of these accessions based on sequence similarity (BLASTP, E-value ≤ 10-10), the availability of EST sequences from haustoria (TBLASTN, e-value ≤ 10-10) and the presence of different motifs conserved in other Avr genes (Kale et al., 2010)  and secreted fungal proteins (Godfrey et al. 2010),  (same as supplementary material 4).

References:

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. DOI:10.1186/1471-2164-11-317

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. DOI:10.1016/j.cell.2010.06.008

This project was supported in part by funds provided through a grant from the Bill & Melinda Gates Foundation and in part by the National Research Initiative Competitive Grant no. 2009-65300-05640 and 2011-68002-30029 (Triticeae-CAP) from the USDA National Institute of Food and Agriculture.