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Title: Next generation sequencing provides rapid access to the genome of wheat stripe rust

Author
item CANTU, DARIO - University Of California
item GOVINDARAJULU, MANJULA - University Of California
item WANG, MEINAN - Washington State University
item Chen, Xianming
item KOJIMA, KENJI - Genetic Information Research Institute (GIRI)
item JURKA, JERZY - Genetic Information Research Institute (GIRI)
item MICHELMORE, RICHARD - University Of California
item DUBCOVSKY, JORGE - University Of California

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/2/2011
Publication Date: 8/31/2011
Citation: Cantu, D., Govindarajulu, M., Wang, M., Chen, X., Kojima, K.K., Jurka, J., Michelmore, R.W., Dubcovsky, J. 2011. Next generation sequencing provides rapid access to the genome of wheat stripe rust. PLoS One. 6(8)e24230. doi:10.1371/journal.pone.0024230.

Interpretive Summary: The wheat stripe rust fungus is responsible for significant yield losses in wheat production worldwide, but its genomic sequence is not currently available. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent race PST-130. We obtained nearly 80 million high quality paired-end reads that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the fungal genes and are available through GenBank. Extensive micro-synteny with the stem rust genome and high sequence similarity with annotated stem rust genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an abinitio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both stripe rust and stem rust and to identify candidate effectors. Finally, the assembled contigs provided an inventory of stripe rust repetitive elements, which were annotated and deposited in Repbase. The assembly of the genome and the predicted proteins provide useful resources to rapidly identify and clone stripe rust genes and their regulatory regions. we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The sequence will also be useful for comparative studies within the stripe rust species as more races are sequenced.

Technical Abstract: Background: The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST) is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS) has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130). Methodology/Principal Findings: 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. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG) genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an abinitio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase. Conclusions/Significance: The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for rapid and efficient access to genomic sequence in non-model organisms.