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

Dario Cantu, Manjula Govindarajulu, Alex Kozik, Meinan Wang, Xianming Chen, Kenji K. Kojima, Jerzy Jurka, Richard W Michelmore, Jorge Dubcovsky

Research output: Contribution to journalArticle

112 Citations (Scopus)

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 ab initio 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.

Original languageEnglish (US)
Article numbere24230
JournalPLoS One
Volume6
Issue number8
DOIs
StatePublished - 2011

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Puccinia striiformis
Triticum
Genes
Genome
wheat
genome
Molecular Sequence Annotation
genes
genomics
application coverage
Synteny
DNA Transposable Elements
Nucleic Acid Regulatory Sequences
Puccinia graminis
Nucleic Acid Databases
power generation
Genomics
prediction
stripe rust
transposons

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust. / Cantu, Dario; Govindarajulu, Manjula; Kozik, Alex; Wang, Meinan; Chen, Xianming; Kojima, Kenji K.; Jurka, Jerzy; Michelmore, Richard W; Dubcovsky, Jorge.

In: PLoS One, Vol. 6, No. 8, e24230, 2011.

Research output: Contribution to journalArticle

Cantu, D, Govindarajulu, M, Kozik, A, Wang, M, Chen, X, Kojima, KK, Jurka, J, Michelmore, RW & Dubcovsky, J 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, vol. 6, no. 8, e24230. https://doi.org/10.1371/journal.pone.0024230
Cantu, Dario ; Govindarajulu, Manjula ; Kozik, Alex ; Wang, Meinan ; Chen, Xianming ; Kojima, Kenji K. ; Jurka, Jerzy ; Michelmore, Richard W ; Dubcovsky, Jorge. / Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust. In: PLoS One. 2011 ; Vol. 6, No. 8.
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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 ab initio 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.",
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