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

<h4>Background</h4>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 Sequ...

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Autores principales:	Dario Cantu, Manjula Govindarajulu, Alex Kozik, Meinan Wang, Xianming Chen, Kenji K Kojima, Jerzy Jurka, Richard W Michelmore, Jorge Dubcovsky
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/46532f859e004b81a77f204d3ae76c0d
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spelling	oai:doaj.org-article:46532f859e004b81a77f204d3ae76c0d2021-11-18T06:46:54ZNext generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.1932-620310.1371/journal.pone.0024230https://doaj.org/article/46532f859e004b81a77f204d3ae76c0d2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21909385/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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).<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.Dario CantuManjula GovindarajuluAlex KozikMeinan WangXianming ChenKenji K KojimaJerzy JurkaRichard W MichelmoreJorge DubcovskyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e24230 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dario Cantu Manjula Govindarajulu Alex Kozik Meinan Wang Xianming Chen Kenji K Kojima Jerzy Jurka Richard W Michelmore Jorge Dubcovsky Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
description	<h4>Background</h4>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).<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.
format	article
author	Dario Cantu Manjula Govindarajulu Alex Kozik Meinan Wang Xianming Chen Kenji K Kojima Jerzy Jurka Richard W Michelmore Jorge Dubcovsky
author_facet	Dario Cantu Manjula Govindarajulu Alex Kozik Meinan Wang Xianming Chen Kenji K Kojima Jerzy Jurka Richard W Michelmore Jorge Dubcovsky
author_sort	Dario Cantu
title	Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
title_short	Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
title_full	Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
title_fullStr	Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
title_full_unstemmed	Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
title_sort	next generation sequencing provides rapid access to the genome of puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/46532f859e004b81a77f204d3ae76c0d
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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.

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