Serveur d'exploration sur les pucciniales

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De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence Genes.

Identifieur interne : 000274 ( Main/Exploration ); précédent : 000273; suivant : 000275

De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence Genes.

Auteurs : Jiapeng Chen [Australie] ; Jingqin Wu [Australie] ; Peng Zhang [Australie] ; Chongmei Dong [Australie] ; Narayana M. Upadhyaya ; Qian Zhou [République populaire de Chine] ; Peter Dodds ; Robert F. Park [Australie]

Source :

RBID : pubmed:31444296

Descripteurs français

English descriptors

Abstract

Puccinia hordei (Ph) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an Australian isolate of Ph ("Ph560") using long-read SMRT sequencing. A total of 838 contigs were assembled, with a total size of 207 Mbp. This included both haplotype collapsed and separated regions, consistent with an estimated haploid genome size of about 150Mbp. An annotation pipeline that combined RNA-Seq of Ph-infected host tissues and homology to proteins from four other Puccinia species predicted 25,543 gene models of which 1,450 genes were classified as encoding secreted proteins based on the prediction of a signal peptide and no transmembrane domain. Genome resequencing using short-read technology was conducted for four additional Australian strains, Ph612, Ph626, Ph608 and Ph584, which are considered to be simple mutational derivatives of Ph560 with added virulence to one or two of three barley leaf rust resistance genes (viz. Rph3, Rph13 and Rph19). To identify candidate genes for the corresponding avirulence genes AvrRph3, AvrRph13 and AvrRph19, genetic variation in predicted secreted protein genes between the strains was correlated to the virulence profiles of each, identifying 35, 29 and 46 candidates for AvrRph13, AvrRph3 and AvrRph19, respectively. The identification of these candidate genes provides a strong foundation for future efforts to isolate these three avirulence genes, investigate their biological properties, and develop new diagnostic tests for monitoring pathogen virulence.

DOI: 10.1534/g3.119.400450
PubMed: 31444296
PubMed Central: PMC6778787


Affiliations:


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Le document en format XML

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Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen
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Identifies Candidates for Three Avirulence Genes.</title>
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Identifies Candidates for Three Avirulence Genes.</title>
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<term>Basidiomycota (genetics)</term>
<term>Computational Biology (methods)</term>
<term>Genes, Fungal (MeSH)</term>
<term>Genome, Fungal (MeSH)</term>
<term>Genomics (methods)</term>
<term>High-Throughput Nucleotide Sequencing (MeSH)</term>
<term>Hordeum (microbiology)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Diseases (microbiology)</term>
<term>Polymorphism, Genetic (MeSH)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
<term>Virulence (genetics)</term>
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<term>Annotation de séquence moléculaire (MeSH)</term>
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<term>Basidiomycota (classification)</term>
<term>Basidiomycota (génétique)</term>
<term>Biologie informatique (méthodes)</term>
<term>Gènes fongiques (MeSH)</term>
<term>Génome fongique (MeSH)</term>
<term>Génomique (méthodes)</term>
<term>Hordeum (microbiologie)</term>
<term>Maladies des plantes (microbiologie)</term>
<term>Phylogenèse (MeSH)</term>
<term>Polymorphisme génétique (MeSH)</term>
<term>Séquençage nucléotidique à haut débit (MeSH)</term>
<term>Virulence (génétique)</term>
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<term>Basidiomycota</term>
<term>Virulence</term>
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<term>Computational Biology</term>
<term>Genomics</term>
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<term>Hordeum</term>
<term>Maladies des plantes</term>
</keywords>
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<term>Hordeum</term>
<term>Plant Diseases</term>
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<term>Biologie informatique</term>
<term>Génomique</term>
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<term>Genes, Fungal</term>
<term>Genome, Fungal</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Molecular Sequence Annotation</term>
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<term>Polymorphism, Genetic</term>
<term>Sequence Analysis, DNA</term>
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<front>
<div type="abstract" xml:lang="en">
<i>Puccinia hordei</i>
(
<i>Ph</i>
) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an Australian isolate of
<i>Ph</i>
("
<i>Ph</i>
560") using long-read SMRT sequencing. A total of 838 contigs were assembled, with a total size of 207 Mbp. This included both haplotype collapsed and separated regions, consistent with an estimated haploid genome size of about 150Mbp. An annotation pipeline that combined RNA-Seq of
<i>Ph</i>
-infected host tissues and homology to proteins from four other
<i>Puccinia</i>
species predicted 25,543 gene models of which 1,450 genes were classified as encoding secreted proteins based on the prediction of a signal peptide and no transmembrane domain. Genome resequencing using short-read technology was conducted for four additional Australian strains,
<i>Ph</i>
612,
<i>Ph</i>
626,
<i>Ph</i>
608 and
<i>Ph</i>
584, which are considered to be simple mutational derivatives of
<i>Ph</i>
560 with added virulence to one or two of three barley leaf rust resistance genes (
<i>viz. Rph3</i>
,
<i>Rph13</i>
and
<i>Rph19</i>
). To identify candidate genes for the corresponding avirulence genes
<i>AvrRph3</i>
,
<i>AvrRph13</i>
and
<i>AvrRph19</i>
, genetic variation in predicted secreted protein genes between the strains was correlated to the virulence profiles of each, identifying 35, 29 and 46 candidates for
<i>AvrRph13</i>
,
<i>AvrRph3</i>
and
<i>AvrRph19</i>
, respectively. The identification of these candidate genes provides a strong foundation for future efforts to isolate these three avirulence genes, investigate their biological properties, and develop new diagnostic tests for monitoring pathogen virulence.</div>
</front>
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<i>De Novo</i>
Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen
<i>Puccinia hordei</i>
Identifies Candidates for Three Avirulence Genes.</ArticleTitle>
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<Abstract>
<AbstractText>
<i>Puccinia hordei</i>
(
<i>Ph</i>
) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an Australian isolate of
<i>Ph</i>
("
<i>Ph</i>
560") using long-read SMRT sequencing. A total of 838 contigs were assembled, with a total size of 207 Mbp. This included both haplotype collapsed and separated regions, consistent with an estimated haploid genome size of about 150Mbp. An annotation pipeline that combined RNA-Seq of
<i>Ph</i>
-infected host tissues and homology to proteins from four other
<i>Puccinia</i>
species predicted 25,543 gene models of which 1,450 genes were classified as encoding secreted proteins based on the prediction of a signal peptide and no transmembrane domain. Genome resequencing using short-read technology was conducted for four additional Australian strains,
<i>Ph</i>
612,
<i>Ph</i>
626,
<i>Ph</i>
608 and
<i>Ph</i>
584, which are considered to be simple mutational derivatives of
<i>Ph</i>
560 with added virulence to one or two of three barley leaf rust resistance genes (
<i>viz. Rph3</i>
,
<i>Rph13</i>
and
<i>Rph19</i>
). To identify candidate genes for the corresponding avirulence genes
<i>AvrRph3</i>
,
<i>AvrRph13</i>
and
<i>AvrRph19</i>
, genetic variation in predicted secreted protein genes between the strains was correlated to the virulence profiles of each, identifying 35, 29 and 46 candidates for
<i>AvrRph13</i>
,
<i>AvrRph3</i>
and
<i>AvrRph19</i>
, respectively. The identification of these candidate genes provides a strong foundation for future efforts to isolate these three avirulence genes, investigate their biological properties, and develop new diagnostic tests for monitoring pathogen virulence.</AbstractText>
<CopyrightInformation>Copyright © 2019 Chen et al.</CopyrightInformation>
</Abstract>
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