scholarly journals Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1107
Author(s):  
Long Song ◽  
Jing Qin Wu ◽  
Chong Mei Dong ◽  
Robert F. Park
Keyword(s):  
Gene Expression ◽  
Leaf Rust ◽  
De Novo ◽  
Puccinia Triticina ◽  
Integrated Analysis ◽  
Avirulence Genes ◽  
Integrated Framework ◽  
Rust Pathogen ◽  
Avr Gene ◽  
Avr Genes

The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt (‘Pt104’) as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27–40 candidates and CNV analysis identified 14–31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available.

scholarly journals Dissecting the first phased dikaryotic genomes of the wheat rust pathogen Puccinia triticina reveals the mechanisms of somatic exchange in nature

2019 ◽  
Author(s):  
Jing Qin Wu ◽  
Chongmei Dong ◽  
Long Song ◽  
Christina A. Cuomo ◽  
Robert F. Park
Keyword(s):  
Leaf Rust ◽  
Somatic Hybridization ◽  
Puccinia Triticina ◽  
Genomic Variation ◽  
Hybrid Wheat ◽  
Wheat Cultivars ◽  
Wheat Leaf Rust ◽  
Virulence Evolution ◽  
Rust Pathogen ◽  
Wheat Leaf

AbstractAlthough somatic hybridization (SH) has been proposed as a means of accelerating rust pathogen virulence evolution in the absence of sexual recombination, previous studies are limited to the laboratory and none have revealed how this process happens. Using long-read sequencing, we generated dikaryotic phased genomes and annotations for three Australian field-collected isolates of the wheat leaf rust pathogen (Puccinia triticina; Pt), including a putative asexual hybrid (Pt64) and two putative parental isolates (Pt104 and Pt53; 132-141 Mb,155-176 contigs, N50 of 1.9-2.1 Mb). The genetic dissection based on the high-quality phased genomes including whole-genome alignments, phylogenetic and syntenic analyses along with short-read sequencing of 27 additional Pt isolates convergently demonstrated that Pt64, which rendered several commercial hybrid wheat cultivars susceptible to leaf rust, arose from SH between isolates within the Pt53 and Pt104 lineages. Parentage analysis demonstrated the role of mitotic crossover in the derivation of both nuclei of Pt64. Within HD mating type genes, the distinct specificity regions in Pt64 and the distinct phylogenetic pattern of the remaining admixed isolates suggested high genetic variation in specificity-related regions on the b locus intrinsically associated with the SH. This study not only provided a fundamental platform for investigating genomic variation underlying virulence evolution in one of the most devastating wheat pathogens, but also offered an in-depth understanding of the mechanisms of naturally occurring SH. This asexual mechanism can be broadly exploited by any dikaryotic pathogen to accelerate virulence evolution, and understanding this process is both urgent and crucial for sustainable pathogen control.ImportanceStrategies to manage plant rust pathogens are challenged by the constant emergence of new virulence. Although somatic hybridization has been proposed as a means by which rusts could overcome host resistance rapidly and cause crop loss, there is very little evidence of this process in nature and the mechanisms underlying it are not known. This study generated and analysed the first dikaryotic phased genomes of the wheat leaf rust pathogen, identifying an isolate as a hybrid and for the first time unveiling parasexuality via mitotic crossover in a rust pathogen. The erosion of the resistance of several hybrid wheat cultivars in agriculture by the hybrid rust has important implications for breeding efforts targeting durable resistance and sustained rust control.

scholarly journals Isolation and Characterization of Avirulence Genes in Magnaporthe oryzae

2017 ◽  
Vol 7 (1) ◽  
pp. 31-42 ◽  
Author(s):  
Mui Sie Jee ◽  
Leonard Whye Kit Lim ◽  
Martina Azelin Dirum ◽  
Sara Ilia Che Hashim ◽  
Muhammad Shafiq Masri ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Fungal Pathogen ◽  
Rice Blast ◽  
Avirulence Gene ◽  
Avirulence Genes ◽  
Isolation And Characterization ◽  
Molecular Pattern ◽  
Avr Gene ◽  
Avr Genes

Magnaporthe oryzae is a fungal pathogen contributing to rice blast diseases globally via their Avr (avirulence) gene. Although the occurrence of M. oryzae has been reported in Sarawak since several decades ago, however, none has focused specifically on Avr genes, which confer resistance against pathogen associated molecular pattern-triggered immunity (PTI) in host. The objective of this study is to isolate Avr genes from M. oryzae 7’ (a Sarawak isolate) that may contribute to susceptibility of rice towards diseases. In this study, AvrPiz-t, AVR-Pik, Avr-Pi54, and AVR-Pita1 genes were isolated via PCR and cloning approaches. The genes were then compared with set of similar genes from related isolates derived from NCBI. Results revealed that all eight Avr genes (including four other global isolates) shared similar N-myristoylation site and a novel motif. 3D modeling revealed similar β-sandwich structure in AvrPiz-t and AVR-Pik despite sequence dissimilarities. In conclusion, it is confirmed of the presence of these genes in the Sarawak (M. oryzae) isolate. This study implies that Sarawak isolate may confer similar avirulence properties as their counterparts worldwide. Further R/Avr gene-for-gene relationship studies may aid in strategic control of rice blast diseases in future.

scholarly journals Wheat Apoplast-Localized Lipid Transfer Protein TaLTP3 Enhances Defense Responses Against Puccinia triticina

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiaojie Zhao ◽  
Weishuai Bi ◽  
Shuqing Zhao ◽  
Jun Su ◽  
Mengyu Li ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Lipid Transfer Protein ◽  
Puccinia Triticina ◽  
Defense Responses ◽  
Transgenic Wheat ◽  
Lipid Transfer ◽  
Transfer Protein ◽  
Pathogenesis Related ◽  
Rust Pathogen ◽  
Wheat Lines

Plant apoplast serves as the frontier battlefield of plant defense in response to different types of pathogens. Many pathogenesis-related (PR) proteins are accumulated in apoplastic space during the onset of plant–pathogen interaction, where they act to suppress pathogen infection. In this study, we found the expression of Triticum aestivum lipid transfer protein 3 (TaLTP3) gene was unregulated during incompatible interaction mediated by leaf rust resistance genes Lr39/41 at the early infection stage. Stable transgenic wheat lines overexpressing TaLTP3 exhibited enhanced resistance to leaf rust pathogen Puccinia triticina. Transcriptome analysis revealed that overexpression of TaLTP3 specifically activated the transcription of pathogenesis-related protein 1a (TaPR1a) and multiple plant hormone pathways, including salicylic acid (SA), jasmonic acid (JA), and auxin, in response to the infection of the model bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Further investigation indicated that TaLTP3 physically associated with wheat TaPR1a protein in the apoplast. Transgenic wheat lines overexpressing TaLTP3 and TaPR1a showed higher accumulations of reactive oxygen species (ROS) during plant defense responses. All these findings suggested that TaLTP3 is involved in wheat resistance against leaf rust pathogen infection and forming a TaLTP3-TaPR1a complex in apoplast against this pathogen, which provides new insights into the functional roles of PR proteins.

scholarly journals New Avirulence Genes in the Phytopathogenic Fungus Leptosphaeria maculans

2002 ◽  
Vol 92 (10) ◽  
pp. 1122-1133 ◽  
Author(s):  
M. H. Balesdent ◽  
A. Attard ◽  
M. L. Kühn ◽  
T. Rouxel
Keyword(s):  
Gene Cluster ◽  
Oilseed Rape ◽  
Single Gene ◽  
Leptosphaeria Maculans ◽  
Phytopathogenic Fungus ◽  
Gene Control ◽  
Avirulence Genes ◽  
Avr Gene ◽  
Avr Genes

Leptosphaeria maculans, the causal agent of stem canker of oilseed rape (Brassica napus), develops gene-for-gene interactions with oilseed rape, and four L. maculans avirulence (AVR) genes (AvrLm1, AvrLm2, AvrLm4, and alm1) were previously genetically characterized. Based on the analysis of progeny of numerous in vitro crosses between L. maculans isolates showing either already characterized or new differential interactions, this work aims to provide an overview of the AVR genes that may specify incompatibility toward B. napus and the related species B. juncea and B. rapa. Two novel differential interactions were thus identified between L. maculans and B. napus genotypes, one of them corresponding to a complete resistance to European races of L. maculans. In both cases, a single gene control of avirulence was established (genes AvrLm3 and AvrLm7). Similarly, a single gene control of avirulence toward a B. rapa genotype, also resistant to European L. maculans isolates, was demonstrated (gene AvrLm8). Finally, a digenic control of avirulence toward B. juncea was established (genes AvrLm5 and AvrLm6). Linkage analyses demonstrated that at least four unlinked L. maculans genomic regions, including at least one AVR gene cluster (AvrLm1-AvrLm2-AvrLm6), are involved in host specificity. The AvrLm3-AvrLm4-AvrLm7 region may correspond either to a second AVR gene cluster or to a multiallelic AVR gene.

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

2019 ◽  
Vol 9 (10) ◽  
pp. 3263-3271 ◽  
Author(s):  
Jiapeng Chen ◽  
Jingqin Wu ◽  
Peng Zhang ◽  
Chongmei Dong ◽  
Narayana M. Upadhyaya ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Candidate Genes ◽  
Reference Genome ◽  
Transmembrane Domain ◽  
De Novo ◽  
Australian Isolate ◽  
Puccinia Hordei ◽  
Avirulence Genes ◽  
Barley Leaf Rust ◽  
Barley Leaf

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.

scholarly journals Agroinfiltration Is a Versatile Tool That Facilitates Comparative Analyses of Avr9/Cf-9-Induced and Avr4/Cf-4-Induced Necrosis

2000 ◽  
Vol 13 (4) ◽  
pp. 439-446 ◽  
Author(s):  
Renier A. L. Van der Hoorn ◽  
Franck Laurent ◽  
Ronelle Roth ◽  
Pierre J. G. M. De Wit
Keyword(s):  
Gene Expression ◽  
Resistance Genes ◽  
Signal Transduction Pathway ◽  
Potato Virus X ◽  
Extracellular Proteins ◽  
Induced Responses ◽  
Avirulence Genes ◽  
Versatile Tool ◽  
Tomato Pathogen ◽  
Avr Gene

The avirulence genes Avr9 and Avr4 from the fungal tomato pathogen Cladosporium fulvum encode extracellular proteins that elicit a hypersensitive response when injected into leaves of tomato plants carrying the matching resistance genes, Cf-9 and Cf-4, respectively. We successfully expressed both Avr9 and Avr4 genes in tobacco with the Agrobacterium tumefaciens transient transformation assay (agroinfiltration). In addition, we expressed the matching resistance genes, Cf-9 and Cf-4, through agroinfiltration. By combining transient Cf gene expression with either transgenic plants expressing one of the gene partners, Potato virus X (PVX)-mediated Avr gene expression, or elicitor injections, we demonstrated that agroinfiltration is a reliable and versatile tool to study Avr/Cf-mediated recognition. Significantly, agroinfiltration can be used to quantify and compare Avr/Cf-induced responses. Comparison of different Avr/Cf-interactions within one tobacco leaf showed that Avr9/Cf-9-induced necrosis developed slower than necrosis induced by Avr4/Cf-4. Quantitative analysis demonstrated that this temporal difference was due to a difference in Avr gene activities. Transient expression of matching Avr/Cf gene pairs in a number of plant families indicated that the signal transduction pathway required for Avr/Cf-induced responses is conserved within solana-ceous species. Most non-solanaceous species did not develop specific Avr/Cf-induced responses. However, co-expression of the Avr4/Cf-4 gene pair in lettuce resulted in necrosis, providing the first proof that a resistance (R) gene can function in a different plant family.

scholarly journals A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Qin Wu ◽  
Long Song ◽  
Yi Ding ◽  
Chongmei Dong ◽  
Mafruha Hasan ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Molecular Mechanisms ◽  
Genetic Relationships ◽  
Durable Resistance ◽  
Puccinia Triticina ◽  
Wheat Leaf Rust ◽  
Structural Variations ◽  
Rust Disease ◽  
Rust Pathogen ◽  
Wheat Leaf

Despite the global economic importance of the wheat leaf rust pathogen Puccinia triticina (Pt), genomic resources for Pt are limited and chromosome-level assemblies of Pt are lacking. Here, we present a complete haplotype-resolved genome assembly at a chromosome-scale for Pt using the Australian pathotype 64-(6),(7),(10),11 (Pt64; North American race LBBQB) built upon the newly developed technologies of PacBio and Hi-C sequencing. PacBio reads with ∼200-fold coverage (29.8 Gb data) were assembled by Falcon and Falcon-unzip and subsequently scaffolded with Hi-C data using Falcon-phase and Proximo. This approach allowed us to construct 18 chromosome pseudomolecules ranging from 3.5 to 12.3 Mb in size for each haplotype of the dikaryotic genome of Pt64. Each haplotype had a total length of ∼147 Mb, scaffold N50 of ∼9.4 Mb, and was ∼93% complete for BUSCOs. Each haplotype had ∼29,800 predicted genes, of which ∼2,000 were predicted as secreted proteins (SPs). The investigation of structural variants (SVs) between haplotypes A and B revealed that 10% of the total genome was spanned by SVs, highlighting variations previously undetected by short-read based assemblies. For the first time, the mating type (MAT) genes on each haplotype of Pt64 were identified, which showed that MAT loci a and b are located on two chromosomes (chromosomes 7 and 14), representing a tetrapolar type. Furthermore, the Pt64 assembly enabled haplotype-based evolutionary analyses for 21 Australian Pt isolates, which highlighted the importance of a haplotype resolved reference when inferring genetic relationships using whole genome SNPs. This Pt64 assembly at chromosome-scale with full phase information provides an invaluable resource for genomic and evolutionary research, which will accelerate the understanding of molecular mechanisms underlying Pt-wheat interactions and facilitate the development of durable resistance to leaf rust in wheat and sustainable control of rust disease.

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