Genetic homogeneity of a recently introduced pathogen of chickpea, Ascochyta rabiei, to Australia

Leo, Audrey E.; Ford, Rebecca; Linde, Celeste C.

doi:10.1007/s10530-014-0752-8

Cited by 23 publications

(27 citation statements)

References 65 publications

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“…The overall low genetic diversity found within the comprehensive assessment of the Australian A. rabiei population in this study is a common finding with Leo et al (2015). Even if compatible mating types were present in the population, it seems likely that the expansion of this population to date has occurred through clonal means, perhaps due to forces suppressing recombination such as an initial imbalance in the mating type ratio of the founder isolates.…”

Section: Discussionmentioning

confidence: 57%

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population

et al. 2017

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The Australian Ascochyta rabiei (Pass.) Labr. (syn. Phoma rabiei) population has low genotypic diversity with only one mating type detected to date, potentially precluding substantial evolution through recombination. However, a large diversity in aggressiveness exists. In an effort to better understand the risk from selective adaptation to currently used resistance sources and chemical control strategies, the population was examined in detail. For this, a total of 598 isolates were quasi-hierarchically sampled between 2013 and 2015 across all major Australian chickpea growing regions and commonly grown host genotypes. Although a large number of haplotypes were identified (66) through short sequence repeat (SSR) genotyping, overall low gene diversity (Hexp = 0.066) and genotypic diversity (D = 0.57) was detected. Almost 70% of the isolates assessed were of a single dominant haplotype (ARH01). Disease screening on a differential host set, including three commonly deployed resistance sources, revealed distinct aggressiveness among the isolates, with 17% of all isolates identified as highly aggressive. Almost 75% of these were of the ARH01 haplotype. A similar pattern was observed at the host level, with 46% of all isolates collected from the commonly grown host genotype Genesis090 (classified as “resistant” during the term of collection) identified as highly aggressive. Of these, 63% belonged to the ARH01 haplotype. In conclusion, the ARH01 haplotype represents a significant risk to the Australian chickpea industry, being not only widely adapted to the diverse agro-geographical environments of the Australian chickpea growing regions, but also containing a disproportionately large number of aggressive isolates, indicating fitness to survive and replicate on the best resistance sources in the Australian germplasm.

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Section: Discussionmentioning

confidence: 57%

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population

et al. 2017

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“…In fact, disease severity measured on the primary host plants showed that isolates Dp-M07-4, Dp-Esc-13, Dp-KHM-13, and Dp-ANN-13 (from Perth, Australia, Escacena del Campo, Spain and both Khemis Miliana and Annaba from Algeria, respectively) were significantly more aggressive, hence dangerous if introduced in other fields. Migration of invasive organisms might lead to selective emergence of adapted isolates in novel geographic regions and on specific host genotypes (Leo et al, 2015 ). The evolutionary potential of pathogens may be increased and subsequently adapt to overcome host resistances (Linde et al, 2009 ).…”

Section: Discussionmentioning

confidence: 99%

Clarification on Host Range of Didymella pinodes the Causal Agent of Pea Ascochyta Blight

2016

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Didymella pinodes is the principal causal agent of ascochyta blight, one of the most important fungal diseases of pea (Pisum sativum) worldwide. Understanding its host specificity has crucial implications in epidemiology and management; however, this has not been clearly delineated yet. In this study we attempt to clarify the host range of D. pinodes and to compare it with that of other close Didymella spp. D. pinodes was very virulent on pea accessions, although differences in virulence were identified among isolates. On the contrary, studied isolates of D. fabae, D. rabiei, and D. lentil showed a reduced ability to infect pea not causing macroscopically visible symptoms on any of the pea accessions tested. D. pinodes isolates were also infective to some extend on almost all species tested including species such as Hedysarum coronarium, Lathyrus sativus, Lupinus albus, Medicago spp., Trifolium spp., Trigonella foenum-graecum, and Vicia articulata which were not mentioned before as hosts of D. pinodes. On the contrary, D. lentil and D. rabiei were more specific, infecting only lentil and chickpea, respectively. D. fabae was intermediate, infecting mainly faba bean, but also slightly other species such as Glycine max, Phaseolus vulgaris, Trifolium spp., Vicia sativa, and V. articulata. DNA sequence analysis of the nuclear ribosomal internal transcribed spacer region (ITS) was performed to confirm identity of the isolates studies and to determine phylogenetic relationship among the Didymella species, revealing the presence of two clearly distinct clades. Clade one was represented by two supported subclusters including D. fabae isolates as well as D. rabiei with D. lentil isolates. Clade two was the largest and included all the D. pinodes isolates as well as Phoma medicaginis var. pinodella. Genetic distance between D. pinodes and the other Didymella spp. isolates was not correlated with overall differences in pathogenicity. Based on evidences presented here, D. pinodes is not specialized on pea and its host range is larger than that of D. fabae, D. lentil, and D. rabiei. This has relevant implications in epidemiology and control as these species might act as alternative hosts for D. pinodes.

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“…In terms of pathogen life cycle and population structure, the two mating types are found in A. rabiei populations in Israel (Lichtenzveig et al 2005), North America (Peever et al 2004) and Canada (Armstrong et al 2001), thus providing a mechanism for sexual recombination. In Australia, most reports suggest the presence of only mating-type MAT1-2 (Leo et al 2015;Mehmood et al 2017) and the absence of mating in the population. SSR genotyping has found the Australian A. rabiei population to be highly homogenous with around 70% of isolates tested being from a single dominant haplotype designated ARH01 (Leo et al 2015;Mehmood et al 2017).…”

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confidence: 99%

Reference Genome Assembly for AustralianAscochyta rabieiIsolate ArME14

Shah

Williams

Hane

et al. 2020

G3 Genes|Genomes|Genetics

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Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.

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Genetic homogeneity of a recently introduced pathogen of chickpea, Ascochyta rabiei, to Australia

Cited by 23 publications

References 65 publications

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population

Clarification on Host Range of Didymella pinodes the Causal Agent of Pea Ascochyta Blight

Reference Genome Assembly for AustralianAscochyta rabieiIsolate ArME14

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