The dispensable chromosome of <i><scp>L</scp>eptosphaeria maculans</i> shelters an effector gene conferring avirulence towards <i><scp>B</scp>rassica rapa</i>

Balesdent, Marie‐Hélène; Fudal, Isabelle; Ollivier, Bénédicte; Bally, Pascal; Grandaubert, Jonathan; Eber, Frédérique; Chèvre, Anne‐Marie; Leflon, Martine; Rouxel, Thierry

doi:10.1111/nph.12178

Cited by 176 publications

(213 citation statements)

References 45 publications

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“…Several resistance genes have been mapped, but only one, LepR3, has been cloned (Delourme et al 2006, van de Wouw et al 2009, Long et al 2011, Larkan et al 2013. Five avirulence genes have been cloned in L. maculans (AvrLm1, AvrLm4-7, AvrLm6, AvrLm11, AvrLmJ1) (Gout et al 2006, Parlange et al 2009, Balesdent et al 2013, van de Wouw et al 2014a). The molecular basis of the interaction between these key proteins in the fungus and the plant is as yet unknown.…”

Section: Blackleg Disease Of Canolamentioning

confidence: 99%

Evolution of virulence in fungal plant pathogens: exploiting fungal genomics to control plant disease

2015

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The propensity of a fungal pathogen to evolve virulence depends on features of its biology (e.g. mode of reproduction) and of its genome (e.g. amount of repetitive DNA). Populations of Leptosphaeria maculans, a pathogen of Brassica napus (canola), can evolve and overcome disease resistance bred into canola within three years of commercial release of a cultivar. Avirulence effector genes are key fungal genes that are complementary to resistance genes. In L. maculans these genes are embedded within inactivated transposable elements in genomic regions where they are readily mutated or deleted. The risk of resistance breakdown in the field can be minimised by monitoring disease severity of canola cultivars and virulence of fungal populations using high throughput molecular assays and by sowing canola cultivars with different resistance genes in subsequent years. This strategy has been exploited to avert yield losses due to blackleg disease in Australia.

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Section: Blackleg Disease Of Canolamentioning

confidence: 99%

Evolution of virulence in fungal plant pathogens: exploiting fungal genomics to control plant disease

2015

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“…The products of these genes are known as effector proteins, and these carry out functions such as plant defence suppression and host cellwall modifications upon infection (Rouxel et al, 2011). Of the eleven L. maculans Avr genes identified, six (AvrLm1, AvrLm6, AvrLm4-7, AvrLm11, AvrLm2 and AvrLm3) (Fudal et al, 2007;Gout et al, 2006b;Parlange et al, 2009;Balesdent et al, 2013;Ghanbarnia et al, 2014;Plissonneau et al, 2015), have been characterised (Table 1.1). A seventh AvrLm gene, AvrLmJ1, virulent on Brassica juncea cultivars, has also been characterised .…”

Section: Avirulence Effector Genesmentioning

confidence: 99%

“…On the other hand, effectors damaging to pathogen fitness can just as easily be lost. Four of the known effector genes, AvrLm1, AvrLm6, AvrLm4-7 and AvrLm11 are hosted in AT-rich isochores of the blackleg genome (Gout et al, 2006b;Fudal et al, 2007;Parlange et al, 2009;Balesdent et al, 2013;Grandaubert et al, 2014b).…”

Section: Avrlmj1mentioning

confidence: 99%

“…In such a scenario, the pathogen needs to overcome resistance and does so because of its high evolutionary potential. The detectable avirulence gene is quickly rendered unrecognisable through methods such as deletion, RIP mutation, point mutation or by conditionally losing the chromosome that contains the avirulence gene (Gout et al, 2006b;Fudal et al, 2007;Fudal et al, 2009;Balesdent et al, 2013;Ghanbarnia et al, 2014;Van de Wouw et al, 2014). This led us to hypothesise that the gene loss tool could highlight candidate effectors that are being lost in the sample set as compared to the reference.…”

Section: Candidate Effector Genesmentioning

confidence: 99%

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Population diversity and genomics of the fungal pathogen of canola Leptosphaeria maculans

Patel¹

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Canola (Brassica napus) is an important agricultural crop in Australia. Its value as an agricultural commodity has dramatically increased over the past few years to >$2000 million (AUD) in 2015.However, the production of this prosperous crop is threatened by up to 34 different pests, including fungal, bacterial and viral pathogens. Diseases caused by these pathogens lead to substantial crop losses that collectively amount to $130 million (AUD) each year. Leptosphaeria maculans (blackleg) is a ubiquitous ascomycete fungus that is the major causal agent of disease on canola plants. It is called blackleg due to its necrotrophic effects that cause stem canker at the base of the stem during the last stages of infection. When canola was first introduced to Australia as an agricultural crop in the 1970s, blackleg disease led to almost 90% crop losses, threatening to drive the nascent canola industry in Australia to the ground. In recent years, crop losses still amount to $76.6 million (AUD) per annum. Therefore, it is imperative to devise methods to control the devastating effects of this pathogen to protect this economically significant crop. In order to do so, we must decipher the genomic content that drives this pathogen to cause large-scale infections in the field.Blackleg disease is a major concern not only in Australia, but also in other parts of the world such as Europe and Canada. Over the past few years, scientists have made significant advances in decoding the genome of this pathogen. It has been established that L. maculans interacts in a genefor-gene manner with its host. It is composed of disease-causing avirulence (Avr) genes that are specifically recognised by the corresponding resistance (R) gene in the host plant. The specific location and characterisation of the Avr genes AvrLm1, AvrLm6, AvrLm4-7, AvrLm11, AvrLmJ1, AvrLm2 and AvrLm3 has been determined. Furthermore, the reference genome for this pathogen was sequenced in 2011. The reference genome based on the strain v23.1.3 is 45.12 Mb and is scaffolded onto 76 supercontigs. It was reported to be bipartite in nature, composed of AT and GCrich blocks and riddled with truncated copies of transposable elements (TEs) that were affected by Repeat-Induced Point (RIP) mutations. The availability of a reference genome has greatly assisted in designing bioinformatics tools to analyse the genomic content of this pathogen. Here we contribute to the growing pool of knowledge of blackleg genomics.This thesis begins by shedding light on the population diversity of this pathogen in Australia. We used Single Nucleotide Polymorphisms (SNPs) and sampled a large variety of isolates from different canola-growing regions across Australia. We were able to conclude that the Australian blackleg population is panmictic in nature, where members of the population interact randomly with one another, leading to high diversity via sexual reproduction. Increased genetic diversity amongst the population contributes significantly to increase the evolutionary potential of thi...

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“…Genetic mapping of avirulence genes revealed four unlinked genomic regions of L. maculans associated with host specificity: the AvrLm1-AvrLm2-AvrLm6 cluster, the AvrLm3-AvrLm4-AvrLm7 cluster, AvrLm5, AvrLm8 and AvrLm11 (Balesdent et al, 2002, Fernando et al, 2007, Balesdent et al, 2013. This cluster of Avr genes in L. maculans has been described as the first example of Avr gene clustering in fungi.…”

Section: Molecular Interaction Between Brassica and L Maculansmentioning

confidence: 99%

Genome wide identification of NBS-LRR genes in Brassica and their association with disease resistance in Brassica napus

Alamery¹

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Brassica napus (canola/rapeseed/oilseed rape) is an important commercial oilseed crop in Australia with an annual production of approximately 1.6 million tons of oil. Canola is an important source of edible vegetable oil and has a broad range of industrial purposes. Blackleg disease (stem canker) caused by the fungal pathogen Leptosphaeria maculans, is one of the most devastating diseases in B. napus. This disease causes significant yield losses with an annual average loss of 15 to 48 %, although losses can reach up to 80% worldwide, mainly in Europe, Australia and Canada.In order to develop an effective strategy to control the blackleg disease, there is a need to identify blackleg resistance genes in Brassica species and understand the genetic interaction between plant resistance genes and the pathogen avirulence genes. Thus, identification of Nucleotide Binding SiteLeucine Rich Repeat (NBS-LRR) resistance genes is one of the most important objectives of understanding resistance. NBS-LRR resistance genes have been extensively studied because they represent the largest class of disease resistance genes and play a critical role in defending plants from pathogens.The objective of this study was to perform comprehensive analysis on identification and characterization of NBS-LRR genes in the B. napus genome and to study the synteny and conservation of NBS-LRR genes between Brassica species. In this study, a total of 641, 249 and 443 NBS-LRR encoding genes in B. napus, B. rapa and B. oleracea, respectively, were identified.The comparative analysis between B. napus and its progenitor species indicated that NBS-LRR genes exhibited similar gene structure, genomic location, arrangement in clusters and syntenic relationships. The results provide evidence that there was a selective advantage to maintaining similar features of NBS-LRR genes in B. napus to both B. rapa and B. oleracea following polyploidization. More than 60% of NBS LRR genes from the progenitor species were conserved.The differences in NBS-LRR gene conservation could be attributed to gene losses or selection pressure to offer species-specific or cultivars-specific resistance.This study found that the NBS-LRR resistance genes are physically clustered and individual genes involved in clusters were more polymorphic and subject to evolutionary process than singleton genes. These clusters, which have been described in many other species, provide a reservoir of genetic variation influenced by tandem duplication and selection pressure. In addition, there was a significant correlation and co-localization between the number of NBS-LRR genes within the disease QTL intervals and the number of genes involved in gene clusters or duplication. This ii correlation provides evidence that NBS-LRR are distributed and clustered throughout the genome and tends to be linked and associated with disease QTL intervals. Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A. P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, ...

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The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa

Cited by 176 publications

References 45 publications

Evolution of virulence in fungal plant pathogens: exploiting fungal genomics to control plant disease

Evolution of virulence in fungal plant pathogens: exploiting fungal genomics to control plant disease

Population diversity and genomics of the fungal pathogen of canola Leptosphaeria maculans

Genome wide identification of NBS-LRR genes in Brassica and their association with disease resistance in Brassica napus

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