Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Rouxel, Thierry; Grandaubert, Jonathan; Hane, James K.; Hoede, Claire; Wouw, Angela P. Van de; Couloux, Arnaud; Dominguez, Victoria M.; Anthouard, Véronique; Bally, Pascal; Bourras, Salim; Cozijnsen, Anton; Ciuffetti, Lynda M.; Degrave, Alexandre; Dilmaghani, Azita; Duret, Laurent; Fudal, Isabelle; Goodwin, Stephen B.; Gout, Lilian; Glaser, Nicolas; Linglin, Juliette; Kema, G.H.J.; Lapalu, Nicolas; Lawrence, Christopher B.; May, K. F.; Meyer, Morgan; Ollivier, Bénédicte; Poulain, Julie; Schoch, Conrad L.; Simon, Adeline; Spatafora, Joseph W.; Stachowiak, A.; Turgeon, B. Gillian; Tyler, Brett M.; Vincent, Delphine; Weissenbach, Jean; Amselem, Joëlle; Quesneville, Hadi; Oliver, Richard P.; Wincker, Patrick; Balesdent, Marie‐Hélène; Howlett, Barbara J.

doi:10.1038/ncomms1189

Cited by 490 publications

(740 citation statements)

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“…9b). CSEP-encoding genes are randomly distributed across the chromosomes of C. graminicola, with no evidence for clustering, enrichment on particular chromosomes or localization near transposable elements or telomeres, as has been reported for some other plant pathogens 8,[20][21][22] (Supplementary Note). An MCL analysis revealed that relatively few Colletotrichum CSEPs (14% in both species) belong to small multigenic families with two to five members ( Supplementary Fig.…”

Section: E T T E R Smentioning

confidence: 73%

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

et al. 2012

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Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types

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Section: E T T E R Smentioning

confidence: 73%

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

et al. 2012

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“…Most of the research on genomics in Hypocreales are mainly focused on gene function related to phylogeny, development and pathogenesis, and has revealed the sophisticated strategies associated with the adaption to various lifestyles (Klosterman et al 2011; Rouxel et al 2011). The subtilisins and chitinases, for example, have been shown to be involved in the pathogenesis of insects (Gao et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.

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“…The genome of L. maculans (v23.1.3 strain) was sequenced using a whole-genome shotgun strategy by Rouxel et al (2011). The total genome of 45.12 Mb was scaffolded onto 76 SuperContigs (SCs).…”

Section: Genomics Of Blacklegmentioning

confidence: 99%

“…Gene prediction analyses revealed 12,469 genes, of which nearly 85% were shown to be expressed (Rouxel et al, 2011). The L. maculans genome is made up of alternating homogenous blocks either rich in adenine and thymine (AT) or guanine and cytosine (GC), lending it its bipartite isochore-like nature.…”

Section: Genomics Of Blacklegmentioning

confidence: 99%

“…Idnurm and Howlett (2003) first described the presence of the RIP mechanism in L. maculans. In blackleg, RIP mainly causes C to T and G to A mutations in transposable elements (TEs) and ribosomal DNA (Rouxel et al, 2011). It was noted that Pholy class 1 transposons degraded by RIP were more frequently located in pericentromeic regions (Attard et al, 2005).…”

Section: Repeat-induced Point (Rip) Mutationsmentioning

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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Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Cited by 490 publications

References 56 publications

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

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

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