Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

Achari, Saidi R.; Edwards, Jacqueline; Mann, Ross; Kaur, Jatinder; Sawbridge, Tim; Summerell, Brett A.

doi:10.1186/s12864-021-08033-y

Cited by 10 publications

(7 citation statements)

References 111 publications

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“…for MoCDIP4, which was first discovered in Magnaporthe oryzae ( Chen et al 2013 ) and since reported in F. oxysporum f. sp. pisi ( Achari et al 2021 )), but most had scattered distributions across the group ( supplementary fig. S6, Supplementary Material online), which may be the result of frequent horizontal gene transfer (e.g., van Dam and Rep 2017 ; Peck et al 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures

Hill

Buggs

Vu³

et al. 2022

Molecular Biology and Evolution

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The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)—both likely to be involved in the host–fungal interaction—and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.

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Section: Discussionmentioning

confidence: 99%

Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures

Hill

Buggs

Vu³

et al. 2022

Molecular Biology and Evolution

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“…Modelling of the MoCDIP4 effector used as template the structure of lytic polysaccharide monooxygenase GH61D from Phanerochaete chrysosporium . MoCDIP4 is a cell death-inducing effector [ 53 ]. Pfam analysis indicates that it corresponds to auxiliary activity family 9, AA9 (formerly GH61) domain, and CATH indicates an enzyme accession EC1.14.99.54, which corresponds to lytic polysaccharide monooxygenase.…”

Section: Resultsmentioning

confidence: 99%

Template-Based Modelling of the Structure of Fungal Effector Proteins

et al. 2023

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The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is that many fungal effector proteins discovered so far lack sequence similarity or conserved sequence motifs. The availability of experimentally determined three-dimensional (3D) structures of a number of effector proteins has recently highlighted structural similarities amongst groups of sequence-dissimilar fungal effectors, enabling the search for similar structural folds amongst effector sequence candidates. We have applied template-based modelling to predict the 3D structures of candidate effector sequences obtained from bioinformatics predictions and the PHI-BASE database. Structural matches were found not only with ToxA- and MAX-like effector candidates but also with non-fungal effector-like proteins—including plant defensins and animal venoms—suggesting the broad conservation of ancestral structural folds amongst cytotoxic peptides from a diverse range of distant species. Accurate modelling of fungal effectors were achieved using RaptorX. The utility of predicted structures of effector proteins lies in the prediction of their interactions with plant receptors through molecular docking, which will improve the understanding of effector–plant interactions.

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“…spp. ( van Dam et al, 2016 ; Czislowski et al, 2018 ; Achari et al, 2021 ; Batson et al, 2021 ), were investigated in this study to assess their presence in the four FOA isolates. The results unveiled a narrow set of these effectors, namely homologs of SIX1, SIX6, SIX9, SIX11, and SIX14, extending the repertoire of known SIX genes within the FOA species.…”

Section: Discussionmentioning

confidence: 99%

Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm

Khayi,

Armitage,

Gaboun

et al. 2023

Front. Microbiol.

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Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.

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Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

Cited by 10 publications

References 111 publications

Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures

Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures

Template-Based Modelling of the Structure of Fungal Effector Proteins

Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm

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