In silico comparative genomic analysis unravels a new candidate protein arsenal specifically associated with Fusarium oxysporum f. sp. albedinis pathogenesis

Abstract

Fusarium oxysporum f. sp albedinis (Foa) is a devastating fungus of date palms. To unravel the genetic characteristics associated with its pathogenesis, the two available genomes of Foa 133 and Foa 9 were compared with 49 genomes of 29 other pathogenic formae speciales belonging to Fusarium oxysporum species complex (FOSC). Foa 133 and Foa 9 have genomes of 56.23 Mb and 65.56 Mb with 17460 and 19514 putative coding genes. Of these genes, 30% lack functional annotation with no similarity to characterized proteins. The remaining genes were involved in pathways essential to the fungi's life and their adaptation. Foa secretome analysis revealed that both Foa strains possess an expanded number of secreted effectors (3003 in Foa 133 and 2418 in Foa 9). Those include effectors encoded by Foa unique genes that are involved in Foa penetration (Egh16-like family), host defense mechanisms suppression (lysM family) and pathogen protection (cysteine-rich protein family). The accessory protein SIX6, which induces plant cell death, was also predicted in Foa. Further analysis of secreted CAZymes revealed an arsenal of enzymes involved in plant cell wall degradation. This arsenal includes an exclusively Foa-specific CAZyme (GH5-7). Transcription factors and membrane transporters (MFS) involved in fungicide efflux have been predicted in Foa, in addition to a variety of secondary metabolites. These comprise mycotoxins as well as chrysogin, the latter provides Foa with resistance against adverse environmental conditions. Our results revealed new Foa proteins that could be targeted in future research in order to manage Bayoud disease.

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

“…However, our analysis of Foa 133 resulted in the presence of 5 SIX genes: SIX1 gene spanning two contigs (2 variants of SIX1 in Rafiqi et al, 2022 ), SIX6, SIX9 (2 variants), SIX11 and SIX14. Therefore, our results confirm the presence of SIX1, SIX9, and SIX11 and expand on the previous findings ( Ayada et al, 2022 ; Rafiqi et al, 2022 ). The homologs of these 14 known SIX genes have been identified in various ff.…”

“…CAZymes annotations showed that the Foa 44 strain genome sequence is enriched with CAZymes accounting a total of 801 families assigned to 763 genes representing 3.72% of the total number of genes. Notably, our analysis revealed a higher number of CAZymes in Foa 44 compared to previous studies conducted on Foa 133 ( Ayada et al, 2022 ; Rafiqi et al, 2022 ). The highest number of CAZyme genes (374) was assigned to Glucoside Hydrolase (GH) family, followed by Carbohydrate Esterases (CE; 128), Auxilary Activities (AA; 119), Glycosyl Transferases (GTs; 103), Polysaccharide Lyases (PL; 27), and Carbohydrate-Binding Modules (CBMs; 12).…”

“…Subsequently, two genome sequences of FOA were sequenced and published in 2020 by Khayi et al (2020) and in 2022 by Khoulassa et al (2022) . While several studies have since been published on FOA, none have yet characterized the genome structure of this important pathogen ( Ayada et al, 2022 ; Rafiqi et al, 2022 ). Hence, a significant knowledge gap persists regarding the arrangement of the FOA genome and the genetic mechanisms driving its pathogenic properties.…”

FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen

“…However, no graph pangenome reference has been available for F. oxysporum which has limited the integration and application of these genomic resources for pathobiological studies. Similar strategies have been employed for F. oxysporum as well ( 7 , 8 ). The pangenomic approach is especially desirable for the compartmentalized genomes of FOSC ( 9 ) given their genetic diversity, host specificity and ability to quickly adapt to diverse environments.…”

High Inhibition for a CoII Tetrazole Bi‐pyrazole Dinuclear Complex against Fusarium Oxysporum f. sp. Albedinis

“…Remarkable activities were observed against Fusarium oxysporum f.sp. albedinis extracted from sick palm trees presenting the ‘Bayoud disease’ [33] …”