Khayi, Slimane, Armitage, Andrew ORCID: 0000-0002-0610-763X, Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)

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Abstract

Date palm ( Phoenix dactylifera) is the most significant crop across North Africaand the Middle East. However, the crop faces a severe threat from Bayoud diseasecaused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOAis 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 basepairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) contentof 17.30%. Through prediction and annotation, we  identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignmentto 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 and14) 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.

Item Type:	Article
Uncontrolled Keywords:	effector; genome; phylogenomics; Phoenix dactylifera; pandemic; accessory chromosome; lineage specific
Subjects:	Q Science > Q Science (General) S Agriculture > S Agriculture (General) S Agriculture > SB Plant culture
Faculty / School / Research Centre / Research Group:	Faculty of Engineering & Science Faculty of Engineering & Science > Natural Resources Institute Faculty of Engineering & Science > Natural Resources Institute > Agriculture, Health & Environment Department Faculty of Engineering & Science > Natural Resources Institute > Molecular Virology and Entomology Research Group
Last Modified:	19 Oct 2023 11:55
URI:	http://gala.gre.ac.uk/id/eprint/44505

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