De Novo
 Genome Sequence of a
 Fusarium xylarioides
 Race Pathogenic to Robusta Coffee (
 Coffea canephora
 ) in Uganda

Olal, S.; Bitalo, Daphne Nyachaki; Olango, Nicholas; Mulindwa, Julius; Ochwo, Silver; Opiyo, Stephen O.; Arinaitwe, Geofrey; Ogwok, Emmanuel

doi:10.1128/mra.00520-19

Cited by 4 publications

(3 citation statements)

References 5 publications

(5 reference statements)

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“…Previous work described the pathology of the epidemics (Flood 2009), clarified molecular taxonomy (Buddie et al 2015, Flood 2005, showed reproductive isolation between the host-specialists (Lepoint et al 2005), and reported the first genome (Olal et al 2019). The genetic basis for successive outbreaks and host-specialisation remains unexplored, however.…”

Section: Introductionmentioning

confidence: 99%

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

Peck

Nowell

Flood

et al. 2020

Preprint

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1AbstractNearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following an initial 1920s outbreak. After successful management, it later re-emerged reaching two separate epidemics by the 2000s on arabica coffee in Ethiopia and robusta coffee in east and central Africa. Here, we use genome sequencing of six historical culture collection strains spanning 70 years to identify the evolutionary processes behind these repeated outbreaks. The robusta population arose from the initial outbreak, whilst the arabica population is divergent and emerged independently. The two populations evolved similar pathologies by separately acquiring different effector genes horizontally via transposable elements from other Fusarium taxa, including F. oxysporum. Thus, historical genomics can help reveal mechanisms that allow fungal pathogens to keep pace with humanity’s efforts to resist them.

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Section: Introductionmentioning

confidence: 99%

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

Peck

Nowell

Flood

et al. 2020

Preprint

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“…Each F. xylarioides MEGAHIT assembly from this study, as well as those assembled previously [26] and the publicly available genomes robusta925 [89] and robustaL0394 [90], were mapped to the reference genome assembly.…”

Section: Methodsmentioning

confidence: 99%

“…Single nucleotide polymorphisms (SNPs) were called against the arabica563 reference genome for each set of F. xylarioides reads. Reads for robusta925 were downloaded from the Sequence Read Archive (accession PRJNA508603, [89]) and robustaL0394 were shared by [90].…”

Section: Methodsmentioning

confidence: 99%

Horizontal transfers between fungalFusariumspecies contributed to successive outbreaks of coffee wilt disease

Peck,

Llewellyn,

Bennetot

et al. 2023

Preprint

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Outbreaks of fungal disease have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogenFusarium xylarioidesseverely impacted coffee production across sub-Saharan Africa. To improve the disease management of such pathogens, it is crucial to understand their genetic structure and evolutionary potential. We compared the genomes of 13 historic strains spanning six decades and multiple disease outbreaks to investigate population structure and host specialisation. We foundF. xylarioidescomprises at least four distinct lineages: one host-specific toCoffea arabica, one toC. canephoravar.robusta, and two historic lineages isolated from variousCoffeaspecies. Mapping variation onto a new long-read reference genome showed that host-specificity appears to be acquired through horizontal transfer of effector genes from members of theF. oxysporumspecies complex. This species complex is known to cause wilt disease in over 100 plant species. Multiple transfers into theF. xylarioidespopulations matched to different parts of theF. oxysporummobile pathogenicity chromosome and were enriched in effector genes and transposons. Effector genes in this region and other horizontally transferred carbohydrate-active enzymes important in the breakdown of plant cell walls were shown by transcriptomics to be highly expressed during infection ofC. arabicaby the fungal arabica strains. Widespread sharing of specific transposons betweenF. xylarioidesandF. oxysporum, and the presence of largeStarshipelements, indicate that transposons were involved in horizontal transfers. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of this fungal disease.

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Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

et al. 2021

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Background Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following its initial outbreak in the 1920s. After successful management, it later re-emerged and by the 2000s comprised two separate epidemics on arabica coffee in Ethiopia and robusta coffee in east and central Africa. Results Here, we use genome sequencing of six historical culture collection strains spanning 52 years to identify the evolutionary processes behind these repeated outbreaks. Phylogenomic reconstruction using 13,782 single copy orthologs shows that the robusta population arose from the initial outbreak, whilst the arabica population is a divergent sister clade to the other strains. A screen for putative effector genes involved in pathogenesis shows that the populations have diverged in gene content and sequence mainly by vertical processes within lineages. However, 15 putative effector genes show evidence of horizontal acquisition, with close homology to genes from F. oxysporum. Most occupy small regions of homology within wider scaffolds, whereas a cluster of four genes occupy a 20Kb scaffold with strong homology to a region on a mobile pathogenicity chromosome in F. oxysporum that houses known effector genes. Lacking a match to the whole mobile chromosome, we nonetheless found close associations with DNA transposons, especially the miniature impala type previously proposed to facilitate horizontal transfer of pathogenicity genes in F. oxysporum. These findings support a working hypothesis that the arabica and robusta populations partly acquired distinct effector genes via transposition-mediated horizontal transfer from F. oxysporum, which shares coffee as a host and lives on other plants intercropped with coffee. Conclusion Our results show how historical genomics can help reveal mechanisms that allow fungal pathogens to keep pace with our efforts to resist them. Our list of putative effector genes identifies possible future targets for fungal control. In turn, knowledge of horizontal transfer mechanisms and putative donor taxa might help to design future intercropping strategies that minimize the risk of transfer of effector genes between closely-related Fusarium taxa.

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De Novo Genome Sequence of a Fusarium xylarioides Race Pathogenic to Robusta Coffee ( Coffea canephora ) in Uganda

Cited by 4 publications

References 5 publications

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

Horizontal transfers between fungalFusariumspecies contributed to successive outbreaks of coffee wilt disease

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

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