Scientists ‘turn up the heat’ on understanding coffee wilt disease which threatens our favourite daily brew

(Press-News.org) Scientists, including those from Imperial College London, University of Oxford and CABI, have ‘turned up the heat’ on how repeated outbreaks of coffee wilt disease threatened arabica and robusta varieties of our favourite daily coffee brew.

The scientists, who present their findings in the journal PLoS Biology, say the fungal pathogen Fusarium xylarioides continues to pose a significant threat to coffee production and incomes across sub-Saharan Africa.

Their work supports earlier findings, based on DNA markers and crossing experiments which suggested that F. xylarioides is a species complex containing distinct, host-specific populations.

The scientists confirm the presence of genetically differentiated lineages with different host-specificity for arabica and robusta coffee and show that the fungal pathogen F. xylarioides repeatedly took up “horizontally transferred” segments of DNA from a related fungal Fusarium taxa which contributed to successive outbreaks of the disease.

Primary source of income for more than 12 million households

Coffee is a primary source of income for more than 12 million households in Africa and contributes a significant proportion of tax revenue in a number of these countries, with Ethiopia, for example, recording an export value of $762.8m annually. Yet repeated outbreaks of coffee wilt disease have continued to decimate coffee production in east and central Africa since the 1920s, affecting yields and farmer incomes.

As part of this study, the scientists compared the genomes of 13 historical strains of F. xylarioides spanning six decades from CABI’s Culture Collection, to identify the evolutionary process behind these repeated outbreaks of coffee wilt disease.

Dr Matthew Ryan, Senior Research Lead, Biological Resources at CABI and a co-author of the paper, co-supervised lead author of the research, Dr Lily Peck, of Imperial College London, together with Professor Tim Barraclough from the University of Oxford.

Crucial to understand genetic structure and evolutionary potential

Dr Peck said, “To improve the disease management of fungal pathogens such as Fusarium xylarioides, it is crucial to understand their genetic structure and evolutionary potential.

“We found that F. xylarioides comprised at least four distinct lineages: one host-specific to arabica, one to robusta and two historic lineages isolated from various coffee species.

“The presence/absence of large genomic regions across these lineages showed that horizontal transfers of effector genes, namely genes that are important in establishing successful infection, contributed to establishing host specificity.”

Dr Peck also said that multiple transfers into F. xylarioides populations matched different parts of the Fusarium oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons.

Transposons, also known as “jumping genes,” are DNA sequences that can move around in genomes. They are found in many organisms, including bacteria, yeasts, humans, mice, fruit flies and frogs.

Shown by transcriptomics to be highly expressed during infection

Effector genes and other carbohydrate-active enzymes important in the breakdown of plant cell walls were shown by transcriptomics to be highly expressed during infection of arabica coffee by the pathogenic arabica strains.

Professor Barraclough said, “Widespread sharing of specific transposons between F. xylarioides and F. oxysporum, and the correspondence of a putative horizontally transferred region to a Starship (recently identified large mobile elements which are involved in fungal horizontal gene transfers), reinforce the inference of horizontal transfers and suggest that mobile elements were involved.

“Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of coffee wilt disease.”

Potentially lucrative export of various coffee varieties

Dr Ryan said the research findings potentially show what is happening more widely in relation to fungi and gives scientists the potential to further build on Dr Peck’s study in the future.

“The fact that horizontal gene transfers between two different species of Fusarium contributed to the repeated emergence of coffee wilt disease is a key mechanism to understand what is happening more widely in fungi – to what extent, we just do not know,” he said.

The scientists suggest that horizontal transfer could have occurred in a ‘shared niche,’ as both F. xylarioides and F. oxysporum are soil-borne pathogens and have been isolated from the roots and wood of coffee wilt-diseased trees in Ethiopia and central Africa, and from the roots of a banana tree in central Africa.

They add that 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.

Full paper reference

Lily D. Peck, Theo Llewellyn, Bastien Bennetot, Samuel O’Donnell, Reuben W. Nowell, Matthew J. Ryan, Julie Flood, Ricardo C. Rodŕıguez de la Vega, Jeanne Ropars, Tatiana Giraud, Pietro D. Spanu, Timothy G. Barraclough, ‘Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease,’ PLoS Biol, 5 December 2024, DOI: 10.1371/journal.pbio.3002480

The paper can be read in full here.

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