publications

2025

1. Drought-associated genes exhibit high constitutive expression in Quercus douglasii, a drought-tolerant California oak

   Stephanie E. Steele, Lily D. Peck, and Victoria L. Sork

   G3: Genes, Genomes, Genetics, Dec 2025

   Equal co-first authors: Steele SE and Peck LD

   Abs DOI

   Drought stress is a strong selective pressure for all plant species. Plants respond to water shortage through various strategies that confer drought tolerance. These strategies may be plastic responses that occur with the onset of stress or may comprise continuously expressed (constitutive) traits regardless of water availability. Here, we used RNA-seq to characterize transcriptional responses to dehydration in seedlings of a drought-tolerant oak, Quercus douglasii, from a local population in the Sierra Nevada Foothills in California. In the greenhouse, we subjected 24 seedlings from 6 maternal families to dry-down or well-watered treatments and prepared RNA libraries from tissue collected before and after each treatment (48 libraries). Upregulated genes were related to known drought response functions, while downregulated genes were enriched for gene ontology terms related to growth and carbohydrate metabolism. We discovered high constitutive expression of many putatively drought-responsive genes that had been found to exhibit gene expression plasticity in a different oak species, which is drought-sensitive. This novel finding demonstrates the potential for constitutive expression of genes involved in drought stress to provide an additional mechanism of drought tolerance for some tree species, such as Q. douglasii.

2024

1. Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease

   Lily D. Peck, Theo Llewellyn, Bastien Bennetot, and 9 more authors

   PLOS Biology, Dec 2024

   Abs DOI

   Outbreaks of fungal diseases have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogen Fusarium xylarioides severely 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 6 decades and multiple disease outbreaks to investigate population structure and host specialisation. We found that F. xylarioides comprised at least 4 distinct lineages: 1 host-specific to Coffea arabica, 1 to C. canephora var. robusta, and 2 historic lineages isolated from various Coffea species. The presence/absence of large genomic regions across populations, the higher genetic similarities of these regions between species than expected based on genome-wide divergence and their locations in different loci in genomes across populations showed that horizontal transfers of effector genes from members of the F. oxysporum species complex contributed to host specificity. Multiple transfers into F. xylarioides populations matched different parts of the F. oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of coffee wilt disease.

2. Can DNA methylation shape climate response in trees?

   Lily D. Peck, and Victoria L. Sork

   Trends in Plant Science, Jun 2024

   DOI
3. Coffee wilt disease: The forgotten threat to coffee

   Lily D. Peck, and Eric Boa

   Plant Pathology, Apr 2024

   Abs DOI

   Coffee is attacked by several highly damaging pests and diseases, which include coffee wilt disease (CWD). Despite a devastating impact in recent years, CWD receives little attention and its importance is downplayed or simply ignored. Memories are short and knowledge of past outbreaks fragmentary. Nearly two decades after the last major outbreaks, CWD has quietly faded into the background. This review describes a series of outbreaks of CWD across Africa, from Uganda to Guinea, from the first discovery in the 1920s to a hugely damaging recurrence that began in the 1970s and lasted through to the 2000s. This second wave had devastating impacts on growers and communities in the Democratic Republic of Congo and in Uganda. This review examines the origins of the disease, how and why it spread, and attempts to manage the outbreaks. Recent work on new pathogen variants is also considered. This review aims to recount these events and to evaluate the strategic successes and failures at national, regional and international levels in tackling the second wave of CWD.

2023

1. Temperature contributes to host specialization of coffee wilt disease (Fusarium xylarioides) on arabica and robusta coffee crops

   Xiuhan Zhang, Lily D. Peck, Julie Flood, and 2 more authors

   Scientific Reports, Jun 2023

   Abs DOI

   Coffee wilt disease, caused by the fungus Fusarium xylarioides, is a vascular wilt disease that has affected coffee production in sub-Saharan Africa over the past century. Today, the disease has two host-specific populations specialising on arabica and robusta coffee crops, which grow at high and low altitude, respectively. Here we test whether adaptation to different temperatures contributes to specialisation of the fungi on each crop. Firstly, climate models show that the severity of the arabica and robusta populations of coffee wilt disease correlates with temperature. The robusta population shows higher peak severity than the arabica population overall, but the latter has greater cold tolerance. Secondly, growth assays of thermal performance of fungal strains in vitro show that, while robusta strains grow faster than arabicas at intermediate temperatures, the arabica strains have higher sporulation and spore germination rates at temperatures below 15ºC. The match between environmental patterns of severity in nature with thermal performance of fungal cultures in the laboratory supports a role for temperature adaptation in specialisation on arabica and robusta coffee. Extrapolating our temperature-models to future climate change predicts that disease severity could decline on average due to increased temperature but could increase in some coffee-growing regions.

2022

1. Culture collections as a source of historic strains for genomic studies in plant pathology

   Matthew J. Ryan, Lily D. Peck, David Smith, and 2 more authors

   Journal of Plant Pathology, Oct 2022

   Abs DOI

   The first microbial culture collection was established in 1890, and subsequently, over the course of the twentieth century, the number of culture collections grew substantially. One such collection was the CABI-IMI Genetic Resources Collection, informally initiated at the origins of the Commonwealth Mycological Institute in 1920 and established as a UK National Collection in 1947. Its holdings reflect the activities of CABI in agriculture and the environment. Like many collections, it was originally established as a taxonomic reference resource. Over the years, deposits have included strains isolated from disease outbreaks in major crops from all parts of the world. Recent developments in genome sequencing technology and bioinformatic analysis have opened up the potential to characterise historic strains to shed more insights on their biology and evolution. In this paper we describe how the resources held within the CABI-IMI culture collection have helped track the emergence and divergence of Fusarium xylarioides, the coffee wilt pathogen, with a specific focus on the evolution of pathogenicity.

2021

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

   Lily D. Peck, Reuben W. Nowell, Julie Flood, and 2 more authors

   BMC Genomics, Jun 2021

   Abs DOI

   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. Here, we use genome sequencing of six historical culture collection strains spanning 52 years to identify the evolutionary processes behind these repeated outbreaks.