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

Abstract

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. Such studies illustrate the value held within the world’s culture collections—their importance in underpinning science and developing our understanding and evolution of plant diseases as well as how the impact of disease can be mitigated in response to climate change, in order to increase yields and feed the world’s burgeoning population.

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

“…Previously, the analysis of historic genetic material involved the use of highly degraded museum specimens and molecular markers and target probes in a small number of genes [49]. However, fungal culture collections contain tens of thousands of fungal isolates collected over the past century and preserved in a living state [50]. If collections are connected with new -omics studies, new HTRs could be investigated at a new inter- and intra-species level.…”