Investigating the role of helitrons in the emergence of novel Fusarium oxysporum f. sp. lactucae isolates

This is one of the funded projects for our 2025 Undergraduate vacation bursary, click here to return to the list of 15 projects.

This project is going to be…	Remote/virtual
Institute	NIAB
Project supervisor	Dr. Jordan Price
Title of Project	Investigating the role of helitrons in the emergence of novel Fusarium oxysporum f. sp. lactucae isolates
Date of Project Commencement	30 June 2025
Duration (weeks)	8
Brief Description of Project	Fusarium oxysporum (Fo) is a species complex (FOSC) comprising both pathogenic and non-pathogenic isolates. Pathogenic isolates are grouped into formae speciales (f. spp.) by host specificity. For example, isolates infecting lettuce are classified as F. oxysporum f. sp. lactucae (Fola). Fusarium wilt of lettuce is a significant threat worldwide, causing crop losses up to 50%. While races 1, 2, and 3 have historically affected warmer regions, race 4 (Fola4) emerged in 2015, spreading across Northern Europe, threatening both glasshouse and open field lettuce production.The FOSC genome is composed of conserved core chromosomes and highly variable accessory chromosomes that are enriched with transposable elements (TEs) and effector genes involved in pathogenicity. Among TEs, helitrons are of particular interest because of their ability to replicate via a rolling circle mechanism and capture gene fragments. Unlike other TEs, helitrons can integrate captured genes into new genomic contexts, potentially creating novel combinations that enhance virulence or adaptation. Our recent study identified differential genomic signatures between Fola1 and Fola4 isolates, suggesting that helitrons may have played a role in the evolution of new races. This project will focus on the bioinformatic investigation of helitrons in Fola isolates (FoHeli). The student will identify helitron-associated protein domains through BLAST and HMM-based searches, followed by phylogenetic analyses to cluster the FoHeli into subgroups. Sequence alignments will be performed to characterise conserved terminal sequences. The student will also estimate FoHeli copy numbers across isolates and assess gene capture events, focussing on identifying captured gene fragments that may contribute to virulence. If time permits, the project will expand to the broader FOSC to determine shared and unique FoHeli elements. This research will provide insights into the genetic mechanisms driving pathogen evolution, potentially informing targeted disease management strategies for lettuce.The 8-week project will be hosted by NIAB, a crop research institute in Cambridge. Working arrangements are flexible, allowing the student to choose between remote, onsite, or hybrid working. Dr Jordan Price, a junior group leader in the Plant Pathology department, will supervise the student. Weekly meetings will provide guidance, set goals, and discuss findings, with support available via email and messaging platforms. The student will require a computer with internet access, and the supervisor will assist with setting up computational resources and bioinformatics tools. This studentship offers an exciting opportunity to contribute to cutting edge research in fungal pathogen genomics. The student will gain practical skills in bioinformatics, as well as transferable skills in scientific communication and independent research, preparing them for postgraduate studies or careers in bioinformatics and plant pathology.Recommended reading for the project Edel-Hermann V, Lecomte C. Current Status of Fusarium oxysporum Formae Speciales and Races. Phytopathology. 2019 Apr;109(4):512-530. doi: 10.1094/PHYTO-08-18-0320-RVW. Epub 2019 Mar 4. PMID: 30461350.Yang H, Yu H, Ma LJ. Accessory Chromosomes in Fusarium oxysporum. Phytopathology. 2020 Sep;110(9):1488-1496. doi: 10.1094/PHYTO-03-20-0069-IA. Epub 2020 Aug 6. PMID: 32692281; PMCID: PMC8086798. Bates HJ, Pike J, Price RJ, Jenkins S, Connell J, Legg A, Armitage A, Harrison RJ, Clarkson JP. Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae. Front Plant Sci. 2024 Oct 10;15:1415534. doi: 10.3389/fpls.2024.1415534. PMID: 39450076; PMCID: PMC11499160.Thomas J, Pritham EJ. Helitrons, the Eukaryotic Rolling-circle Transposable Elements. Microbiol Spectr. 2015 Aug;3(4). doi: 10.1128/microbiolspec.MDNA3-0049-2014. PMID: 26350323. Chellapan BV, van Dam P, Rep M, Cornelissen BJ, Fokkens L. Non-canonical Helitrons in Fusarium oxysporum. Mob DNA. 2016 Dec 9;7:27. doi: 10.1186/s13100-016-0083-7. PMID: 27990178; PMCID: PMC5148889.van Dam P, Fokkens L, Ayukawa Y, van der Gragt M, Ter Horst A, Brankovics B, Houterman PM, Arie T, Rep M. A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species. Sci Rep. 2017 Aug 22;7(1):9042. doi: 10.1038/s41598-017-07995-y. PMID: 28831051; PMCID: PMC5567276. https://sandbox.bio/ (particularly the Terminal Basics and Terminal Exercises tutorials)