Two De Novo genome assemblies from pathogenic fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) isolates from California

Authors: Jobe, Timothy; Ulloa, Mauricio; ELLIS, MARGARET - California State University

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2023
Publication Date: 11/30/2023
Citation: Jobe, T.O., Ulloa, M., Ellis, M.L. 2023. Two De Novo genome assemblies from pathogenic fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) isolates from California. Microbiology Resource Announcements. 13(1). https://doi.org/10.1128/mra.00760-23.
DOI: https://doi.org/10.1128/mra.00760-23

Interpretive Summary: The most severe Fusarium wilt (FOV) disease of cotton in the USA is caused by a soilborne fungal pathogen known as FOV race 4 (FOV4). This disease is responsible for substantial crop losses in California, far West Texas, and New Mexico. Molecular information or complete information of genes or proteins is limited for pathogens causing diseases. A molecular blueprint of this pathogen or high-quality whole DNA genome sequence, structural assembly, and gene annotation of two FOV4 strains or isolates from California were obtained by ARS and University scientists. Performed analyses suggest that these structural assemblies are of high quality. Overall, this obtained information from FOV4 will help us develop diagnostic tools of identification and specifically target this pathogen. In addition, resources like this are used by researchers, biologist, pathologists, geneticist and breeders, and are crucial to facilitate the identification of genes important for causing this disease, pathogen-plant interactions, and for improving cotton resistance to diseases such as Fusarium wilt.

Technical Abstract: While multiple races of Fusarium oxysporum f. sp vasinfectum (FOV) have been identified, FOV race 4 (FOV4) is considered the most virulent cotton wilt pathogen in the US. FOV4 infestations have disrupted cotton production in California, far West Texas, and New Mexico. Recent efforts aimed at rapid identification and classification of FOV and FOV-specific races have focused on DNA sequencing of the translation elongation factor (EF-1a), phosphate permease (PHO), and ß-tubulin (BT) genes, and intergenic spacer (ITS) regions. Interestingly, these efforts have identified four distinct genotypes of FOV4 based on the absence (N-type) or presence of the transposable element Tfo1 in the PHO gene (T-type). For this study, two previously described FOV4 isolates from California designated Tm2 (N-type) and 15-2J (T-type) were used. The pathogenicity of these isolates was previously documented using several assays. Cultures of each isolate were grown and high molecular weight DNA appropriate for Oxford Nanopore sequencing was extracted and used for library preparation. Base calling was performed using MinKNOW v22.12.5. We generated a high-quality whole genome sequence, assembly, and gene annotation of these two FOV4 isolates from California. A total sequencing coverage of 117x was generated for isolate Tm2 and 197x sequencing coverage was generated for isolate 15-2J. We discuss key parameters that suggest this assembly is of high quality. As FOV races are continuing to change, there is currently an urgent need for additional genetic markers to improve and accelerate our diagnostic capabilities, especially for FOV4. To achieve this goal, whole genome sequencing of many diverse FOV and FOV4 isolates is needed. In addition, resources like this are crucial to facilitate the identification of genes important in host-plant interactions and for improving crop resistance to diseases such as Fusarium wilt.