A high-quality draft genome sequence, assembly, and gene annotation of a [Fusarium oxysporum f. sp. vasinfectum (FOV)] race 1 isolate 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: 11/25/2023
Publication Date: 12/15/2023
Citation: Jobe, T.O., Ulloa, M., Ellis, M.L. 2023. A high-quality draft genome sequence, assembly, and gene annotation of a [Fusarium oxysporum f. sp. vasinfectum (FOV)] race 1 isolate from California. Microbiology Resource Announcements. 13(1). https://doi.org/10.1128/mra.00702-23.
DOI: https://doi.org/10.1128/mra.00702-23

Interpretive Summary: Fusarium wilt of cotton is a plant disease caused by a soilborne fungal pathogen known as Fusarium (FOV). This widespread disease is responsible for substantial crop losses and is found in virtually all cotton producing regions worldwide. There are different types or races of this fungus that can infect the cotton plants, producing typical symptoms such as yellowing of the leaves and root death. FOV race 1 (FOV1) is well established across almost all cotton production regions, especially in the US. There is limited molecular information or complete information of genes or proteins from this or other FOV races that cause this disease in cotton. ARS and university scientists were able to obtain the molecular blueprint of this pathogen or whole DNA sequence, assembly, and gene annotation of FOV1 isolate from California. Analyses indicated that this assembly is nearly complete. This information or resources like this are crucial to facilitate the identification of infection-genes important in host-plant interactions and for improving crop resistance to diseases such as Fusarium wilt. In addition, this information will be used by researchers involved in diagnostic of plant disorders or diseases, plant pathogen infection-identification, and breeding and genetics.

Technical Abstract: Fusarium wilt of cotton (Gossypium spp.) is a vascular plant disease caused by the soilborne pathogen Fusarium oxysporum f. sp. vasinfectum (FOV). This widespread disease is responsible for substantial crop losses worldwide and is found in virtually all cotton producing regions worldwide. There are currently six recognized races of FOV, and FOV race 1 (FOV1) is well established across almost all cotton production regions, especially in the US. In addition, it is well known that there is a detrimental synergistic role of root-know nematode [Meloidogyne incognita (RKN)] with FOV1 where root damage caused by the RKN increases the incidence and severity of FOV1 infection. Herein, we report a high-quality whole genome sequence, assembly, and gene annotation of FOV1 from California. High molecular weight DNA was extracted from mycelia produced from a single spore isolation. Oxford Nanopore sequencing libraries were prepared and sequenced using a MinION Mk1C (Oxford Nanopore). The consensus assembly was annotated using the GenSAS annotation server (https://www.gensas.org). The final gene set was evaluated using BUSCO v5. The FOV1 isolate ME-23 assembly consists of 13 contigs having an N50 value of 4,885,915bp and a total length of 49,876,382bp with no gaps. We discuss several quality indicators that suggest this assembly is approaching chromosome level with a predicted total of 17,019 genes. Genomic resources like this are crucial to facilitate the identification of genes (effector and receptors) and alleles important in host-plant interactions and for improving selection signatures relevant for resistance to diseases such as Fusarium wilt.