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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #407284
Research Project: Development of Climate Resilient Germplasm and Management Tools for Sustainable Row Crop Production

Location: Plant Stress and Germplasm Development Research

Title: High-quality de novo genome assembly of two pathogenic Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) Isolates from California

Author
item Jobe, Timothy
item Ulloa, Mauricio
item ELLIS, MARGARET - California State University

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 10/25/2023
Publication Date: 12/15/2023
Citation: Jobe, T.O., Ulloa, M., Ellis, M.L. 2023. High-quality de novo genome assembly of two pathogenic Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) Isolates from California. National Center for Biotechnology Information (NCBI).

Interpretive Summary:

Technical Abstract: Fusarium oxysporum f. sp vasinfectum (FOV) race 4 (FOV4) is the most virulent cotton wilt pathogen in the U.S. FOV4 field-infestations have disrupted cotton production in California, far West Texas, and New Mexico. There is an urgent need for improved detection and diagnostics to combat the spread of FOV4. To help meet this challenge, we report the de novo assembly of two pathogenic isolates designated Tm2 (N-type) and 15-2J (T-type) of FOV4 from California. 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. For each genome, putative gene sets were predicted using Augustus, GeneMarkES, SNAP and GlimmerM. Each of these putative gene sets was evaluated using BUSCO v5 with the fungi_odb10 dataset and GeneMarkES and features were selected as the final gene set based on the superior BUSCO results. The final results of the assembly process generated 16 contigs for Tm2 having a BUSCO score of 98.5 and 18 contigs for 15-2J having a BUSCO score of 98. Interestingly, the N-type isolate Tm2 genome contains only 17,540 putative genes compared to 18,080 putative genes in the T-type isolate 15-2J. 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. High-quality FOV genomes like these will help us better understand the molecular basis of Fusarium pathogenicity. 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.