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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 #405305
Research Project: Development of Climate Resilient Germplasm and Management Tools for Sustainable Row Crop Production

Location: Plant Stress and Germplasm Development Research

Title: A high-quality whole genome sequence, assembly, and gene annotation of [Fusarium oxysporum f. sp. vasinfectum (FOV)] race 1 from California

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

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 8/14/2023
Publication Date: 12/15/2023
Citation: Jobe, T.O., Ulloa, M., Elllis, M.L. 2023. A high-quality whole genome sequence, assembly, and gene annotation of [Fusarium oxysporum f. sp. vasinfectum (FOV)] race 1 from California. National Center for Biotechnology Information (NCBI).

Interpretive Summary:

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.