Skip to main content
ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #413800
Research Project: Development of Climate Resilient Germplasm and Management Tools for Sustainable Row Crop Production

Location: Plant Stress and Germplasm Development Research

Title: Whole genome sequencing of California and Texas FOV4 isolates from cotton roots for genomic comparisons with a composite Fusarium genome from Uzbekistan

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: 5/17/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Fusarium wilt caused by the fungus Fusarium oxysporum f. sp vasinfectum (FOV) is a global disease responsible for sizeable crop losses annually and is found in many cotton-producing regions, including the Republic of Uzbekistan. In California, New Mexico, and far west Texas, FOV race 4 (FOV4) has been a substantial cotton pathogen causing production disruptions with plant vascular wilt, browning of the vascular tissues, plant death in the most severe cases. Whole-genome sequencing was used characterize FOV4 isolates causing disease in the main cotton producing region of Uzbekistan. The results were compared with FOV4 isolates from California and Texas cotton. To this end, two FOV4 isolates from California (CSU1 and CSU63) and one FOV4 isolate from El Paso, Texas (TX1) were sequenced. High molecular weight DNA was extracted from mycelia produced from a single spore isolation. Oxford Nanopore sequencing libraries were prepared and sequenced using 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 CSU1 isolate assembly consists of 26 contigs having an N50 value of 4,970,333bp, a total length of 58,896,445bp and a final BUSCO of 94.4%. The CSU63 isolate assembly consists of 24 contigs having an N50 value of 5,106,020bp, a total length of 63,907,682bp, and a final BUSCO of 98.9%. The TX1 isolate assembly had 18 contigs with an N50 of 4495885bp, a total length of 64195881bp, and a final BUSCO of 94.3%. Genomic resources like this should play a crucial role in facilitating identification of genes (effectors and receptors) and alleles important in host-plant interactions, and in improving selection signatures relevant for resistance to diseases such as Fusarium wilt.