Cotton Microbiome El Paso, TX 2023 Raw sequence reads

Cotton (Gossypium spp.) is a globally important crop whose productivity is increasingly threatened by Fusarium oxysporum f. sp. vasinfectum (FOV), a soil-borne pathogen responsible for Fusarium wilt race 4 (FOV4). FOV4 has negatively affected cotton production in California over the past two decades and was confirmed in the far west Texas region of El Paso in 2017, where it has caused similar disruptions. These developments highlight the urgent need for improved management strategies and the development of resistant cotton cultivars to maintain agricultural productivity. Understanding the relationships among soil properties, microbial communities, and disease incidence is essential for developing sustainable disease management strategies and breeding resistant cultivars. This study examined fungal microbiome diversity in five cotton fields in the lower valley of El Paso, Texas, which exhibited varying levels of Fusarium wilt incidence caused by FOV4. Comparative analysis was conducted between high-FOV4-incidence fields (F1, F2, and F5) and low-FOV4-incidence fields (F3 and F4). High-throughput amplicon-based metagenomic analysis identified marked differences in microbial community composition and diversity between the fields.