Genome Resources of Four Distinct Pathogenic Races Within Fusarium oxysporum f. sp. vasinfectum that Cause Vascular Wilt Disease of Cotton

• Published in: Phytopathology 2021-03, Vol.111 (3), p.593-596
• Main Authors: Srivastava, Subodh K, Zeller, Kurt A, Sobieraj, James H, Nakhla, Mark K
• Format: Article
• Language: English
• Subjects: Fusarium - genetics; Phylogeny; Plant Diseases; Quantitative Trait Loci
• ISSN: 0031-949X; 1943-7684
• DOI: 10.1094/PHYTO-07-20-0298-A

Whole genome sequence (WGS) based identifications are being increasingly used by regulatory and public health agencies to facilitate the detection, investigation, and control of pathogens and pests. f. sp. is a significant vascular wilt pathogen of cultivated cotton and consists of several pathogenic races that are not each other's closest phylogenetic relatives. We have developed WGS assemblies for isolates of f. sp. race 1 (FOV1), race 4 (FOV4), race 5 (FOV5), and race 8 (FOV8) using a combination of Nanopore (MinION) and Illumina sequencing technology (Mi-Seq). This resulted in assembled contigs with more than 100× coverage for each of the f. sp. races and estimated genome sizes of FOV1 52 Mb, FOV4 68 Mb, FOV5 68 Mb, and FOV8 55 Mb. The AUGUSTUS gene prediction program predicted 16,263 genes in FOV1, 20,259 genes in FOV4, 20,375 genes in FOV5 and 16,615 genes in FOV8. We were able to identify 525 genes unique to FOV1, 570 unique to FOV4, 1,242 unique to FOV5, and 383 unique to FOV8. We expect that these findings will help in comparative genomics and in the identification of unique genes as candidate targets for diagnostic marker and methods development to permit rapid differentiation of f. sp. subgroups.