Fusarium oxysporum f. sp. vasinfectum race 1 (ME23) Genome sequencing and assembly

Diseases such as Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny &Hans) in cotton represent expanding threats to crop production. FOV is a widespread soilborne pathogen that causes vascular plant disease and is responsible for substantial crop losses worldwide. There are currently six recognized races of FOV, and FOV race 1 (FOV1) is well established worldwide 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-knot 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 an FOV1 isolate from California. High molecular weight DNA was extracted from mycelia produced from a single spore isolation. Oxford Nanopore sequencing was performed to generate a consensus assembly having 13 contigs with an N50 value of 4,885,915bp and a total length of 49,876,382bp with no gaps. Annotation using the GenSAS annotation server (https://www.gensas.org) generated a final gene set with a predicted total of 16,304 genes. Several indicators suggest this assembly is approaching chromosome level. 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.

棉花上的尖孢镰刀菌萎蔫专化型（Fusarium oxysporum f. sp. vasinfectum (FOV) Atk. Sny & Hans）等病害，正对作物生产构成日益扩大的威胁。FOV是一种分布广泛的土传维管束病原菌，在全球范围内造成严重的作物减产。目前已确认FOV存在6个公认的生理小种，其中FOV1（小种1）已在全球几乎所有棉花主产区广泛定殖，尤其在美国地区发生严重。此外，学界公认根结线虫（Meloidogyne incognita (RKN)）与FOV1存在有害的协同致病作用：RKN造成的根系损伤会提升FOV1侵染的发生率与严重程度。本研究报道了一株来自加利福尼亚州的FOV1分离株的高质量全基因组序列、组装结果及基因注释信息。研究人员从单孢子分离培养的菌丝体中提取了高分子量DNA，通过牛津纳米孔（Oxford Nanopore）测序技术完成测序，最终获得包含13个重叠群（contig）的一致性组装序列，其N50值为4,885,915bp，总长度为49,876,382bp，无间隙序列。利用GenSAS注释服务器（https://www.gensas.org）进行注释，最终得到包含16,304个预测基因的基因集。多项指标表明该组装结果已接近染色体水平。此类基因组资源对于鉴定参与寄主-植物互作的关键基因（效应蛋白与受体）及等位基因，以及优化与枯萎病等病害抗性相关的选择标记具有至关重要的作用。