Table_3_Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China.XLSX

Cabbage Fusarium wilt (CFW) caused by Fusarium oxysporum f. sp. conglutinans (FOC) is known to significantly affect yield and quality of cabbages worldwide. CFW was first detected in New York, NY, United States, and has now spread to almost all cabbage-planting areas, including a recent outbreak of the disease in China. However, it was unknown whether the FOC strains emerged in China differed from the strains in other areas of the world. From 2009 to 2018, we collected Chinese FOC isolates and compared them to the races 1 and 2 strains in other areas to define their characteristics. Race tests indicated that most of the Chinese FOC strains belonged to race 1 and were more virulent than type strain 52557. To evaluate the genome level diversity, we performed next-generation sequencing and genome assembly for the race 2 strain 58385. Based on the assembled genome, we discovered abundant single-nucleotide polymorphisms and 645 insertion–deletions (InDels) compared with the race 1 strain FGL03-6 by comparative genomic analysis and showed that all FOC race 1 strains have a low genetic variability, with a genomic background distinct from 58385. Furthermore, the internal transcribed spacer, elongation factor-1α, and whole-genome InDel variation studies suggested that the last might be a powerful tool in phylogenetic as well as evolution analysis for F. oxysporum Schlechtend.: Fr. The race, virulence, and genome-based variation profiles could contribute to our knowledge of FOC diversity and support the studies of pathogen characterization in genomic era and also provide clues for CFW-resistance breeding. To our knowledge, this is the first extensive survey conducted for FOC strains.

大白菜立枯病（CFW），由尖孢镰刀菌菌丝菌（Fusarium oxysporum f. sp. conglutinans，简称FOC）引起，已知其严重影响了全球范围内大白菜的产量与品质。CFW最初在美国纽约州被发现，现已蔓延至几乎所有的大白菜种植区，包括近期中国地区该病的暴发。然而，关于FOC菌株在中国是否与其他地区的菌株存在差异尚无定论。自2009年至2018年，我们收集了中国FOC菌株，并将其与其他地区的1型和2型菌株进行对比，以定义其特征。通过品种测试，我们发现大多数中国FOC菌株属于1型，其致病性比52557型菌株更强。为了评估基因组水平的多样性，我们对2型菌株58385进行了下一代测序和基因组组装。基于组装的基因组，我们通过比较基因组分析发现了与1型菌株FGL03-6相比，58385菌株中存在丰富的单核苷酸多态性和645个插入-缺失（InDels）。此外，通过内转录间隔区、延长因子-1α和全基因组InDels变异的研究表明，后者可能是F. oxysporum Schlechtend.: Fr.系统发育及进化分析的有力工具。品种、致病性和基于基因组的变异谱可能有助于我们了解FOC的多样性，支持基因组时代病原体特征的 研究，并为CFW抗病育种提供线索。据我们所知，这是首次对FOC菌株进行的广泛调查。