Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China
Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China
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DOI：
10.3389/fmicb.2019.01373
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发表时间：
2019-06-25
影响因子：
5.2
通讯作者：
Lv, Honghao
中科院分区：
文献类型：
--
作者：
Liu, Xing;Xing, Miaomiao;Lv, Honghao
甘蓝枯萎病 (CFW) 由尖孢镰刀菌 (Fusarium oxysporum) 引起。 sp。众所周知，球菌凝集素 (FOC) 会显着影响全世界卷心菜的产量和质量。 CFW首先在美国纽约州发现，目前已蔓延至几乎所有卷心菜种植区，包括最近在中国爆发的该病害。然而，尚不清楚中国出现的FOC毒株是否与世界其他地区的毒株不同。 2009年至2018年，我们收集了中国FOC分离株，并将其与其他地区的小种1和2菌株进行比较，以确定其特征。种族测试表明，大多数中国FOC菌株属于小种1，比标准菌株52557毒力更强。为了评估基因组水平的多样性，我们对小种2菌株58385进行了新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，发现与小种1菌株FGL03-6相比丰富的单核苷酸多态性和645个插入缺失（InDels），并表明所有FOC race 1 菌株具有较低的遗传变异性，其基因组背景与 58385 不同。此外，内部转录间隔区、延伸因子 1 α 和全基因组 InDel 变异研究表明，后者可能是 F. oxysporum Schlechtend 系统发育和进化分析的强大工具。种族、毒力和基于基因组的变异谱有助于我们了解 FOC 多样性，支持基因组时代病原体特征研究，并为 CFW 抗性育种提供线索。据我们所知，这是首次针对 FOC 菌株进行广泛调查。
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-1 alpha, 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.