NIAB-EMR, New Road, East Malling, Kent, ME19 6BJ, UK.
Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK.
Sci Rep. 2018 Sep 10;8(1):13530. doi: 10.1038/s41598-018-30335-7.
A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core. RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta.
已经生成了洋葱基底腐烂病病原体洋葱镰孢菌 f. 孢子 (Foc) 的参考质量组装，以及其他致病和非致病洋葱分离物的基因组。系统发育分析证实 Foc 致病谱系具有单一起源。与其他 F. oxysporum ff. spp. 和非病原体的基因组比对显示核心染色体的高度同线性保守，但谱系特异性 (LS) 染色体之间很少有同线性。Foc 中的四个 LS 连续体总计 3.9 Mb 被指定为病原体特异性 (PS)。与核心区域或从 LS 区域到核心区域相比，在基因组的 LS 区域之间观察到两倍的片段重复事件增加。RNA-seq 表达研究鉴定了在植物体内表达的候选效应子，包括已知的效应子同源物和新的候选物。发现 FTF1 和其他一些参与效应子表达调控的转录因子在植物体内表达。
