A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem.
A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem.
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DOI：
10.1534/g3.120.401375
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发表时间：
2020-10-05
期刊：
影响因子：
--
通讯作者：
Croll D
中科院分区：
文献类型：
--
作者：
Fokkens L;Guo L;Dora S;Wang B;Ye K;Sánchez-Rodríguez C;Croll D
植物病原体在农业中引起广泛的产量损失。理解植物-病原体相互作用的驱动因素需要解码导致抗性或疾病的分子对话。然而，在破译致病基因的进展已严重阻碍了合适的模型系统和不完整的真菌基因组组装。在这里，我们报告了一个显着的改进的组装和注释的尖孢镰刀菌（Fo）菌株Fo 5176的基因组。Fo包括数十种植物物种上的大量严重植物病原体，其致病性因素基本上未得到解决。菌株Fo 5176感染拟南芥，因此，构成了一个非常有前途的模式系统。我们使用高覆盖率的Pacific Biosciences Sequel长读和Hi-C测序数据将基因组组装成19条染色体，总基因组大小为67.98 Mb。基因组具有4 Mb的N50和99.1%的完整BUSCO评分。基于单拷贝直向同源物的系统基因组分析清楚地将Fo 5176菌株如预期地置于Fo f sp. concilians进化枝中。我们从培养基和植物感染中生成RNAseq数据来训练基因预测，并鉴定了18,000个基因，包括10个来自其他Fo进化枝的效应基因。我们表明，Fo 5176能够感染甘蓝和甘蓝芽，扩大了Fo 5176模型致病系统的有用性。最后，我们进行了大规模的比较基因组学分析，比较Fo 5176和103个额外的Fo基因组，以确定核心和辅助基因组区域。结合可用于A. Fo 5176基因组和注释为建立一个非常有前途的致病系统提供了关键的一步。
Plant pathogens cause widespread yield losses in agriculture. Understanding the drivers of plant-pathogen interactions requires decoding the molecular dialog leading to either resistance or disease. However, progress in deciphering pathogenicity genes has been severely hampered by suitable model systems and incomplete fungal genome assemblies. Here, we report a significant improvement of the assembly and annotation of the genome of the Fusarium oxysporum (Fo) strain Fo5176. Fo comprises a large number of serious plant pathogens on dozens of plant species with largely unresolved pathogenicity factors. The strain Fo5176 infects Arabidopsis thaliana and, hence, constitutes a highly promising model system. We use high-coverage Pacific Biosciences Sequel long-read and Hi-C sequencing data to assemble the genome into 19 chromosomes and a total genome size of 67.98 Mb. The genome has a N50 of 4 Mb and a 99.1% complete BUSCO score. Phylogenomic analyses based on single-copy orthologs clearly place the Fo5176 strain in the Fo f sp. conglutinans clade as expected. We generated RNAseq data from culture medium and plant infections to train gene predictions and identified ∼18,000 genes including ten effector genes known from other Fo clades. We show that Fo5176 is able to infect cabbage and Brussel sprouts of the Brassica oleracea, expanding the usefulness of the Fo5176 model pathosystem. Finally, we performed large-scale comparative genomics analyses comparing the Fo5176 to 103 additional Fo genomes to define core and accessory genomic regions. In conjunction with the molecular tool sets available for A. thaliana, the Fo5176 genome and annotation provides a crucial step toward the establishment of a highly promising pathosystem.
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影响因子：
4.6
作者：
Chen YC;Wong CL;Muzzi F;Vlaardingerbroek I;Kidd BN;Schenk PM
通讯作者：
Schenk PM
影响因子：
9.3
作者：
Durand NC;Shamim MS;Machol I;Rao SS;Huntley MH;Lander ES;Aiden EL
通讯作者：
Aiden EL
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ
影响因子：
5.2
作者：
Liu, Xing;Xing, Miaomiao;Lv, Honghao
通讯作者：
Lv, Honghao