Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae.
Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae.
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DOI：
10.1038/s41598-018-30335-7
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发表时间：
2018-09-10
影响因子：
4.6
通讯作者：
Clarkson JP
中科院分区：
文献类型：
--
作者：
Armitage AD;Taylor A;Sobczyk MK;Baxter L;Greenfield BPJ;Bates HJ;Wilson F;Jackson AC;Ott S;Harrison RJ;Clarkson JP
洋葱基腐病病原菌尖孢镰刀菌（Fusarium oxysporum f. sp. cepae, Foc）的基因组与其他洋葱致病和非致病分离株的基因组已被合成。系统发育分析证实了Foc致病谱系的单一起源。与其他尖孢菌的基因组比对。spp.和非病原体显示核心染色体的高水平共生性保守，但谱系特异性（LS）染色体之间的共生性很少。在Foc中鉴定出4个总长度为3.9 Mb的LS序列为病原菌特异性（pathogen specific， PS）。与核心区域内或从LS区域到核心区域相比，在基因组的LS区域之间观察到的片段重复事件增加了两倍。RNA-seq表达研究确定了植物中表达的候选效应物，包括已知的效应物同源物和新的候选效应物。发现FTF1和其他转录因子的一个子集参与调控效应表达在植物中表达。
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.
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DOI：
10.1093/bioinformatics/btv562
发表时间：
2016-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gel B;Díez-Villanueva A;Serra E;Buschbeck M;Peinado MA;Malinverni R
通讯作者：
Malinverni R
影响因子：
3.2
作者：
Baayen, RP;O'Donnell, K;Waalwijk, C
通讯作者：
Waalwijk, C
影响因子：
4
作者：
Dong, Suomeng;Raffaele, Sylvain;Kamoun, Sophien
通讯作者：
Kamoun, Sophien
影响因子：
1.5
作者：
Bayraktar, Harun;Dolar, Fatma Sara
通讯作者：
Dolar, Fatma Sara
影响因子：
3.7
作者：
Jiang SY;González JM;Ramachandran S
通讯作者：
Ramachandran S