Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida.
Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida.
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DOI：
10.1186/1471-2164-15-923
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发表时间：
2014-10-23
期刊：
影响因子：
4.4
通讯作者：
Jones JT
中科院分区：
文献类型：
--
作者：
Thorpe P;Mantelin S;Cock PJ;Blok VC;Coke MC;Eves-van den Akker S;Guzeeva E;Lilley CJ;Smant G;Reid AJ;Wright KM;Urwin PE;Jones JT
马铃薯囊肿线虫与寄主有生物营养相互作用。线虫诱导了一种进食结构——合胞体，它在整个生命周期中保持合胞体的活力，并依靠合胞体获得发育到成虫阶段所需的所有营养。苍螺菌与寄主的相互作用是由效应器介导的，效应器在两组腺体细胞中产生。这些效应物抑制宿主防御，促进迁移并诱导合胞体的形成。最近完成的苍白藻基因组序列使我们能够从该物种中识别出效应补体。我们从其他线虫中鉴定出128个效应物的同源物以及117个新的候选效应物。我们已经使用原位杂交来确认这些效应物的一个子集的腺体细胞表达，证明了我们的效应物鉴定方法的有效性。我们使用RNAseq检测了所有候选效应物的表达谱；该分析表明，大多数效应子属于具有保守表达特征的三组序列之一（仅侵袭期线虫，仅寄生期或仅侵袭期和成年雄性）。我们证明了效应池的进一步多样性是由选择性剪接产生的。此外，我们表明，效应物靶向植物细胞中的多种结构，包括过氧化物酶体。这是首次从任何植物病原体中鉴定出针对该结构的效应物。这是第一次对任何植物寄生线虫的效应物进行基因组规模的搜索，并结合生命周期表达分析。我们发现，与其他系统发育无关的植物病原体一样，植物寄生线虫为了寄生植物部署了数百种效应物，在感染过程的不同阶段需要不同的效应物。本文的在线版本（doi:10.1186/1471-2164-15-923）包含补充材料，可供授权用户使用。
The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure – the syncytium – which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium. The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure. This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process. The online version of this article (doi:10.1186/1471-2164-15-923) contains supplementary material, which is available to authorized users.
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Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
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影响因子：
9.4
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影响因子：
3.5
作者：
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影响因子：
12.3
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DOI：
10.1073/pnas.0604698103
发表时间：
2006-09-26
影响因子：
11.1
作者：
Huang, Guozhong;Allen, Rex;Hussey, Richard S.
通讯作者：
Hussey, Richard S.