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| 1 | clusterProfiler 4.0:A universal enrichment tool for interpreting omics data显示文摘Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life science.It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible.To meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler 4.0.This package has been enhanced considerably compared with its original version published 9 years ago.The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases.It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization.Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists.We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms. | Tianzhi Wu Erqiang Hu Shuangbin Xu Meijun Chen Pingfan Guo Zehan Dai Tingze Feng Lang Zhou Wenli Tang Li Zhan Xiaocong Fu Shanshan Liu Xiaochen Bo Guangchuang Yu | 2021 | The Innovation2021，2，3： | 40 |
| 2 | The Phytophthora effector Avh241 interacts with host NDR1-like proteins to manipulate plant immunity显示文摘Plant pathogens rely on effector proteins to suppress host innate immune responses and facilitate colonization.Although the Phytophthora sojae RxLR effector Avh241 promotes Phytophthora infection,the molecular basis of Avh241 virulence remains poorly understood.Here we identified non-race specific disease resistance 1(NDR1)-like proteins,the critical components in plant effector-triggered immunity(ETI)responses,as host targets of Avh241.Avh241 interacts with NDR1 in the plasma membrane and suppresses NDR1-participated ETI responses.Silencing of GmNDR1s increases the susceptibility of soybean to P.sojae infection,and overexpression of GmNDR1s reduces infection,which supports its positive role in plant immunity against P.sojae.Furthermore,we demonstrate that GmNDR1 interacts with itself,and Avh241 probably disrupts the self-association of GmNDR1.These data highlight an effective counter-defense mechanism by which a Phytophthora effector suppresses plant immune responses,likely by disturbing the function of NDR1 during infection. | Bo Yang Sen Yang Baodian Guo Yuyin Wang Wenyue Zheng Mengjun Tian Kaixin Dai Zehan Liu Haonan Wang Zhenchuan Ma Yan Wang Wenwu Ye Suomeng Dong Yuanchao Wang | 2021 | Journal of Integrative Plant Biology2021，63，7： | 1 |
| 3 | Fg12 ribonuclease secretion contributes to Fusarium graminearum virulence and induces plant cell death显示文摘Filamentous fungal pathogens secrete effectors that modulate host immunity and facilitate infection. Fusarium graminearum is an important plant pathogen responsible for various devastating diseases. However, little is known about the function of effector proteins secreted by F. graminearum. Herein, we identified several effector candidates in the F. graminearum secretome. Among them, the secreted ribonuclease Fg12 was highly upregulated during the early stages of F. graminearum infection in soybean;its deletion compromised the virulence of F. graminearum. Transient expression of Fg12 in Nicotiana benthamiana induced cell death in a light-dependent manner. Fg12 possessed ribonuclease(RNase) activity, degrading total RNA. The enzymatic activity of Fg12 was required for its cell death-promoting effects. Importantly, the ability of Fg12 to induce cell death was independent of BAK1/SOBIR1, and treatment of soybean with recombinant Fg12 protein induced resistance to various pathogens, including F. graminearum and Phytophthora sojae. Overall, our results provide evidence that RNase effectors not only contribute to pathogen virulence but also induce plant cell death. | Bo Yang Yuyin Wang Mengjun Tian Kaixin Dai Wenyue Zheng Zehan Liu Sen Yang Xinyu Liu Dongya Shi Haifeng Zhang Yan Wang Wenwu Ye Yuanchao Wang | 2021 | Journal of Integrative Plant Biology2021，63，2： | 0 |
| 4 | MicrobiotaProcess:A comprehensive R package for deep mining microbiome显示文摘The data output from microbiome research is growing at an accelerating rate,yet mining the data quickly and efficiently remains difficult.There is still a lack of an effective data structure to represent and manage data,as well as flexible and composable analysis methods.In response to these two issues,we designed and developed the MicrobiotaProcess package.It provides a comprehensive data structure,MPSE,to better integrate the primary and intermediate data,which improves the integration and exploration of the downstream data.Around this data structure,the downstream analysis tasks are decomposed and a set of functions are designed under a tidy framework.These functions independently perform simple tasks and can be combined to perform complex tasks. | Shuangbin Xu Li Zhan Wenli Tang Qianwen Wang Zehan Dai Lang Zhou Tingze Feng Meijun Chen Tianzhi Wu Erqiang Hu Guangchuang Yu | 2023 | The Innovation2023，4，2： | 0 |
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