A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems
文献类型： 外文期刊
作者： Kim, Hanhae 1 ; Joe, Anna 2 ; Lee, Muyoung 1 ; Yang, Sunmo 1 ; Ma, Xiaozhi 4 ; Ronald, Pamela C. 2 ; Lee, Insuk 1 ;
作者机构： 1.Yonsei Univ, Dept Biotechnol, Coll Life Sci & Biotechnol, Seoul, South Korea
2.Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA
3.Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA
4.Guangdong Acad Agr Sci, Rice Res Inst, Guangzhou, Guangdong, Peoples R China
5.Korea Inst S&T Evaluat & Planning, Bio & Basic Sci R&D Coordinat Div, Seoul, South Korea
6.Joint Bioenergy Inst, Feedstocks Div, Oakland, CA 94608 USA
关键词： co-functional network; plant bacterial pathogen; Xanthomonas oryzae pv. oryzae
期刊名称：MOLECULES AND CELLS （ 影响因子：5.034； 五年影响因子：4.932 ）
ISSN： 1016-8478
年卷期： 2019 年 42 卷 2 期
页码：
收录情况： SCI
摘要： Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.
- 相关文献
作者其他论文 更多>>
-
Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice
作者：Fu, Chongyun;Zhu, Manshan;Liu, Wuge;Ma, Xiaozhi;Li, Jinhua;Liao, Yilong;Liu, Dilin;Wang, Feng;Fu, Chongyun;Zhu, Manshan;Liu, Wuge;Ma, Xiaozhi;Li, Jinhua;Liao, Yilong;Liu, Dilin;Wang, Feng;Fu, Chongyun;Zhu, Manshan;Liu, Wuge;Ma, Xiaozhi;Li, Jinhua;Liao, Yilong;Liu, Dilin;Wang, Feng;Fu, Chongyun;Zhu, Manshan;Liu, Wuge;Ma, Xiaozhi;Li, Jinhua;Liao, Yilong;Liu, Dilin;Wang, Feng;Ma, Ce;Gu, Xiaofeng;Wang, Haiyang
关键词：Indica rice; heterosis; prediction; transcriptome; methylome
-
Comprehensive transcriptomic analysis of three varieties with different brown planthopper-resistance identifies leaf sheath lncRNAs in rice
作者：Liu, Kai;Zhao, Luyao;Lai, Xiaofeng;Chen, Jie;Lang, Xingxuan;Han, Qunxin;Wan, Xiaorong;Li, Chunmei;Liu, Kai;Zhao, Luyao;Lai, Xiaofeng;Chen, Jie;Lang, Xingxuan;Han, Qunxin;Wan, Xiaorong;Li, Chunmei;Ma, Xiaozhi
关键词：Resistant rice; Nilaparvata lugens; Transcriptome; Long non-coding RNAs; Expression analysis
-
Bulk segregant analysis coupled with transcriptomics and metabolomics revealed key regulators of bacterial leaf blight resistance in rice
作者：Ma, Xiaozhi;Zhu, Manshan;Liu, Wuge;Li, Jinhua;Liao, Yilong;Liu, Dilin;Jin, Mengya;Fu, Chongyun;Wang, Feng;Ma, Xiaozhi;Zhu, Manshan;Liu, Wuge;Li, Jinhua;Liao, Yilong;Liu, Dilin;Jin, Mengya;Fu, Chongyun;Wang, Feng;Ma, Xiaozhi;Zhu, Manshan;Liu, Wuge;Li, Jinhua;Liao, Yilong;Liu, Dilin;Jin, Mengya;Fu, Chongyun;Wang, Feng
关键词：Bacterial leaf blight; Rice; Disease resistance; Genetics; R genes
-
The grain yield regulator NOG1 plays a dual role in latitudinal adaptation and cold tolerance during rice domestication
作者：Huo, Xing;Xiao, Junyi;Peng, Xin;Liu, Dilin;Liu, Wuge;Liao, Yilong;Li, Jinhua;Zhu, Manshan;Fu, Chongyun;Zeng, Xueqin;Ma, Xiaozhi;Kong, Le;Wang, Feng;Xiao, Junyi;Lin, Yanhui
关键词：NOG1; cold stress; domestication; differentially expressed genes; RNA-seq
-
Rice Brittle Culm19 Encoding Cellulose Synthase Subunit CESA4 Causes Dominant Brittle Phenotype But has No Distinct Influence on Growth and Grain Yield
作者：Ma, Xiaozhi;Li, Chunmei;Huang, Rui;Zhang, Kuan;Wang, Qian;Sun, Changhui;Wang, Pingrong;Deng, Xiaojian;Ma, Xiaozhi;Fu, Chongyun;Liu, Wuge;Wang, Feng;Li, Chunmei;Huang, Rui
关键词：Rice; Dominant mutation; Brittle culm; Cellulose synthase; Secondary cell wall
-
QTL mapping using an ultra-high-density SNP map reveals a major locus for grain yield in an elite rice restorer R998
作者：Zhu, Manshan;Liu, Dilin;Liu, Wuge;Li, Dan;Liao, Yilong;Li, Jinhua;Fu, Chongyun;Fu, Fuhong;Huang, Huijun;Zeng, Xueqin;Ma, Xiaozhi;Wang, Feng;Zhu, Manshan;Liu, Dilin;Liu, Wuge;Li, Dan;Liao, Yilong;Li, Jinhua;Fu, Chongyun;Fu, Fuhong;Huang, Huijun;Zeng, Xueqin;Ma, Xiaozhi;Wang, Feng
关键词：
