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A haplotype block associated with thousand-kernel weight on chromosome 5DS in common wheat(Triticum aestivum L.)

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Journal of integrative Plant Biology 2015年第8期57卷 662-672页

作者： Yuquan Wang Chenyang Hao Jun Zheng Hongmei Ge Yang Zhou Zhengqiang Ma Xueyong Zhang Crop Genomics and bioinformatics center and National Key Lab of Crop Genetics and Germplasm Enhancement College of Agricultural SciencesNanjing Agricultural University Key Laboratory of Crop Gene Resources and Germplasm Enhancement Ministry of Agriculture/Institute of Crop Science the Chinese Academy of Agricultural Sciences

Spike number per unit area, number of grains per spike, and thousand-kernel weight（TKW） are important yield components for wheat（Triticum aestivum L.）. TKW has the highest heritability among the three components. We validated 27 simple sequence repeat（SSR） loci associated with TKW in an F2：5breeding population grown in four environments. A cfd78265 bpmarker on chromosome 5DS showed the strongest association with TKW and had a significantly positive effect on TKW compared to allele cfd78259 bp, with mean increases of 5.17, 3.63, 4.11, and 5.16 g in the four environments. Markers cfd67 and cfd40 flanking cfd78 also showed significantly positive associations with TKW with increases of 5.11, 3.29, 4.31, and 4.50 g for cfd67205, and4.98, 3.49, 4.06, and 4.84 g for cfd40187 compared with cfd67203 and cfd40190in the four environments, respectively. A major quantitative trait locus for TKW spanning 2.94 c M on chromosome 5DS was detected by association *** linkage disequilibrium（LD）（r2〉 0.2） was detected Resear among the three linked markers, which formed three haplotype blocks in the F2：5breeding population. Mean TKW differences between Hap B-I and Hap B-II were 5.80, 4.41, 4.02,and 5.06 g in the four environments, respectively. Moreover,significant LD was detected only between cfd78 and cfd67 and between cfd67 and cfd40 in a germplasm collection. This study provides a base for cloning genes related to TKW on chromosome 5DS.

关键词： Association mapping haplotype thousand-kernel weight Triticum oestivum

<i>In Silico</i>Modeling of C1 Metabolism

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American Journal of Plant Sciences 2015年第9期6卷 1444-1465页

作者： Santhiya Kothandaram Prabhakar Deonikar Mrudhuula Mohan Vyshali Venugopal V. A. Shiva Ayyadurai Systems Biology Group International Center for Integrative Systems Cambridge MA USA

An integrative computational, in silico, model of C1 metabolism is developed from molecular pathway systems identified from a recent, comprehensive systematic bioinformatics review of C1 metabolism. C1 metabolism is essential for all organisms to provide one-carbon units for methylation and other types of modifications, as well as for nucleic acid, amino acid, and other biomolecule syntheses. C1 metabolism consists of three important molecular pathway systems: 1) methionine biosynthesis, 2) methylation cycle, and 3) formaldehyde detoxification. Each of the three molecular pathway systems is individually modeled using the CytoSolve?? Collaboratory?, a proven and scalable computational systems biology platform for in silico modeling of complex molecular pathway systems. The individual models predict the temporal behavior of formaldehyde, formate, sarcosine, glutathione (GSH), and many other key biomolecules involved in C1 metabolism, which may be hard to measure experimentally. The individual models are then coupled and integrated dynamically using CytoSolve to produce, to the authors’ knowledge, the first comprehensive computational model of C1 metabolism. In silico modeling of the individual and integrated C1 metabolism models enables the identification of the most sensitive parameters involved in the detoxification of formaldehyde. This integrative model of C1 metabolism, giving its systems-based nature, can likely serve as a platform for: 1) generalized research and study of C1 metabolism, 2) hypothesis generation that motivates focused and specific in vitro and in vivo testing in perhaps a more efficient manner, 3) expanding a systems biology understanding of plant bio-molecular systems by integrating other known molecular pathway systems associated with C1 metabolism, and 4) exploring and testing the potential effects of exogenous inputs on the C1 metabolism system.

关键词： In Silico Modeling C1 Metabolism CytoSolve Computational Systems Biology bioinformatics Molecular Pathway Formaldehyde Detoxification Maize Methionine Biosynthesis Activated Methyl Cycle Folate-Mediated Pathways

Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks

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Journal of Molecular Cell Biology 2017年第6期9卷 436-452页

作者： Mengmeng Wu Zhixiang Lin Shining Ma Ting Chen Rui Jiang Wing Hung Wong Department of Computer Science Tsinghua University Beijing 100084 China Ministry of Education Key Laboratory of bioinformatics and bioinformatics Division Tsinghua National Laboratory for Information Science and Technology Beijing 100084 China Department of Statistics Stanford University CA 94305 USA Department of Automation Tsinghua University Beijing 100084 China

Although genome-wide association studies （GWAS） have successfully identified thousands of genomic loci associated with hun- dreds of complex traits in the past decade, the debate about such problems as missing heritabiUty and weak interpretability has been appealing for effective computational methods to facilitate the advanced analysis of the vast volume of existing and antici- pated genetic data. Towards this goal, gene-tevel integrative GWAS analysis with the assumption that genes associated with a phenotype tend to be enriched in biological gene sets or gene networks has recently attracted much attention, due to such advan- tages as straightforward interpretation, tess multiple testing burdens, and robustness across studies. However, existing methods in this category usually exploit non-tissue-specific gene networks and thus lack the ability to utilize informative tissue-specific characteristics. To overcome this limitation, we proposed a Bayesian approach called SIGNET （Simultaneously Inference of GeNEs and Tissues） to integrate GWAS data and multiple tissue-specific gene networks for the simultaneous inference of phenotype- associated genes and relevant tissues. Through extensive simulation studies, we showed the effectiveness of our method in find- ing both associated genes and relevant tissues for a phenotype. In applications to real GWAS data of 14 complex phenotypes, we demonstrated the power of our method in both deciphering genetic basis and discovering biological insights of a phenotype. With this understanding, we expect to see SIGNET as a valuable tool for integrative GWAS analysis, thereby boosting the preven- tion, diagnosis, and treatment of human inherited diseases and eventually facilitating precision medicine.

关键词： GWAS tissue-specific gene networks Markov random field

Molecular and in vitro biochemical assessment of chemosensory protein 10 from brown planthopper Nilaparvata lugens at acidic pH

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Journal of integrative Agriculture 2022年第3期21卷 781-796页

作者： Muhammad Irfan WARIS Aneela YOUNAS Rana Muhammad Kaleem ULLAH Fatima RASOOL Muhammad Muzammal ADEEL WANG Man-qun College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070P.R.China National center for bioinformatics Quaid-i-Azam UniversityIslamaba 45320Pakistan College of Informatics Huazhong Agricultural UniversityWuhan 430070P.R.China

Chemosensory proteins(CSPs)are important molecular components of the insect olfactory system,which are involved in capturing,binding,and transporting hydrophobic odour molecules across the sensillum in sensillar lymph in regulating insect *** protein family(CSPs)is also involved in many other systems that are not linked to olfactory receptors in olfactory *** brown planthopper(BPH)is a monophagous pest of rice that causes damage by sucking phloem sap and transmitting a number of diseases caused by *** this study,fluorescence competitive binding assay and fluorescence quenching assay at acidic p H were performed as well as homology modelling to describe the binding affinity of Nlug *** competitive binding assay(FCBA)demonstrated that Nlug CSP10 bound strongly to nonadecane,farnesene,and 2-tridecanone at acidic p *** results of FCBA indicated that Nlug CSP10 bound different ligands at the physiological p H(5.0)of the bulk sensillum *** quenching assay demonstrated that Nlug CSP10 generated a stable complex with 2-tridecanone,while two ligands nonadecane and farnesene collided due to molecular *** interaction of selected ligands with the modelled structure of Nlug CSP10 was also analyzed,which found the key amino acids(Gln23,Gln24,Gln25,Asn27,Met33,Ser34,Ile35,Tyr36,Asn42,Met43,Val45,Asn46,Asn93,Arg96,Ala97,Lys99,and Ala100)in Nlug CSP10 that were involved in binding of volatile *** present study contributes to the binding profile of Nlug CSP10 that promotes the development of behaviorally active ligands based on BPH olfactory system.

关键词： insect olfaction chemosensory protein Nilaparvata lugens fluorescence competitive binding assay fluorescence quenching assay molecular docking

Gene Expression Profiling Related to Hyphal Growth in a Temperature-Sensitive Mutant of Magnaporthe oryzae

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Journal of integrative Agriculture 2013年第12期12卷 2189-2196页

作者： LI Xue-song XU Fei WANG Hong-kai LIN Fu-cheng State Key Laboratory for Rice Biology Biotechnology InstituteZhejiang University bioinformatics Lab Institute of Digital AgricultureZhejiang Academy of Agricultural Sciences

The rice blast,caused by fungus Magnaporthe oryzae,is a major constraint to the world food *** growth is the foundation of fungal development and proliferation of *** investigate genes involved in hyphal growth of this fungus,digital gene expression tag profiling was used to compare a previously generated temperature-sensitive mutant which defect at hyphae growth and reduction on pathogenicity,with its related wildtype strain.416 genes were detected as differential expression,178 of which were specifically expressed in Guy-11 but down-regulated expression in the *** classification analysis revealed the phenotype mutation may be mainly caused by a defection in translational and vacuole- related *** results and the protocol used will improve our knowledge on morphogenesis and promote the further study on *** pathogenesis.

关键词： differential expressed gene qRT-PCR gene ontology hyphal growth vacuole

Phylogenomic reconstruction addressing the Peltigeralean backbone(Lecanoromycetes,Ascomycota)

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Fungal Diversity 2021年第5期110卷 59-73页

作者： Todd J.Widhelm Felix Grewe Bernard Goffinet Mats Wedin Trevor Goward Luis F.Coca Isabel Distefano Alica Košuthová· H.Thorsten Lumbsch Science&Education The Grainger Bioinformatics CenterNegaunee Integrative Research CenterGantz Family Collections Centerand Pritzker Laboratory for Molecular SystematicsThe Field Museum1400 S.Lake Shore DriveChicagoIL 60605USA Department of Ecology and Evolutionary Biology University of Connecticut75 North Eagleville RoadStorrsCT 06269-3043USA Department of Botany Swedish Museum of Natural HistoryP.O.Box 5000710405 StockholmSweden Herbarium Beaty MuseumUniversity of British ColumbiaVancouverBC V6T 1Z4Canada Herbario Univ Caldas FAUC Edificio BicentenarioCalle 6526-10275 ManizalesColombia

Rapid radiations in Fungi are only beginning to be studied with phylogenomic *** evolutionary history of the lichenized fungal order Peltigerales has not been well resolved,particularly for the ***,we used concatenation and coalescent-based species tree methods to reconstruct the phylogeny of the Peltigerales based on sequences of 125 nuclear single-copy exon sequences among 60 samples,representing 58 *** uneven,lineage-specific missing data and significant topological incongruence of individual exon trees,the resulting phylogenies were concordant and successfully resolved the phylogenetic relationships of the *** in the Collematineae were defined by short branches and lower nodal support than in other parts of the tree,due in part to conflicting signal in exon trees,suggesting rapid diversification events in the early evolution of the *** tree distance measures,we were able to identify a minimum subset of exons that could reconstruct phylogenetic relationships in Peltigerales with higher support than the 125-exon *** between the minimum and complete datasets in species tree inferences,bipartition analyses,and divergence time estimations displayed similar results,although the minimum dataset was characterized by higher levels of error in estimations of divergence *** our inferences from the complete and minimum datasets to those derived from few nuclear and mitochondrial loci reveal that our topology is concordant with topologies reconstructed using the nuclear large subunit and mitochondrial small subunit ribosomal DNA markers,but the target capture datasets had much higher support *** demonstrated how target capture approaches can effectively decipher ancient rapid radiations in cases where well resolved individual exon trees are sufficiently sampled and how to identify subsets of loci that are appropriate for fungal order-level phylogenetics.

关键词： Lichenized fungi Phylogenomics Rapid radiations High-throughput sequencing

Global Analysis of Non-coding Small RNAs in Arabidopsis in Response to Jasmonate Treatment by Deep Sequencing Technology

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Journal of integrative Plant Biology 2012年第2期54卷 73-86页

作者： Bosen Zhang Zhiping Jin Daoxin Xie School of Life Sciences TsinghuaUniversityBeijing 100084China MOE Key Laboratory of bioinformatics Tsinghua UniversityBeijing 100084China State Key Laboratory of Plant Genomics and National center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. Thirty new miRNAs and 27 new miRNA candidates were identified through bioinformatics approach. Forty-nine known miRNAs （belonging to 24 families）, 15 new miRNAs and new miRNA candidates （belonging to 11 families） and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs （belonging to 9 families） were repressed by JA.

关键词： Non-coding small RNAs jasmonate Arabidopsis Solexa deep sequencing

Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus

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Molecular Plant 2021年第4期14卷 604-619页

作者： Qing Zhang Pengpeng Guan Lun Zhao Meng Ma Liang Xie Yue Li Ruiqin Zheng Weizhi Ouyang Shunyao Wang Hongmeijuan Li Ying Zhang Yong Peng Zhilin Cao Wei Zhang Qin Xiao Yuanling Xiao Tingdong Fu Guoliang Li Xingwang Li Jinxiong Shen National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China National Engineering Research center of Rapeseed Huazhong Agricultural UniversityWuhan 430070China Agicultural bioinformatics Key Laboratory of Hubei Province Hubei Engineering Technology Research Center of Agricutural Big Data3D Genomics Research CenterCollge of InformaticsHuazhong Agricultural UniversityWuhan 430070China These authors contributed equally to this article.

The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization,which drives genome evolution and contributes to the increased adaptability to diverse ***,a comprehensive epigenome map of Brassica napus is still *** this study,we performed integrative analysis of five histone modifications,RNA polymerase Ⅱ CCU-pancy,DNA methylation,and transcriptomes in two *** lines(2063A and B409),and established global maps of regulatory elements,chromatin states,and their dynamics for the whole genome(including the An and Cn subgenomes)in four tissue types(young leaf,flower bud,silique,and root)of these two *** 65.8% of the genome was annotated with different epigenomic *** with the Cn subgenome,the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic *** from subgenome-unique regions contribute to the major differences between the An and Cn *** histone modifications between homeologous gene pairs reflect their biased expression *** identified a novel bivalent chromatin state(with H3K4me1 and H3K27me3)in *** that is associated with tissue-specific gene ***,we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation ***,our findings provide a valuable epigenetic resource for allopolyploid plants.

关键词： Brassica napus epigenome ChlP-seq gene expression

Analysis of Pathway Activity in Primary Tumors and NCI60 Cell Lines Using Gene Expression Profiling Data

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Genomics, Proteomics & bioinformatics 2007年第1期5卷 15-24页

作者： Xing-Dong Feng Shu-Guang Huang Jian-Yong Shou Bi-Rong Liao Jonathan M. Yingling Xiang Ye Xi Lin Lawrence M. Gelbert Eric W. Su Jude E. Onyia Shu-Yu Li integrative Biology Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA Global Discovery ＆ Development Statistics Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA Cancer Discovery Research Lilly Research Laboratories Eli Lilly and Company Lilly Corporate Center Indianapolis IN 46285 USA

To determine cancer pathway activities in nine types of primary tumors and NCI60 cell lines, we applied an in silico approach by examining gene signatures reflective of consequent pathway activation using gene expression data. Supervised learning approaches predicted that the Ras pathway is active in -70% of lung adenocarcinomas but inactive in most squamous cell carcinomas, pulmonary carcinoids, and small cell lung carcinomas. In contrast, the TGF-β, TNF-α, Src, Myc, E2F3, and β-catenin pathways are inactive in lung adenocarcinomas. We predicted an active Ras, Myc, Src, and/or E2F3 pathway in significant percentages of breast cancer, colorectal carcinoma, and gliomas. Our results also suggest that Ras may be the most prevailing oncogenic pathway. Additionally, many NCI60 cell lines exhibited a gene signature indicative of an active Ras, Myc, and/or Src, but not E2F3, β-catenin, TNF-α, or TGF-β pathway. To our knowledge, this is the first comprehensive survey of cancer pathway activities in nine major tumor types and the most widely used NCI60 cell lines. The ＂gene expression pathway signatures＂ we have defined could facilitate the understanding of molecular mechanisms in cancer development and provide guidance to the selection of appropriate cell lines for cancer research and pharmaceutical compound screening.

关键词： cancer pathways gene expression profiling supervised learning classification