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PlantCFG:A comprehensive database with web tools for analyzing candidate flowering genes in multiple plants

Plant Communications 2024年第2期5卷 11-14页

作者： Dongxu Liu Jiawei Li Shengbo Wang Tingting Huang Fangting Tao Yuchen Lin Wei Lin Xinle Zhao Yiming Huang Yupeng Jia Zhiquan Yang Chengfang Luo Qiang Zhu Wing-Kin Sung Jian Wu Qing-Yong Yang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hong Kong Genome Institute Hong Kong Science ParkShatinHong KongChina State Key Laboratory of Biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhou 510275China School of Life Sciences University of Science and Technology of ChinaHefei 230026China Key Laboratory of Plant Functional Genomics of the Ministry of Education Yangzhou UniversityYangzhou 225009China

Dear Editor,The transition from the vegetative to the reproductive phase of plant development,known as the floral transition,plays important roles in the plant life *** is a vulnerable but crucial phase for building crop yield,and proper timing of this period is therefore vital for obtaining optimal yields(Jung and Muller,2009).Analysis of flowering time is currently an important research topic in several fields,including plant molecular genetics,evolutionary biology,ecology,and crop breeding(Huang et al.,2011).

关键词： database web breeding

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3D segmentation and quantification of mouse embryonic stem cells in fluorescence microscopy images

3D segmentation and quantification of mouse embryonic stem c...

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IEEE International Symposium on Biomedical Imaging

作者： Nathalie Harder Megan Bodnar Roland Eils David L. Spector Karl Rohr BIOQUANT IPMB and DKFZ Heidelberg Department Bioinformatics and Functional Genomics University of Heidelberg Heidelberg Germany Cold Spring Harbor Laboratory Cold Spring Harbor NY USA

We present an automatic approach for 3D segmentation of mouse embryonic stem cell nuclei based on level set active contours. Due to the specific properties of these cells, standard methods for cell nucleus segmentation and splitting of cell clusters cannot be applied. Our segmentation approach combines information from two different channels which represent the nuclear region and the nuclear membrane. Moreover, we perform segmentation of gene loci within two other channels which enables single cell quantification of gene distances.

关键词： Image segmentation Three dimensional displays Marine animals Transforms Active contours Level set Mice

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Feature Selection for Evaluating Fluorescence Microscopy Images in Genome-Wide Cell Screens

Feature Selection for Evaluating Fluorescence Microscopy Ima...

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Conference on Computer Vision and Pattern Recognition (CVPR)

作者： V. Kovalev N. Harder B. Neumann M. Held U. Liebel H. Erfle J. Ellenberg R. Eils K. Rohr IPMB and DKFZ Heidelberg Department Bioinformatics and Functional Genomics University of Heidelberg Heidelberg Germany Gene Expression and Cell Biology/Biophysics Programmes European Molecular Biology Laboratory Heidelberg Germany

We investigate different approaches for efficient feature space reduction and compare different methods for cell classification. The application context is the development of automatic methods for analysing fluorescence microscopy images with the goal to identify those genes that are involved in the mitosis of human cells (cell division). We distinguish four cell classes comprising interphase cells, mitotic cells, apoptotic cells, and cells with clustered nuclei. Feature space reduction was performed using the Principal Component Analysis and Independent Component Analysis methods. Six classification methods were examined including unsupervised clustering algorithms such as K-means, Hard Competitive Learning, and Neural Gas as well as Hierarchical Clustering, Support Vector Machines, and Random Forests classifiers. Detailed results on the cell image classification accuracy and computational efficiency achieved using different feature sets and different classification methods are reported.

关键词： Fluorescence Microscopy genomics bioinformatics Independent component analysis Image analysis Humans Principal component analysis Clustering algorithms Machine learning

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0414 Recurrent chimeric transcripts in human and mouseGet access

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Journal of Animal Science 2016年第SUPPL_5期94卷 200–201页

作者： Djebali, S. Rodríguez Martín, B. Palumbo, E. Pervouchine, D. D. Breschi, A. Davis, C. Dobin, A. Alonso, G. Rastrojo, A. Aguado, B. Gingeras, T. R. Guigó, R. GenPhySE INRA Castanet-Tolosan France Universitat Pompeu Fabra (UPF) Barcelona Spain Bioinformatics and Genomics Program Centre for Genomic Regulation (CRG) Barcelona Spain Cold Spring Harbor Laboratory Functional Genomics NY Centro de Biología Molecular Severo Ochoa (CSIC- UAM) Madrid Spain

The formation of chimeric transcripts (chimeras) has been widely reported. Some of them reflect underlying chromosomal rearrangements, or are the results of the propensity of reverse transcriptase to engage in template switching, however, a proportion of cases genuinely appear to correspond totrans-splicing of RNAs, as has previously been *** we use ENCODE and mouse ENCODE deeply sequenced and bio-replicated RNaseq data from 18 human and 30 mouse samples, and the ChimPipe program, to identify chimeras occurring in multiple biological samples (recurrent), and between the same pairs of genes in human and mouse, since they are more likely to be transcriptionally induced and *** common chimeras tend to connect gene pairs located on the same chromosome and relatively near to each other ( < 100kb), therefore pointing to polymerase read-through, however interchromosomal chimeras are also observed, pointing totrans-splicing. Importantly, these recurrent chimeras tend to maintain an open reading frame, and could therefore generate chimeric proteins. We also observe that not only the gene-to-gene connection is conserved, but strikingly so are specific junction sites. The genes connected in common chimeras tend to be involved in morphogenesis and body plan formation, and consistently tend to be detected in cell lines of embryonic *** of human chimeras by RT-PCR yielded a success rate of 50%, and subsequent cloning and sequencing revealed novel transcript structures, of which some preserve the domains from the two parent genes. Applying this method to multiple animal species and breeds will help us understanding chimera evolution as well as reveal some links between genotype and phenotype.

关键词： chimeras transcripts trans-splicing

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Automated recognition of mitotic patterns in fluorescence microscopy images of human cells

Automated recognition of mitotic patterns in fluorescence mi...

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IEEE International Symposium on Biomedical Imaging

作者： N. Harder B. Neumann M. Held U. Liebel H. Erfle J. Ellenberg R. Eils K. Rohr IPMB DKFZ Heidelberg Department Bioinformatics and Functional Genomics Biomedical Computer Vision Group University of Heidelberg Heidelberg Germany Gene Expression and Cell Biology/Biophysics Programmes European Molecular Biology Laboratory Heidelberg Germany

High-throughput screens of the gene function provide rapidly increasing amounts of data. In particular, the analysis of image data acquired in genome-wide cell phenotype screens constitutes a substantial bottleneck in the evaluation process and motivates the development of automated image analysis tools for large-scale experiments. Here we introduce a computational scheme to process multi-cell images as they are produced in high-throughput screens. We describe an approach to automatically segment and classify cell nuclei into different mitotic phenotypes. This enables automated identification of cell cultures that show an abnormal mitotic behavior. Our scheme proves a high classification accuracy, suggesting a promising future for automating the evaluation of high-throughput experiments

关键词： Pattern recognition Image recognition Fluorescence Microscopy Humans Image analysis Data analysis genomics bioinformatics Large-scale systems

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The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

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Molecular Plant 2019年第7期12卷 935-950页

作者： Qing Zhao Jun Yang Meng-Ying Cui Jie Liu Yumin Fang Mengxiao Yan Wenqing Qiu Huiwen Shang Zhicheng Xu Reheman Yidiresi Jing-Ke Weng Tomas Pluskal Marielle Vigouroux Burkhard Steuernagel Yukun Wei Lei Yang Yonghong Hu Xiao-Ya Chen Cathie Martin Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical Garden Shanghai Chenshan Plant Science Research Center Chinese Academy of Sciences Shanghai China State Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China Key Laboratory of Metabolism and Molecular Medicine Department of Biochemistry and Molecular Biology School of Basic Medical Sciences Fudan University Shanghai China Novogene Bioinformatics Institute Beijing China Whitehead Institute for Biomedical Research 455 Main Street Cambridge MA 02142 USA Department of Biology Massachusetts Institute of Technology Cambridge MA 02139 USA John Innes Centre Norwich NR4 7UH UK

Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots,"Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, sesamum indicum and Salvia splendens,revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scu-tellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its newfunc- tion following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionaliza-tions were involved in the evolution of 4'-deoxyflavone synthesis in the genus Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.

关键词： genome skullcap 4’-deoxyflavone traditional Chinese medicine Huang Qin:evolution specialized metabolism

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DETERMINATION OF MITOTIC DELAYS IN 3D FLUORESCENCE MICROSCOPY IMAGES OF HUMAN CELLS USING AN ERROR-CORRECTING FINITE STATE MACHINE

DETERMINATION OF MITOTIC DELAYS IN 3D FLUORESCENCE MICROSCOP...

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IEEE International Symposium on Biomedical Imaging

作者： N. Harder F. Mora-Bermudez W.J. Godinez J. Ellenberg R. Eils K. Rohr IPMB University of Heidelberg Germany DKFZ Heidelberg Department Bioinformatics and Functional Genomics Biomed Computer Vision Group Heidelberg Germany Gene Expression and Cell Biology/Biophysics Programmes European Molecular Biology Laboratory Heidelberg Germany

ISBN: (纸本)9781424406715;1424406714

In high-throughput cell phenotype screens large amounts of image data are acquired. The evaluation of these microscopy images constitutes a bottleneck and motivates the development of automated image analysis methods. Here we introduce a computational scheme to process 3D multi-cell image sequences as they are produced in large-scale RNAi experiments. We describe an approach to automatically segment, track, and classify cell nuclei into seven different mitotic phases. In particular, we present an algorithm based on a finite state machine to check the consistency of the resulting sequence of mitotic phases and to correct classification errors. Our approach enables automated determination of the duration of the single phases and thus the identification of cell cultures with delayed mitotic progression.

关键词： Delay Fluorescence Microscopy Humans Automata Image sequence analysis Image sequences Large-scale systems Image segmentation Error correction

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Ancient genomics and the origin, dispersal, and development of domestic sheep

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Science (New York, N.Y.) 2025年第6733期387卷 492-497页

作者： Daly, Kevin G. Mullin, Victoria E. Hare, Andrew J. Halpin, Áine Mattiangeli, Valeria Teasdale, Matthew D. Rossi, Conor Geiger, Sheila Krebs, Stefan Medugorac, Ivica Sandoval-Castellanos, Edson Özbaşaran, Mihriban Duru, Güneş Gülcür, Sevil Pöllath, Nadja Collins, Matthew Frantz, Laurent Vila, Emmanuelle Zidarov, Peter Stoddart, Simon Boldgiv, Bazartseren Orlando, Ludovic Pearson, Mike Parker Mullville, Jacqui Askeyev, Igor V. Askeyev, Arthur O. Askeyev, Oleg V. Shaymuratova, Dilyara N. Van den Hurk, Youri Zeeb-Lanz, Andrea Arbogast, Rose-Marie Hemmer, Helmut Davoudi, Hossein Amiri, Sarieh Doost, Sanaz Beizaee Decruyenaere, Delphine Fathi, Homa Khazaeli, Roya Hassanzadeh, Yousef Sardari, Alireza Lhuillier, Johanna Abdolahi, Mostafa Summers, Geoffrey D. Marro, Catherine Bahshaliyev, Veli Berthon, Rémi Çakirlar, Canan Benecke, Norbert Scheu, Amelie Burger, Joachim Sauer, Eberhard Horwitz, Liora Kolska Arbuckle, Benjamin Buitenhuis, Hijlke Gourichon, Lionel Bulatović, Jelena Orton, David Jalabadze, Mindia Rhodes, Stephen Chazan, Michael Özkaya, Vecihi Zeder, Melinda Atıcı, Levent Mashkour, Marjan Peters, Joris Bradley, Daniel G. Smurfit Institute of Genetics Trinity College Dublin Dublin Ireland UCD School of Agricultural and Food Science University College Dublin Belfield Ireland Bioinformatics Support Unit Faculty of Medical Sciences Newcastle University Newcastle upon Tyne United Kingdom Institute of Palaeoanatomy Domestication Research and the History of Veterinary Medicine LMU Munich Munich Germany Laboratory for Functional Genome Analysis (LAFUGA) Gene Center LMU Munich Feodor-Lynen-Straße 25 Munich Germany LMU Munich Munich Germany Population Genomics Group Department of Veterinary Sciences LMU Munich Martinsried Germany Prehistory Department Faculty of Letters Istanbul University Istanbul Türkiye Department of Archaeology Mimar Sinan Fine Arts University Bavarian Natural History Collections State Collection of Palaeoanatomy Munich Munich Germany Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark McDonald Institute for Archaeological Research University of Cambridge West Tower Downing Street Cambridge United Kingdom School of Biological and Behavioural Sciences Queen Mary University of London London United Kingdom Maison de l'Orient et la Méditerranée Université Lumière Lyon 2 Lyon France Institute of Prehistory Early History and Medieval Archaeology Eberhard-Karls Universität Tübingen Tübingen Germany Department of Archaeology University of Cambridge Cambridge United Kingdom Laboratory of Ecological and Evolutionary Synthesis Department of Biology School of Arts and Sciences National University of Mongolia Ulaanbaatar Mongolia Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR 5288) Université Paul Sabatier Toulouse France Institute of Archaeology University College London London United Kingdom School of History Archaeology and Religion Cardiff University Cardiff Wales United Kingdom Laboratory of Biomonitoring Institute of Problems in Ecology and Mineral Wealth Tatarstan Academy of Sciences Daurskaya Street 28 Ka

The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood;to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Genomes from Central Türkiye ~8000 BCE are genetically proximal to the domestic origins of sheep but do not fully explain the ancestry of later populations, suggesting a mosaic of wild ancestries. Genomic signatures indicate selection by ancient herders for pigmentation patterns, hornedness, and growth rate. Although the first European sheep flocks derive from Türkiye, in a notable parallel with ancient human genome discoveries, we detected a major influx of Western steppe-related ancestry in the Bronze Age.

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The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae

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Molecular Plant 2023年第3期16卷 549-570页

作者： Haixiu Li Song Wu Ruoxi Lin Yiren Xiao Ana Luisa Malaco Morotti Ya Wang Meytal Galilee Haowen Qin Tao Huang Yong Zhao Xun Zhou Jun Yang Qing Zhao Angelos K.Kanellis Cathie Martin Evangelos C.Tatsis National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China Novogene Bioinformatics Institute BeijingChina Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai Chenshan Plant Science Research CenterChinese Academy of SciencesShanghai 201602 Group of Biotechnology of Pharmaceutical Plants Lab.of PharmacognosyDepartment of Pharmaceutical SciencesAristotle University of Thessaloniki54124 ThessalonikiGreece John Innes Centre Norwich NR47UHUK CEPAMS-CAS-JIC Centre of Excellence for Plant and Microbial Sciences Shanghai 200032China

The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata,although the molecular mechanisms behind clerodane biosynthesis are ***,we report a high-quality assembly of the 414.98 Mb genome of *** into 13 *** phylogenomic and biochemical data,we mapped the plastidial metabolism of kaurene(gibberellins),abietane,and clerodane diterpenes in three species of the family Lamiaceae(Scutellaria barbata,Scutellaria baicalensis,and Salvia splendens),facilitating the identification of genes involved in the biosynthesis of the clerodanes,kolavenol,and *** show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane *** the assumed monophyletic origin of clerodane biosynthesis,which is widespread in species of the Lamiaceae,our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family *** study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family,Lamiaceae,but also will facilitate the production of anticancer clerodanes through future metabolic engineering efforts.

关键词： Scutellaria barbata genome clerodane diterpenoids biosynthesis specialized metabolism evolution

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First Crotonyl-proteome Profiling and Genome-wide Mapping Reveals the Involvement of crotonylation in Oryza sativa

First Crotonyl-proteome Profiling and Genome-wide Mapping Re...

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江苏省遗传学会2016年学术年会

作者： Shuai Liu hao Xue Guanqing Liu Yuan Fang Rui Guo Xiaoyu Liu Yong Zhou Gang Chen Yufeng Wu Zhiyun Gong Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou University The State Key Laboratory of Crop Genetics and Germplasm Enhancement Bioinformatics CenterNanjing Agricultural University

Lysine crotonylation(Kcr) is a newly discovered posttranslational modification(PTM) existing in mammalian cell *** Kcr of the animals is generally enriched on active promoters and potential enhancers,both in somatic and male germ ***,crotonyl-proteome was rarely reported in high ***,we performed a global crotonylome analysis of Oryza sativa *** by using high accuracy nano-LC-MS/MS in combination with the enrichment of crotonylated *** total,1265 lysine crotonylation sites on 690 proteins were identified in rice seedling,out of which 63.4% proteins contain one crotonylation *** further characterize this modification,we classified crotonylated proteins into several groups according to biological *** location of the crotonylated proteins showed that 50% identified crotonylated proteins were predicted to be *** proteins involved in photosynthesis were also mostly enriched,as determined through the KEGG pathway ***,we focused on genomic localization of histone Kcr by ChIP-seq *** Kcr marks was positively correlated with gene *** 10923 identified peak regions,the majority(86.7%) enriched around gene bodys,especially on ***,these results firstly provide a rich resource for functional analyses of lysine crotonylation in *** findings reinforce the notion that lysine crotonylation plays a critical regulatory role in diverse aspects of cellular process,especially in photosynthesis and Calvin cycle,and histone Kcr marks active genes in *** also found 6 Kcr sites of rice histones,including 4 H3 Kcr PTM sites and 2 H4 PTM *** is different form Histone Kcr in ***-located with the all histone modifications,Kcr is associated with active genes in this study and implied that did not mark the enhancersin rice *** found 69%～95% histone Kcr regions were overlapped with regions associated with the active histone modifications.

关键词： Rice Post Translational Modification Crotonyllysine Photosynthesis Histone Kcr

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