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37 results on '"Lu, Fu-Hao"'

2. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Author

Luo, Ming-Cheng, Gu, Yong Q, Puiu, Daniela, Wang, Hao, Twardziok, Sven O, Deal, Karin R, Huo, Naxin, Zhu, Tingting, Wang, Le, Wang, Yi, McGuire, Patrick E, Liu, Shuyang, Long, Hai, Ramasamy, Ramesh K, Rodriguez, Juan C, Van, Sonny L, Yuan, Luxia, Wang, Zhenzhong, Xia, Zhiqiang, Xiao, Lichan, Anderson, Olin D, Ouyang, Shuhong, Liang, Yong, Zimin, Aleksey V, Pertea, Geo, Qi, Peng, Bennetzen, Jeffrey L, Dai, Xiongtao, Dawson, Matthew W, Müller, Hans-Georg, Kugler, Karl, Rivarola-Duarte, Lorena, Spannagl, Manuel, Mayer, Klaus FX, Lu, Fu-Hao, Bevan, Michael W, Leroy, Philippe, Li, Pingchuan, You, Frank M, Sun, Qixin, Liu, Zhiyong, Lyons, Eric, Wicker, Thomas, Salzberg, Steven L, Devos, Katrien M, and Dvořák, Jan

Subjects
Biological Sciences, Genetics, Chromosome Mapping, Diploidy, Evolution, Molecular, Gene Duplication, Genes, Plant, Genome, Plant, Genomics, Phylogeny, Poaceae, Recombination, Genetic, Sequence Analysis, DNA, Triticum, General Science & Technology
Abstract

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

Published
2017

3. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Author

Clavijo, Bernardo J, Venturini, Luca, Schudoma, Christian, Accinelli, Gonzalo Garcia, Kaithakottil, Gemy, Wright, Jonathan, Borrill, Philippa, Kettleborough, George, Heavens, Darren, Chapman, Helen, Lipscombe, James, Barker, Tom, Lu, Fu-Hao, McKenzie, Neil, Raats, Dina, Ramirez-Gonzalez, Ricardo H, Coince, Aurore, Peel, Ned, Percival-Alwyn, Lawrence, Duncan, Owen, Trösch, Josua, Yu, Guotai, Bolser, Dan M, Namaati, Guy, Kerhornou, Arnaud, Spannagl, Manuel, Gundlach, Heidrun, Haberer, Georg, Davey, Robert P, Fosker, Christine, Di Palma, Federica, Phillips, Andrew L, Millar, A Harvey, Kersey, Paul J, Uauy, Cristobal, Krasileva, Ksenia V, Swarbreck, David, Bevan, Michael W, and Clark, Matthew D

Subjects
Genetics, Biotechnology, Human Genome, Algorithms, Contig Mapping, Genome, Plant, Molecular Sequence Annotation, Plant Proteins, Polymorphism, Genetic, Polyploidy, Translocation, Genetic, Triticum, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

Published
2017

12. Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat

Author

Lu, Fu-Hao, McKenzie, Neil, Gardiner, Laura-Jayne, Luo, Ming-Cheng, Hall, Anthony, and Bevan, Michael W

Subjects
chr3DL, AcademicSubjects/SCI02254, Aegilops, Triticum aestivum, Health Informatics, Chromosomes, Plant, Evolution, Molecular, Gene Expression Regulation, Plant, wheat, Gene expression, Homologous chromosome, Aegilops tauschii, Gene, Triticum, Genetics, Ploidies, biology, Research, synteny, Computational Biology, food and beverages, Chromosome, Genomics, DNA Methylation, Chromatin Assembly and Disassembly, biology.organism_classification, ATAC, Chromatin, Computer Science Applications, Chromosome Arm, AcademicSubjects/SCI00960, gene expression in polyploids, Ploidy, Genome, Plant, Pseudogenes
Abstract

BackgroundPolyploidy is centrally important in the evolution and domestication of plants because it leads to major genomic changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are not well understood.ResultsUsing a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3 L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was ∼40% of the levels observed in diploid Ae tauschii. Several genes showed elevated expression during the later stages of grain development in wheat compared with Ae tauschii. Gene sequence and methylation differences probably accounted for only a few cases of differences in gene expression. In contrast, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression.ConclusionsOur pilot-scale analyses show that chromatin compaction may orchestrate reduced gene expression levels in the hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm.

Published
2020

24. Bisulphite Sequencing v1

Author

Lu, Fu-Hao, primary, McKenzie, Neil, additional, Gardiner, Laura-Jayne, additional, Luo, Ming-Cheng, additional, Hall, Anthony, additional, and W, Michael, additional

Published
2019
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25. Transcription Analyses v1

Author

Lu, Fu-Hao, primary, McKenzie, Neil, additional, Gardiner, Laura-Jayne, additional, Luo, Ming-Cheng, additional, Hall, Anthony, additional, and W, Michael, additional

Published
2019
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27. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis

Author

Dong, Hui, Dumenil, Jack, Lu, Fu-Hao, Na, Li, Vanhaeren, Hannes, Naumann, Christin, Klecker, Maria, Prior, Rachel, Smith, Caroline, McKenzie, Neil, Saalbach, Gerhard, Chen, Liangliang, Xia, Tian, Gonzalez, Nathalie, Seguela, Mathilde, Inze, Dirk, Dissmeyer, Nico, Li, Yunhai, Bevan, Michael W., Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)

Subjects
[SDV]Life Sciences [q-bio], human activities
Abstract

Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis

Published
2017

30. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis

Author

Dong, Hui, primary, Dumenil, Jack, additional, Lu, Fu-Hao, additional, Na, Li, additional, Vanhaeren, Hannes, additional, Naumann, Christin, additional, Klecker, Maria, additional, Prior, Rachel, additional, Smith, Caroline, additional, McKenzie, Neil, additional, Saalbach, Gerhard, additional, Chen, Liangliang, additional, Xia, Tian, additional, Gonzalez, Nathalie, additional, Seguela, Mathilde, additional, Inze, Dirk, additional, Dissmeyer, Nico, additional, Li, Yunhai, additional, and Bevan, Michael W., additional

Published
2016
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31. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Author

Clavijo, Bernardo J., primary, Venturini, Luca, additional, Schudoma, Christian, additional, Accinelli, Gonzalo Garcia, additional, Kaithakottil, Gemy, additional, Wright, Jonathan, additional, Borrill, Philippa, additional, Kettleborough, George, additional, Heavens, Darren, additional, Chapman, Helen, additional, Lipscombe, James, additional, Barker, Tom, additional, Lu, Fu-Hao, additional, McKenzie, Neil, additional, Raats, Dina, additional, Ramirez-Gonzalez, Ricardo H., additional, Coince, Aurore, additional, Peel, Ned, additional, Percival-Alwyn, Lawrence, additional, Duncan, Owen, additional, Trösch, Josua, additional, Yu, Guotai, additional, Bolser, Dan, additional, Namaati, Guy, additional, Kerhornou, Arnaud, additional, Spannagl, Manuel, additional, Gundlach, Heidrun, additional, Haberer, Georg, additional, Davey, Robert P., additional, Fosker, Christine, additional, Di Palma, Federica, additional, Phillips, Andrew, additional, Millar, A. Harvey, additional, Kersey, Paul J., additional, Uauy, Cristobal, additional, Krasileva, Ksenia V., additional, Swarbreck, David, additional, Bevan, Michael W., additional, and Clark, Matthew D., additional

Published
2016
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37. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis .

Author

Dong H, Dumenil J, Lu FH, Na L, Vanhaeren H, Naumann C, Klecker M, Prior R, Smith C, McKenzie N, Saalbach G, Chen L, Xia T, Gonzalez N, Seguela M, Inze D, Dissmeyer N, Li Y, and Bevan MW

Subjects
Arabidopsis genetics, Arabidopsis Proteins genetics, Cell Proliferation, Enzyme Activation, LIM Domain Proteins genetics, Protein Stability, Arabidopsis enzymology, Arabidopsis growth & development, Arabidopsis Proteins metabolism, LIM Domain Proteins metabolism, Ubiquitin-Protein Ligases metabolism, Ubiquitination
Abstract

The characteristic shapes and sizes of organs are established by cell proliferation patterns and final cell sizes, but the underlying molecular mechanisms coordinating these are poorly understood. Here we characterize a ubiquitin-activated peptidase called DA1 that limits the duration of cell proliferation during organ growth in Arabidopsis thaliana The peptidase is activated by two RING E3 ligases, Big Brother (BB) and DA2, which are subsequently cleaved by the activated peptidase and destabilized. In the case of BB, cleavage leads to destabilization by the RING E3 ligase PROTEOLYSIS 1 (PRT1) of the N-end rule pathway. DA1 peptidase activity also cleaves the deubiquitylase UBP15, which promotes cell proliferation, and the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22, which promote cell proliferation and repress endoreduplication. We propose that DA1 peptidase activity regulates the duration of cell proliferation and the transition to endoreduplication and differentiation during organ formation in plants by coordinating the destabilization of regulatory proteins., (© 2017 Dong et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2017
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