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Thiébaut A, Altenhoff AM, Campli G, Glover N, Dessimoz C, Waterhouse RM. DrosOMA: the Drosophila Orthologous Matrix browser. F1000Res 2024; 12:936. [PMID: 38434623 PMCID: PMC10905159 DOI: 10.12688/f1000research.135250.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2024] [Indexed: 03/05/2024] Open
Abstract
Background Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Methods Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. Results DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. Conclusions The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.
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Affiliation(s)
- Antonin Thiébaut
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Adrian M. Altenhoff
- Department of Computer Science, SIB Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Giulia Campli
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Natasha Glover
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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2
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Altenhoff A, Bairoch A, Bansal P, Baratin D, Bastian F, Bolleman* J, Bridge A, Burdet F, Crameri K, Dauvillier J, Dessimoz C, Gehant S, Glover N, Gnodtke K, Hayes C, Ibberson M, Kriventseva E, Kuznetsov D, Frédérique L, Mehl F, Mendes de Farias* T, Michel PA, Moretti S, Morgat A, Österle S, Pagni M, Redaschi N, Robinson-Rechavi M, Samarasinghe K, Sima AC, Szklarczyk D, Topalov O, Touré V, Unni D, von Mering C, Wollbrett J, Zahn-Zabal* M, Zdobnov E. The SIB Swiss Institute of Bioinformatics Semantic Web of data. Nucleic Acids Res 2024; 52:D44-D51. [PMID: 37878411 PMCID: PMC10767860 DOI: 10.1093/nar/gkad902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023] Open
Abstract
The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation of bioinformatics research and service groups. The international life science community in academia and industry has been accessing the freely available databases provided by SIB since its inception in 1998. In this paper we present the 11 databases which currently offer semantically enriched data in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable), as well as the Swiss Personalized Health Network initiative (SPHN) which also employs this enrichment. The semantic enrichment facilitates the manipulation of large data sets from public databases and private data sets. Examples are provided to illustrate that the data from the SIB databases can not only be queried using precise criteria individually, but also across multiple databases, including a variety of non-SIB databases. Data manipulation, be it exploration, extraction, annotation, combination, and publication, is possible using the SPARQL query language. Providing documentation, tutorials and sample queries makes it easier to navigate this web of semantic data. Through this paper, the reader will discover how the existing SIB knowledge graphs can be leveraged to tackle the complex biological or clinical questions that are being addressed today.
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3
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Blatter MC, Zahn-Zabal M, Moix S, Pichon B, Dessimoz C, Glover N. Bringing science to the public in the light of evolution. Biol Methods Protoc 2023; 8:bpad040. [PMID: 38152108 PMCID: PMC10752581 DOI: 10.1093/biomethods/bpad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/24/2023] [Indexed: 12/29/2023] Open
Abstract
Evolution stands as a foundational pillar within modern biology, shaping our understanding of life. Studies related to evolution, for example constructing phylogenetic trees, are often carried out using DNA or protein sequences. These data, readily accessible from public databases, represent a treasure trove of resources that can be harnessed to create engaging activities with the public. At the heart of our project lies a collection of "stories" about evolution, each rooted in genuine scientific publications that furnish both biological context and supporting evidence. These narratives serve as the focal point of our LightOfEvolution.org website. Each story is accompanied by a dedicated "Your Turn to Play" section. Within this section, we furnish user-friendly activities and step-by-step guidelines, equipping visitors with the means to replicate analyses showcased in the highlighted publications. For example, the website OhMyGenes.org, relying on authentic scientific data, provides the capability to compute the proportion of shared genes across different species. Here, visitors can address the captivating question: "How many genes do we share with a banana?" To extend the educational reach, we have developed a series of modular activities, also related to the stories. These activities have been thoughtfully designed to be adaptable for face-to-face workshops held in classrooms or presented during public events. We aim to create stories and activities that resonate with participants, offering a tangible and enjoyable experience. By providing opportunities that reflect real-world scientific practices, we seek to offer participants valuable insights into the current workings of scientists "in the light of evolution."
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Affiliation(s)
| | | | - Samuel Moix
- SIB Swiss Institute of Bioinformatics, Lausanne and Geneva, Switzerland
- Department of Computational Biology, University of Lausanne, Switzerland
| | - Béatrice Pichon
- SIB Swiss Institute of Bioinformatics, Lausanne and Geneva, Switzerland
- Department of Computational Biology, University of Lausanne, Switzerland
| | - Christophe Dessimoz
- SIB Swiss Institute of Bioinformatics, Lausanne and Geneva, Switzerland
- Department of Computational Biology, University of Lausanne, Switzerland
| | - Natasha Glover
- SIB Swiss Institute of Bioinformatics, Lausanne and Geneva, Switzerland
- Department of Computational Biology, University of Lausanne, Switzerland
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4
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Lopez Vazquez A, Allenbach Petrolati L, Legris M, Dessimoz C, Lampugnani ER, Glover N, Fankhauser C. Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE. Plant Cell 2023:koad096. [PMID: 36972404 DOI: 10.1093/plcell/koad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
PHYTOCHROME KINASE SUBSTRATE (PKS) proteins are involved in light-modulated changes in growth orientation. They act downstream of phytochromes to control hypocotyl gravitropism in the light and act early in phototropin signaling. Despite their importance for plant development, little is known about their molecular mode of action, except that they belong to a protein complex comprising phototropins at the plasma membrane. Identifying evolutionary conservation is one approach to reveal biologically important protein motifs. Here, we show that PKS sequences are restricted to seed plants and that these proteins share six motifs (A to F from the N to the C terminus). Motifs A and D are also present in BIG GRAIN, while the remaining four are specific to PKSs. We provide evidence that motif C is S-acylated on highly conserved cysteines, which mediates the association of PKS proteins with the plasma membrane. Motif C is also required for PKS4-mediated phototropism and light-regulated hypocotyl gravitropism. Finally, our data suggest that the mode of PKS4 association with the plasma membrane is important for its biological activity. Our work therefore identifies conserved cysteines contributing to plasma membrane association of PKS proteins and strongly suggests that this is their site of action to modulate environmentally regulated organ positioning.
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Affiliation(s)
- Ana Lopez Vazquez
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Laure Allenbach Petrolati
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Martina Legris
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, Faculty of Biology and Medicine, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Edwin R Lampugnani
- School of BioScience, University of Melbourne, Parkville, Victoria 3010, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Natasha Glover
- Department of Computational Biology, Faculty of Biology and Medicine, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Fankhauser
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode Building, University of Lausanne, CH-1015 Lausanne, Switzerland
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5
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Sarton-Lohéac G, Nunes da Silva CG, Mazel F, Baud G, de Bakker V, Das S, El Chazli Y, Ellegaard K, Garcia-Garcera M, Glover N, Liberti J, Nacif Marçal L, Prasad A, Somerville V, Bonilla-Rosso G, Engel P. Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees. mBio 2023; 14:e0353822. [PMID: 36939321 PMCID: PMC10128065 DOI: 10.1128/mbio.03538-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiotas presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here, we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumblebee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host, indicating that the evolution of the social bee gut microbiota was not driven by strict codiversification but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumblebee microbiotas, we found substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. IMPORTANCE Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumblebees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees, which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major members of the gut microbiotas of six stingless bee species and sequenced their genomes. We found that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumblebees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents a basis for characterizing the symbiotic relationships between gut bacteria and stingless bees.
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Affiliation(s)
- Garance Sarton-Lohéac
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gilles Baud
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent de Bakker
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sudip Das
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yassine El Chazli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joanito Liberti
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lorena Nacif Marçal
- Department of Morphology, Instituto de Ciências Biológicas, Federal University of Amazonas, Manaus, Brazil
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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6
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Glover N, Sheppard S, Dessimoz C. Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs. Genome Biol Evol 2021; 13:6237894. [PMID: 33871639 PMCID: PMC8214411 DOI: 10.1093/gbe/evab077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Homoeologs are pairs of genes or chromosomes in the same species that originated by speciation and were brought back together in the same genome by allopolyploidization. Bioinformatic methods for accurate homoeology inference are crucial for studying the evolutionary consequences of polyploidization, and homoeology is typically inferred on the basis of bidirectional best hit (BBH) and/or positional conservation (synteny). However, these methods neglect the fact that genes can duplicate and move, both prior to and after the allopolyploidization event. These duplications and movements can result in many-to-many and/or nonsyntenic homoeologs-which thus remain undetected and unstudied. Here, using the allotetraploid upland cotton (Gossypium hirsutum) as a case study, we show that conventional approaches indeed miss a substantial proportion of homoeologs. Additionally, we found that many of the missed pairs of homoeologs are broadly and highly expressed. A gene ontology analysis revealed a high proportion of the nonsyntenic and non-BBH homoeologs to be involved in protein translation and are likely to contribute to the functional repertoire of cotton. Thus, from an evolutionary and functional genomics standpoint, choosing a homoeolog inference method which does not solely rely on 1:1 relationship cardinality or synteny is crucial for not missing these potentially important homoeolog pairs.
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Affiliation(s)
- Natasha Glover
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Switzerland
| | | | - Christophe Dessimoz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Switzerland.,Department of Genetics, Evolution, and Environment, University College London, United Kingdom.,Department of Computer Science, University College London, United Kingdom
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7
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Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten Years of Collaborative Progress in the Quest for Orthologs. Mol Biol Evol 2021; 38:3033-3045. [PMID: 33822172 PMCID: PMC8321534 DOI: 10.1093/molbev/msab098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/07/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit-from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
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Affiliation(s)
- Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tomohiro Mochizuki
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Yannis Nevers
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Jordi Girona, Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Department of Computer Science, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ikuo Uchiyama
- Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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8
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Zajac N, Zoller S, Seppälä K, Moi D, Dessimoz C, Jokela J, Hartikainen H, Glover N. Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism. Genome Biol Evol 2021; 13:evab010. [PMID: 33484570 PMCID: PMC7936022 DOI: 10.1093/gbe/evab010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2021] [Indexed: 01/10/2023] Open
Abstract
Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host-parasite adaptation.
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Affiliation(s)
- Natalia Zajac
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Stefan Zoller
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Katri Seppälä
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - David Moi
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
- Centre for Life’s Origins and Evolution, Department of Genetics Evolution and Environment, University College London, United Kingdom
- Department of Computer Science, University College London, United Kingdom
| | - Jukka Jokela
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
| | - Hanna Hartikainen
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- ETH Zurich, Department of Environmental Systems Science, Institute of Integrative Biology, Zurich, Switzerland
- School of Life Sciences, University of Nottingham, University Park, United Kingdom
| | - Natasha Glover
- Department of Computational Biology, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, Lausanne, Switzerland
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9
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Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Advances and Applications in the Quest for Orthologs. Mol Biol Evol 2020; 36:2157-2164. [PMID: 31241141 PMCID: PMC6759064 DOI: 10.1093/molbev/msz150] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
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Affiliation(s)
- Natasha Glover
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Genetics, Evolution & Environment, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (BIK-F), Frankfurt, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany.,Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität u Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Maria-Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Cécile Pereira
- Eura Nova, Marseille, France.,Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Alan Sousa da Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Yan Wang
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA
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Ellegaard KM, Brochet S, Bonilla‐Rosso G, Emery O, Glover N, Hadadi N, Jaron KS, Meer JR, Robinson‐Rechavi M, Sentchilo V, Tagini F, Engel P. Genomic changes underlying host specialization in the bee gut symbiont
Lactobacillus
Firm5. Mol Ecol 2019; 28:2224-2237. [DOI: 10.1111/mec.15075] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Kirsten M. Ellegaard
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Silvia Brochet
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - German Bonilla‐Rosso
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Olivier Emery
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Natasha Glover
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Jan R. Meer
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Florian Tagini
- Institute of Microbiology, Department of Laboratory Medicine University of Lausanne & Lausanne University Hospital Lausanne Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
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11
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Lindert JM, Pozzorini S, Boughezal R, Campbell JM, Denner A, Dittmaier S, Gehrmann-De Ridder A, Gehrmann T, Glover N, Huss A, Kallweit S, Maierhöfer P, Mangano ML, Morgan TA, Mück A, Petriello F, Salam GP, Schönherr M, Williams C. Precise predictions for V + jets dark matter backgrounds. Eur Phys J C Part Fields 2017; 77:829. [PMID: 31997935 PMCID: PMC6956894 DOI: 10.1140/epjc/s10052-017-5389-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/15/2017] [Indexed: 06/08/2023]
Abstract
High-energy jets recoiling against missing transverse energy (MET) are powerful probes of dark matter at the LHC. Searches based on large MET signatures require a precise control of the Z ( ν ν ¯ ) + jet background in the signal region. This can be achieved by taking accurate data in control regions dominated by Z ( ℓ + ℓ - ) + jet, W ( ℓ ν ) + jet and γ + jet production, and extrapolating to the Z ( ν ν ¯ ) + jet background by means of precise theoretical predictions. In this context, recent advances in perturbative calculations open the door to significant sensitivity improvements in dark matter searches. In this spirit, we present a combination of state-of-the-art calculations for all relevant V + jets processes, including throughout NNLO QCD corrections and NLO electroweak corrections supplemented by Sudakov logarithms at two loops. Predictions at parton level are provided together with detailed recommendations for their usage in experimental analyses based on the reweighting of Monte Carlo samples. Particular attention is devoted to the estimate of theoretical uncertainties in the framework of dark matter searches, where subtle aspects such as correlations across different V + jet processes play a key role. The anticipated theoretical uncertainty in the Z ( ν ν ¯ ) + jet background is at the few percent level up to the TeV range.
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Affiliation(s)
- J. M. Lindert
- Department of Physics, Institute for Particle Physics Phenomenology, University of Durham, Durham, DH1 3LE UK
| | - S. Pozzorini
- Physik-Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - R. Boughezal
- High Energy Physics Division, Argonne National Laboratory, Argonne, IL 60439 USA
| | | | - A. Denner
- Institut für Theoretische Physik und Astrophysik, Universität Würzburg, 97074 Würzburg, Germany
| | - S. Dittmaier
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - A. Gehrmann-De Ridder
- Physik-Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute for Theoretical Physics, ETH, 8093 Zurich, Switzerland
| | - T. Gehrmann
- Physik-Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - N. Glover
- Department of Physics, Institute for Particle Physics Phenomenology, University of Durham, Durham, DH1 3LE UK
| | - A. Huss
- Institute for Theoretical Physics, ETH, 8093 Zurich, Switzerland
| | - S. Kallweit
- Theoretical Physics Department, CERN, 1211 Geneva 23, Switzerland
| | - P. Maierhöfer
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - M. L. Mangano
- Theoretical Physics Department, CERN, 1211 Geneva 23, Switzerland
| | - T. A. Morgan
- Department of Physics, Institute for Particle Physics Phenomenology, University of Durham, Durham, DH1 3LE UK
| | - A. Mück
- Institut für Theoretische Teilchenphysik und Kosmologie, RWTH Aachen University, 52056 Aachen, Germany
| | - F. Petriello
- High Energy Physics Division, Argonne National Laboratory, Argonne, IL 60439 USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208 USA
| | - G. P. Salam
- Theoretical Physics Department, CERN, 1211 Geneva 23, Switzerland
| | - M. Schönherr
- Physik-Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - C. Williams
- Department of Physics, University at Buffalo, The State University of New York, Buffalo, 14260 USA
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12
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Hamblin A, Greenfield DM, Gilleece M, Salooja N, Kenyon M, Morris E, Glover N, Miller P, Braund H, Peniket A, Shaw BE, Snowden JA. Provision of long-term monitoring and late effects services following adult allogeneic haematopoietic stem cell transplant: a survey of UK NHS-based programmes. Bone Marrow Transplant 2017; 52:889-894. [DOI: 10.1038/bmt.2017.67] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/15/2017] [Accepted: 01/23/2017] [Indexed: 12/28/2022]
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13
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Pingault L, Choulet F, Alberti A, Glover N, Wincker P, Feuillet C, Paux E. Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome. Genome Biol 2015; 16:29. [PMID: 25853487 PMCID: PMC4355351 DOI: 10.1186/s13059-015-0601-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/28/2015] [Indexed: 12/19/2022] Open
Abstract
Background Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. Results By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Conclusions Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0601-9) contains supplementary material, which is available to authorized users.
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14
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Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res 2014; 43:D240-9. [PMID: 25399418 PMCID: PMC4383958 DOI: 10.1093/nar/gku1158] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org.
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Affiliation(s)
- Adrian M Altenhoff
- University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Nives Škunca
- University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Natasha Glover
- University College London, Gower Street, London WC1E 6BT, UK Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium
| | | | - Anna Sueki
- University College London, Gower Street, London WC1E 6BT, UK
| | - Ivana Piližota
- University College London, Gower Street, London WC1E 6BT, UK
| | - Kevin Gori
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Steven Müller
- University College London, Gower Street, London WC1E 6BT, UK
| | | | - Gaston H Gonnet
- Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland
| | - Christophe Dessimoz
- University College London, Gower Street, London WC1E 6BT, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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15
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Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science 2014; 345:1249721. [PMID: 25035497 DOI: 10.1126/science.1249721] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
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Affiliation(s)
- Frédéric Choulet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France.
| | - Adriana Alberti
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Sébastien Theil
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Natasha Glover
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Josquin Daron
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Lise Pingault
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Etienne Paux
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Philippe Leroy
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Nicolas Guilhot
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jacques Le Gouis
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Francois Balfourier
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Michael Alaux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Véronique Jamilloux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Céline Durand
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Christine Gaspin
- Biométrie et Intelligence Artificielle, INRA, Chemin de Borde Rouge, BP 27, 31326 Castanet-Tolosan, France
| | - Jan Safar
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jane Rogers
- The Genome Analysis Centre, Norwich, Norwich Research Park, Norwich NR4 7UH, UK
| | - Klaas Vandepoele
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052 Gent, Belgium
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Klaus Mayer
- Munich Information Center for Protein Sequences, Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - Hélène Berges
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Hadi Quesneville
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France. CNRS UMR 8030, 2 Rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, CP5706 Evry, France
| | - Catherine Feuillet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
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16
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Lloyd AH, Ranoux M, Vautrin S, Glover N, Fourment J, Charif D, Choulet F, Lassalle G, Marande W, Tran J, Granier F, Pingault L, Remay A, Marquis C, Belcram H, Chalhoub B, Feuillet C, Bergès H, Sourdille P, Jenczewski E. Meiotic Gene Evolution: Can You Teach a New Dog New Tricks? Mol Biol Evol 2014; 31:1724-7. [DOI: 10.1093/molbev/msu119] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Daron J, Glover N, Pingault L, Theil S, Jamilloux V, Paux E, Barbe V, Mangenot S, Alberti A, Wincker P, Quesneville H, Feuillet C, Choulet F. Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome Biol 2014; 15:546. [PMID: 25476263 PMCID: PMC4290129 DOI: 10.1186/s13059-014-0546-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/17/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far. RESULTS We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation. CONCLUSION Accurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.
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Affiliation(s)
- Josquin Daron
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Natasha Glover
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Lise Pingault
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Sébastien Theil
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Véronique Jamilloux
- />INRA-URGI, Centre de Versailles, Route de Saint Cyr, 78026 Versailles, France
| | - Etienne Paux
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
| | - Sophie Mangenot
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
| | - Adriana Alberti
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
| | - Patrick Wincker
- />CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, 91000 Evry, France
- />CNRS UMR 8030, 2 rue Gaston Crémieux, 91000 Evry, France
- />Université d’Evry, P5706 Evry, France
| | - Hadi Quesneville
- />INRA-URGI, Centre de Versailles, Route de Saint Cyr, 78026 Versailles, France
| | - Catherine Feuillet
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Frédéric Choulet
- />INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
- />University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France
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Wawrzynski A, Ashfield T, Chen NWG, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Howell S, Ilut D, Lai H, Del Campo SM, Metcalf M, O'Bleness M, Pfeil BE, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Tucker DM, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MAS, Young ND, Innes RW. Replication of nonautonomous retroelements in soybean appears to be both recent and common. Plant Physiol 2008; 148:1760-71. [PMID: 18952860 PMCID: PMC2593652 DOI: 10.1104/pp.108.127910] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Accepted: 10/22/2008] [Indexed: 05/19/2023]
Abstract
Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.
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Affiliation(s)
- Adam Wawrzynski
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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19
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Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NWG, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MAS, Young ND. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol 2008; 148:1740-59. [PMID: 18842825 PMCID: PMC2593655 DOI: 10.1104/pp.108.127902] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Accepted: 10/06/2008] [Indexed: 05/18/2023]
Abstract
The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
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Affiliation(s)
- Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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20
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Kowalski M, Brazas L, Zaretsky R, Rasamoelisolo M, MacDonald G, Cuthbert W, Glover N. A phase I study of VB6–845, an anti-EpCAM fusion protein targeting advanced solid tumours of epithelial origin: preliminary results. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.14663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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21
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Glover N, Ah-Chan JJ, Frith P, Downes S, Atan D. Unremitting sympathetic ophthalmia associated with homozygous interleukin-10-1082A single nucleotide polymorphism. Br J Ophthalmol 2008; 92:155-6. [PMID: 18156390 DOI: 10.1136/bjo.2007.116756] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- N Glover
- Oxford Eye Hospital, Radcliffe Infirmary, Oxford, UK
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22
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Fitsialos D, Seitz S, Wiecek E, Rasamoelisolo M, Entwistle J, Jewett M, MacDonald GC, Glover N. Phase I/II study of vicinium given by intravesical administration in patients with superficial transitional cell carcinoma of the bladder: Phase I results. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.4580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4580 Background: Vicinium is a fusion protein comprised of a humanized scFv, specific for Ep-CAM (epithelial cell adhesion molecule), and a truncated fragment of Pseudomonas exotoxin A. Ep-CAM is highly expressed on carcinoma cells including superficial transitional cell carcinomas (TCC) of the bladder. Vicinium targets and kills Ep-CAM-positive tumors. Results from the Phase I arm of a Phase I/II trial where Vicinium was instilled into the bladders of patients with superficial TCC of the bladder showed the drug to be very well tolerated and showed promising clinical results. Methods: 64 patients with Ep-CAM positive superficial TCC of the bladder, Ta, Tis or T1, Grades 2 or 3 who were refractory or intolerant to BCG therapy were admitted into the study. Dosing comprised a minimum of 3 subjects per dose level through 12 escalating doses. Vicinium was given once/week for 6 consecutive weeks by intravesical administration into the bladder via a catheter at escalating dose levels of 0.1, 0.2, 0.33, 0.66, 1.32, 2.64, 5.28, 10.56, 13.73, 17.85, 23.2 and 30.16 mg/week. All toxicities were assessed according to the NCI CTC v3. Blood samples were collected at different times in the study to determine systemic drug exposure and to assess immunogenicity. Efficacy was explored via biopsy, cystoscopy, urine cytology and FISH. Results: Vicinium was very well tolerated at all doses. Almost all (64/65) patients were positive for the Ep-CAM antigen. Pharmacokinetic analysis showed no evidence of Vicinium in the circulation of any of the patients; however, the majority of patients developed an anti-Vicinium response. Most patients, in particular at the higher doses, showed decreased tumor cell numbers by FISH analysis by the final day of treatment with the greatest sustained effect being observed in patients with the higher percentage Ep-CAM-positive tumors. Conclusions: Vicinium dosed on a weekly basis for 6 weeks was very well tolerated at all dose levels. The early clinical benefit observed with Vicinium strongly supports its development as a promising therapy for superficial transitional cell carcinoma of the bladder. The phase II arm of the trial will confirm the safety and further assess the efficacy of Vicinium at a recommended Phase II dose. [Table: see text]
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Affiliation(s)
- D. Fitsialos
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - S. Seitz
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - E. Wiecek
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - M. Rasamoelisolo
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - J. Entwistle
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - M. Jewett
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - G. C. MacDonald
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - N. Glover
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
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Kheradpour A, Glover N. 122 Long-term management and safety of oral posaconazole for progressive zygomycosis in a pediatric oncology patient following ambisome intolerance. Int J Infect Dis 2006. [DOI: 10.1016/s1201-9712(06)80118-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Fitsialos D, Quenneville J, Rasamoelisolo M, Cross M, Glover N, MacDonald G. A phase I study of VB4–845 in patients with advanced, recurrent head and neck cancer on a weekly dosing scheme. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.5569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- D. Fitsialos
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - J. Quenneville
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - M. Rasamoelisolo
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - M. Cross
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - N. Glover
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - G. MacDonald
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
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25
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Quenneville J, Fitsialos D, Rasamoelisolo M, Cross M, Glover N, MacDonald G. A phase I open-label study to evaluate safety, tolerability and pharmacokinetic (PK) profile of VB4–845, an anti-EpCAM immunotoxin, in subjects with SCCHN. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.5539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- J. Quenneville
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - D. Fitsialos
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - M. Rasamoelisolo
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - M. Cross
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - N. Glover
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
| | - G. MacDonald
- Viventia Biotech, Toronto, ON, Canada; Viventia Biotech, Winnipeg, MB, Canada
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26
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Abstract
The uptake of faecal occult blood testing in a workplace based colorectal cancer screening programme was investigated. Altogether 1828 employees aged 41-65 years at a large British industrial company were invited to receive a free faecal occult blood test (Haemoccult). Faecal occult blood tests were completed on three separate days. Patients with positive results were invited to undergo colonoscopy. The number of employees completing kits was measured and differences in compliance according to age, sex, and occupation were tested with a chi2 test. Compliance was 25.4%, and similar in men (25.0%) and women (32.0%, chi2=3.0, not significant). In men, compliance was highest in those aged 51-60 years (30.5% chi2>1.6, p<0.001). Compliance in women aged 41-50 years, 51-60 years, and 61-65 years was similar (Yates's corrected chi2<2.08, not significant). Managers returned more kits than clerical and blue collar workers (28.6% v 23.5%, chi2=5.6, p<0.02). One percent of tests were positive and one patient had a tubular adenoma. Compliance in employees aged 51-60 years was comparable to that achieved in one-off British general practice programmes, but less than that in the large randomised trial of screening in general practices in Nottinghamshire. Health education of large numbers of people is easier at the workplace than in the community. Future screening must target older employees and those with clerical and blue collar jobs.
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Affiliation(s)
- A R Hart
- Gastroenterology Research Unit, Leicester General Hospital, Leicester.
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27
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Argueta C, Yoder S, Holtzman AE, Aronson TW, Glover N, Berlin OG, Stelma GN, Froman S, Tomasek P. Isolation and identification of nontuberculous mycobacteria from foods as possible exposure sources. J Food Prot 2000; 63:930-3. [PMID: 10914663 DOI: 10.4315/0362-028x-63.7.930] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A variety of foods collected from local supermarkets and produce stands were examined as possible sources of nontuberculous mycobacterial exposure. Food samples were combined with sterile ultrapure water and manually shaken. To remove large particles, the suspensions were filtered through a sterile strainer, centrifuged, and the supernatants were discarded. The food pellets were stored at -75 degrees C. The pellets were treated with either oxalic acid or sodium hydroxide-sodium citrate solutions to reduce contamination by nonmycobacterial organisms. Decontaminated pellets were cultured on both Middlebrook 7H10C agar and Middlebrook 7H10C agar with supplemental malachite green. Plates were observed for growth at 2 and 8 weeks. Isolates demonstrating acid-fastness were identified to species using polymerase chain reaction and restriction enzyme analysis. Nontuberculous mycobacteria (NTM) were recovered from 25 of 121 foods. Six different species of NTM were isolated, the most predominant being Mycobacterium avium.
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Affiliation(s)
- C Argueta
- Education and Research Institute, Olive View-UCLA Medical Center, Sylmar, California 91342, USA.
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28
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Gonzalez-Ryan L, Van Syckle K, Coyne KD, Glover N. Umbilical cord blood banking: procedural and ethical concerns for this new birth option. Pediatr Nurs 2000; 26:105-10. [PMID: 12026311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
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29
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Yoder S, Argueta C, Holtzman A, Aronson T, Berlin OG, Tomasek P, Glover N, Froman S, Stelma G. PCR comparison of Mycobacterium avium isolates obtained from patients and foods. Appl Environ Microbiol 1999; 65:2650-3. [PMID: 10347056 PMCID: PMC91391 DOI: 10.1128/aem.65.6.2650-2653.1999] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium avium is a cause of disseminated disease in AIDS patients. A need for a better understanding of possible sources and routes of transmission of this organism has arisen. This study utilized a PCR typing method designed to amplify DNA segments located between the insertion sequences IS1245 and IS1311 to compare levels of relatedness of M. avium isolates found in patients and foods. Twenty-five of 121 food samples yielded 29 mycobacterial isolates, of which 12 were M. avium. Twelve food and 103 clinical M. avium isolates were tested. A clinical isolate was found to be identical to a food isolate, and close relationships were found between two patient isolates and two food isolates. Relatedness between food isolates and patient isolates suggests the possibility that food is a potential source of M. avium infection. This study demonstrates a rapid, inexpensive method for typing M. avium, possibly replacing pulsed-field gel electrophoresis.
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Affiliation(s)
- S Yoder
- Education and Research Institute, Olive View-UCLA Medical Center, Sylmar, California 91342, USA.
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30
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Aronson T, Holtzman A, Glover N, Boian M, Froman S, Berlin OG, Hill H, Stelma G. Comparison of large restriction fragments of Mycobacterium avium isolates recovered from AIDS and non-AIDS patients with those of isolates from potable water. J Clin Microbiol 1999; 37:1008-12. [PMID: 10074518 PMCID: PMC88641 DOI: 10.1128/jcm.37.4.1008-1012.1999] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/1998] [Accepted: 12/30/1998] [Indexed: 11/20/2022] Open
Abstract
We examined potable water in Los Angeles, California, as a possible source of infection in AIDS and non-AIDS patients. Nontuberculous mycobacteria were recovered from 12 (92%) of 13 reservoirs, 45 (82%) of 55 homes, 31 (100%) of 31 commercial buildings, and 15 (100%) of 15 hospitals. Large-restriction-fragment (LRF) pattern analyses were done with AseI. The LRF patterns of Mycobacterium avium isolates recovered from potable water in three homes, two commercial buildings, one reservoir, and eight hospitals had varying degrees of relatedness to 19 clinical isolates recovered from 17 patients. The high number of M. avium isolates recovered from hospital water and their close relationship with clinical isolates suggests the potential threat of nosocomial spread. This study supports the possibility that potable water is a source for the acquisition of M. avium infections.
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Affiliation(s)
- T Aronson
- Education and Research Institute, Olive View-University of California, Los Angeles, California, USA
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31
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Abstract
A negative image of community care prevails. This method of care is perceived to be a relatively novel phenomenon and has received mixed media coverage. The negative image of community care has led to the growing belief that this care method has failed. This failure has largely been ascribed to the lack of powers available to control patients in the community and to the method's relative novelty. However, this paper contends that there are two flaws to the above assertion: first, community care is far from new, and second, the inherent problem is not the lack of powers available to control patients in the community, but, essentially, the absence of a secure and stable environment within the community.
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Affiliation(s)
- N Glover
- Faculty of Law, University of Manchester
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32
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Yuen VG, Caravan P, Gelmini L, Glover N, McNeill JH, Setyawati IA, Zhou Y, Orvig C. Glucose-lowering properties of vanadium compounds: comparison of coordination complexes with maltol or kojic acid as ligands. J Inorg Biochem 1997; 68:109-16. [PMID: 9336969 DOI: 10.1016/s0162-0134(97)00082-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bis(kojato)oxovanadium(IV) [abbreviated VO(ka)2], a close chemical analog of the insulin-mimetic lead compound bis(maltolato)oxovanadium(IV)--abbreviated BMOV or VO(ma)2--is reported and its reaction chemistry and insulin-mimetic properties are presented. VO(ka)2 [log K1 = 7.61(10), log K2 = 6.89(6), log beta 2 = 14.50(16)] has a reaction chemistry which directly parallels that of VO(ma)2. In aqueous solution it is more slowly oxidized by molecular oxygen to [VO2(ka)2]- than is VO(ma)2 to [VO2(ma)2]-. Variable pH electrochemistry and variable pH 51V NMR of solutions of VO(ka)2 are presented and contrasted with the corresponding results for VO(ma)2. Time course studies (24 hr) in STZ-diabetic rats following the oral or i.p. administration of VO(ka)2, VO(ma)2, VO2+ (vanadyl) as vanadyl sulfate (VOSO4), and [VO2(ma)2]- as its [NH4]+ salt have been performed, as have chronic oral studies comparing VO(ka)2 and VO(ma)2 over a six week period. In all studies, the most potent form of vanadium was the neutrally charged, water soluble, complex VO(ma)2.
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Affiliation(s)
- V G Yuen
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
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33
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Boian M, Avaniss-Aghajani E, Walker R, Aronson T, Tran T, Glover N, Berlin OG, Woods L, Brunk C, Li JL, Froman S, Holtzman A. Identification of Mycobacterium genavense in intestinal tissue from a parakeet using two polymerase chain reaction methods: are pets a reservoir of infection in AIDS patients? AIDS 1997; 11:255-6. [PMID: 9030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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34
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Avaniss-Aghajani E, Jones K, Holtzman A, Aronson T, Glover N, Boian M, Froman S, Brunk CF. Molecular technique for rapid identification of mycobacteria. J Clin Microbiol 1996; 34:98-102. [PMID: 8748282 PMCID: PMC228739 DOI: 10.1128/jcm.34.1.98-102.1996] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Identification of mycobacteria through conventional microbiological methods is cumbersome and time-consuming. Recently we have developed a novel bacterial identification method to accurately and rapidly identify different mycobacteria directly from water and clinical isolates. The method utilizes the PCR to amplify a portion of the small subunit rRNA from mycobacteria. The 5' PCR primer has a fluorescent label to allow detection of the amplified product. The PCR product is digested with restriction endonucleases, and an automated DNA sequencer is employed to determine the size of the labeled restriction fragments. Since the PCR product is labeled only at the 5' end, the analysis identifies only the restriction fragment proximal to the 5' end. Each mycobacterial species has a unique 5' restriction fragment length for each specific endonuclease. However, frequently the 5' restriction fragments from different species have similar or identical lengths for a given endonuclease. A set of judiciously chosen restriction enzymes produces a unique set of fragments for each species, providing us with an identification signature. Using this method, we produced a library of 5' restriction fragment sizes corresponding to different clinically important mycobacteria. We have characterized mycobacterial isolates which had been previously identified by biochemical test and/or nucleic acid probes. An analysis of these data demonstrates that this protocol is effective in identifying 13 different mycobacterial species accurately. This protocol has the potential of rapidly (less than 36 h) identifying mycobacterial species directly from clinical specimens. In addition, this protocol is accurate, sensitive, and capable of identifying multiple organisms in a single sample.
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Affiliation(s)
- E Avaniss-Aghajani
- Department of Biology, University of California, Los Angeles 90024-1606, USA
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Allen AD, Mathisen GE, Glover N. A pilot study on the use of self-mononuclear cell vaccines for tertiary prevention in early HIV disease. AIDS 1993; 7:743-4. [PMID: 8318184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Abstract
Malaria during pregnancy may be associated with significant morbidity and mortality in both mother and fetus. Treatment of severe chloroquine-resistant malaria during pregnancy may be problematic since quinine and related compounds may have a deleterious effect on the course of labor. This article reports the case of a 21-year-old primigravida Liberian woman who presented with high-grade (greater than 12%) parasitemia with Plasmodium falciparum. The patient was initially treated with chloroquine; however, she developed bilateral pulmonary infiltrates and premature labor, and her condition appeared to clinically deteriorate. Therapy was changed to intravenous quinidine, and red blood cell exchange transfusion was instituted. This resulted in a decreased parasitemia and clinical improvement. The patient underwent a cesarean section, and a healthy child was delivered. Although most cases of malaria may be managed with conventional chemotherapy, the use of intravenous quinidine in combination with exchange transfusion with careful monitoring should be considered in selected cases of severe, complicated malaria in pregnant women.
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Affiliation(s)
- R D Wong
- Department of Medicine, Sepulveda Veterans Administration Medical Center, California
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Bendaña N, Glover N, Skolnick S, Barba D, Mascola L, Yakrus M. Pseudoepidemic of mycobacterium fortuitum associated with a contaminated on-site hospital water reservoir. Am J Infect Control 1991. [DOI: 10.1016/0196-6553(91)90062-h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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