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Herson J, Krummenacker M, Spaulding A, O'Maille P, Karp PD. The Genome Explorer genome browser. mSystems 2024:e0026724. [PMID: 38958457 DOI: 10.1128/msystems.00267-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024] Open
Abstract
Are two adjacent genes in the same operon? What are the order and spacing between several transcription factor binding sites? Genome browsers are software data visualization and exploration tools that enable biologists to answer questions such as these. In this paper, we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest. The user can rapidly move between scales that depict the entire genome, individual genes, and the sequence; Genome Explorer presents the most relevant detail and context for each scale. By downloading the data for the entire genome to the user's web browser and dynamically generating visualizations locally, we enable fine control of zoom and pan functions and real-time redrawing of the visualization, resulting in smoother and more intuitive exploration of a genome than is possible with other browsers. Further, genome features are presented together, in-line, using familiar graphical depictions. In contrast, many other browsers depict genome features using data tracks, which have low information density and can visually obscure the relative positions of features. Genome Explorer diagrams have a high information density that provides larger amounts of genome context and sequence information to be presented in a given-sized monitor than for tracks-based browsers. Genome Explorer provides optional data tracks for the analysis of large-scale data sets and a unique comparative mode that aligns genomes at orthologous genes with synchronized zooming. IMPORTANCE Genome browsers provide graphical depictions of genome information to speed the uptake of complex genome data by scientists. They provide search operations to help scientists find information and zoom operations to enable scientists to view genome features at different resolutions. We introduce the Genome Explorer browser, which provides extremely fast zooming and panning of genome visualizations and displays with high information density.
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Affiliation(s)
- James Herson
- Advanced Technology and Systems Division, SRI International, Menlo Park, California, USA
| | - Markus Krummenacker
- Artificial Intelligence Center, SRI International, Menlo Park, California, USA
| | - Aaron Spaulding
- Artificial Intelligence Center, SRI International, Menlo Park, California, USA
| | - Paul O'Maille
- BioSciences Division, SRI International, Menlo Park, California, USA
| | - Peter D Karp
- Artificial Intelligence Center, SRI International, Menlo Park, California, USA
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2
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Hu H, Li R, Zhao J, Batley J, Edwards D. Technological Development and Advances for Constructing and Analyzing Plant Pangenomes. Genome Biol Evol 2024; 16:evae081. [PMID: 38669452 PMCID: PMC11058698 DOI: 10.1093/gbe/evae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Risheng Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA 6009, Australia
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3
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Schuster M, Schweizer G, Reißmann S, Happel P, Aßmann D, Rössel N, Güldener U, Mannhaupt G, Ludwig N, Winterberg S, Pellegrin C, Tanaka S, Vincon V, Presti LL, Wang L, Bender L, Gonzalez C, Vranes M, Kämper J, Seong K, Krasileva K, Kahmann R. Novel Secreted Effectors Conserved Among Smut Fungi Contribute to the Virulence of Ustilago maydis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:250-263. [PMID: 38416124 DOI: 10.1094/mpmi-09-23-0139-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Fungal pathogens deploy a set of molecules (proteins, specialized metabolites, and sRNAs), so-called effectors, to aid the infection process. In comparison to other plant pathogens, smut fungi have small genomes and secretomes of 20 Mb and around 500 proteins, respectively. Previous comparative genomic studies have shown that many secreted effector proteins without known domains, i.e., novel, are conserved only in the Ustilaginaceae family. By analyzing the secretomes of 11 species within Ustilaginaceae, we identified 53 core homologous groups commonly present in this lineage. By collecting existing mutants and generating additional ones, we gathered 44 Ustilago maydis strains lacking single core effectors as well as 9 strains containing multiple deletions of core effector gene families. Pathogenicity assays revealed that 20 of these 53 mutant strains were affected in virulence. Among the 33 mutants that had no obvious phenotypic changes, 13 carried additional, sequence-divergent, structurally similar paralogs. We report a virulence contribution of seven previously uncharacterized single core effectors and of one effector family. Our results help to prioritize effectors for understanding U. maydis virulence and provide genetic resources for further characterization. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Gabriel Schweizer
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Independent Data Lab UG, 80937 Munich, Germany
| | - Stefanie Reißmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Petra Happel
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Daniela Aßmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Nicole Rössel
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Ulrich Güldener
- Deutsches Herzzentrum München, Technische Universität München, 80636 München, Germany
| | - Gertrud Mannhaupt
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Nicole Ludwig
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Research & Development, Weed Control Bayer AG, Crop Science Division, 65926 Frankfurt am Main, Germany
| | - Sarah Winterberg
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Clément Pellegrin
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Shigeyuki Tanaka
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Volker Vincon
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lei Wang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lena Bender
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Department of Pharmaceutics and Biopharmaceutics, Phillips-University Marburg, 35037 Marburg, Germany
| | - Carla Gonzalez
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Miroslav Vranes
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, 76131 Karlsruhe, Germany
| | - Jörg Kämper
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, 76131 Karlsruhe, Germany
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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Genome Sequence of the Wine Yeast Saccharomycodes ludwigii UTAD17. Microbiol Resour Announc 2018; 7:MRA01195-18. [PMID: 30533777 PMCID: PMC6256542 DOI: 10.1128/mra.01195-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/09/2018] [Indexed: 01/24/2023] Open
Abstract
This work describes, for the first time, the genome sequence of a Saccharomycodes ludwigii strain. Although usually seen as a wine spoilage yeast, S. ludwigii has been of interest for the production of fermented beverages because it harbors several interesting properties, including the production of beneficial aroma compounds. This work describes, for the first time, the genome sequence of a Saccharomycodes ludwigii strain. Although usually seen as a wine spoilage yeast, S. ludwigii has been of interest for the production of fermented beverages because it harbors several interesting properties, including the production of beneficial aroma compounds.
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Abstract
An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .
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Golicz AA, Batley J, Edwards D. Towards plant pangenomics. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1099-105. [PMID: 26593040 DOI: 10.1111/pbi.12499] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/18/2015] [Accepted: 10/04/2015] [Indexed: 05/05/2023]
Abstract
As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.
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Affiliation(s)
- Agnieszka A Golicz
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD, Australia
- School of Plant Biology, University of Western Australia, Perth, WA, Australia
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7
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Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga. Genetics 2016; 203:255-68. [PMID: 27017627 DOI: 10.1534/genetics.116.186734] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/21/2016] [Indexed: 12/12/2022] Open
Abstract
RNA-mediated silencing processes play a key role in silencing of transposable elements, especially in the germ line, where piwi-interacting RNAs (piRNAs) are responsible for suppressing transposon mobility and maintaining genome integrity. We previously reported that the genome of Adineta vaga, the first sequenced representative of the phylum Rotifera (class Bdelloidea), is characterized by massive levels of horizontal gene transfer, by unusually low transposon content, and by highly diversified RNA-mediated silencing machinery. Here, we investigate genome-wide distribution of pi-like small RNAs, which in A. vaga are 25-31 nucleotides in length and have a strong 5'-uridine bias, while lacking ping-pong amplification signatures. In agreement with expectations, 71% of mapped reads corresponded to annotated transposons, with 93% of these reads being in the antisense orientation. Unexpectedly, a significant fraction of piRNAs originate from predicted coding regions corresponding to genes of putatively foreign origin. The distribution of piRNAs across foreign genes is not biased toward 3'-UTRs, instead resembling transposons in uniform distribution pattern throughout the gene body, and in predominantly antisense orientation. We also find that genes with small RNA coverage, including a number of genes of metazoan origin, are characterized by higher occurrence of telomeric repeats in the surrounding genomic regions, and by higher density of transposons in the vicinity, which have the potential to promote antisense transcription. Our findings highlight the complex interplay between RNA-based silencing processes and acquisition of genes at the genome periphery, which can result either in their loss or eventual domestication and integration into the host genome.
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Shifman AR, Johnson RM, Wilhelm BT. Cascade: an RNA-seq visualization tool for cancer genomics. BMC Genomics 2016; 17:75. [PMID: 26810393 PMCID: PMC4727405 DOI: 10.1186/s12864-016-2389-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/11/2016] [Indexed: 12/20/2022] Open
Abstract
Background Cancer genomics projects are producing ever-increasing amounts of rich and diverse data from patient samples. The ability to easily visualize this data in an integrated an intuitive way is currently limited by the current software available. As a result, users typically must use several different tools to view the different data types for their cohort, making it difficult to have a simple unified view of their data. Results Here we present Cascade, a novel web based tool for the intuitive 3D visualization of RNA-seq data from cancer genomics experiments. The Cascade viewer allows multiple data types (e.g. mutation, gene expression, alternative splicing frequency) to be simultaneously displayed, allowing a simplified view of the data in a way that is tuneable based on user specified parameters. The main webpage of Cascade provides a primary view of user data which is overlaid onto known biological pathways that are either predefined or added by users. A space-saving menu for data selection and parameter adjustment allows users to access an underlying MySQL database and customize the features presented in the main view. Conclusions There is currently a pressing need for new software tools to allow researchers to easily explore large cancer genomics datasets and generate hypotheses. Cascade represents a simple yet intuitive interface for data visualization that is both scalable and customizable. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2389-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aaron R Shifman
- Laboratory for high throughput genomics, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.
| | - Radia M Johnson
- Laboratory for high throughput genomics, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.
| | - Brian T Wilhelm
- Laboratory for high throughput genomics, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.
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Yu B, Doraiswamy H, Chen X, Miraldi E, Arrieta-Ortiz ML, Hafemeister C, Madar A, Bonneau R, Silva CT. Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2014; 20:1903-1912. [PMID: 26356904 DOI: 10.1109/tvcg.2014.2346753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Elucidation of transcriptional regulatory networks (TRNs) is a fundamental goal in biology, and one of the most important components of TRNs are transcription factors (TFs), proteins that specifically bind to gene promoter and enhancer regions to alter target gene expression patterns. Advances in genomic technologies as well as advances in computational biology have led to multiple large regulatory network models (directed networks) each with a large corpus of supporting data and gene-annotation. There are multiple possible biological motivations for exploring large regulatory network models, including: validating TF-target gene relationships, figuring out co-regulation patterns, and exploring the coordination of cell processes in response to changes in cell state or environment. Here we focus on queries aimed at validating regulatory network models, and on coordinating visualization of primary data and directed weighted gene regulatory networks. The large size of both the network models and the primary data can make such coordinated queries cumbersome with existing tools and, in particular, inhibits the sharing of results between collaborators. In this work, we develop and demonstrate a web-based framework for coordinating visualization and exploration of expression data (RNA-seq, microarray), network models and gene-binding data (ChIP-seq). Using specialized data structures and multiple coordinated views, we design an efficient querying model to support interactive analysis of the data. Finally, we show the effectiveness of our framework through case studies for the mouse immune system (a dataset focused on a subset of key cellular functions) and a model bacteria (a small genome with high data-completeness).
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10
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Fan Y, Yu D, Yao YG. Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. Sci Rep 2014; 4:7145. [PMID: 25413576 PMCID: PMC5382678 DOI: 10.1038/srep07145] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/30/2014] [Indexed: 11/10/2022] Open
Abstract
The tree shrew (Tupaia belangeri) is a small mammal with a close relationship to primates and it has been proposed as an alternative experimental animal to primates in biomedical research. The recent release of a high-quality Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies. With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including an updated gene set, with a systematic functional annotation and a mRNA expression pattern. In addition, to assist with automatic gene sequence analysis, we have integrated the common programs Blast, Muscle, GBrowse, GeneWise and codeml, into TreeshrewDB. We have also developed a pipeline for the analysis of positive selection. The user-friendly interface of TreeshrewDB, which is available at http://www.treeshrewdb.org, will undoubtedly help in many areas of biological research into the tree shrew.
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Affiliation(s)
- Yu Fan
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Yong-Gang Yao
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China [3] Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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11
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Billis K, Billini M, Tripp HJ, Kyrpides NC, Mavromatis K. Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation. PLoS One 2014; 9:e109738. [PMID: 25340743 PMCID: PMC4207680 DOI: 10.1371/journal.pone.0109738] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/13/2014] [Indexed: 12/13/2022] Open
Abstract
Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 are model cyanobacteria from which the metabolism and adaptive responses of other cyanobacteria are inferred. Using stranded and 5' enriched libraries, we measured the gene expression response of cells transferred from reference conditions to stress conditions of decreased inorganic carbon, increased salinity, increased pH, and decreased illumination at 1-h and 24-h after transfer. We found that the specific responses of the two strains were by no means identical. Transcriptome profiles allowed us to improve the structural annotation of the genome i.e. identify possible missed genes (including anti-sense), alter gene coordinates and determine transcriptional units (operons). Finally, we predicted associations between proteins of unknown function and biochemical pathways by revealing proteins of known functions that are co-regulated with the unknowns. Future studies of these model organisms will benefit from the cataloging of their responses to environmentally relevant stresses, and improvements in their genome annotations found here.
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Affiliation(s)
- Konstantinos Billis
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Billini
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Group of Prokaryotic Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Faculty of Biology, Philipps-Universität, Marburg, Germany
| | - H. James Tripp
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
| | - Nikos C. Kyrpides
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Konstantinos Mavromatis
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Computational Biology Group, Celgene Corp, San Francisco, California, United States of America
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Jung S, Main D. Genomics and bioinformatics resources for translational science in Rosaceae. PLANT BIOTECHNOLOGY REPORTS 2014; 8:49-64. [PMID: 24634697 PMCID: PMC3951882 DOI: 10.1007/s11816-013-0282-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/22/2013] [Indexed: 05/22/2023]
Abstract
Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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Evans K, Jung S, Lee T, Brutcher L, Cho I, Peace C, Main D. Addition of a breeding database in the Genome Database for Rosaceae. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat078. [PMID: 24247530 PMCID: PMC3831303 DOI: 10.1093/database/bat078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox.
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Affiliation(s)
- Kate Evans
- Washington State University Tree Fruit Research and Extension Center, 1100 N. Western Ave, Wenatchee, WA 98801; Department of Horticulture, Washington State University, Johnson Hall, Pullman WA 99164 and Department of Computer Science, Saginaw Valley State University, University Center, MI 48710, USA
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Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J. Genome Maps, a new generation genome browser. Nucleic Acids Res 2013; 41:W41-6. [PMID: 23748955 PMCID: PMC3692043 DOI: 10.1093/nar/gkt530] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.
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Affiliation(s)
- Ignacio Medina
- Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
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15
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Lee CC, Chen YPP, Yao TJ, Ma CY, Lo WC, Lyu PC, Tang CY. GI-POP: A combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. Gene 2013; 518:114-23. [DOI: 10.1016/j.gene.2012.11.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
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16
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Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O'Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Güldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, Zeng Z. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genet 2013; 9:e1003323. [PMID: 23468653 PMCID: PMC3585121 DOI: 10.1371/journal.pgen.1003323] [Citation(s) in RCA: 271] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/31/2012] [Indexed: 01/01/2023] Open
Abstract
The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.
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17
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Huang Y, Chen W, Wang X, Liu H, Chen Y, Guo L, Luo F, Sun J, Mao Q, Liang P, Xie Z, Zhou C, Tian Y, Lv X, Huang L, Zhou J, Hu Y, Li R, Zhang F, Lei H, Li W, Hu X, Liang C, Xu J, Li X, Yu X. The carcinogenic liver fluke, Clonorchis sinensis: new assembly, reannotation and analysis of the genome and characterization of tissue transcriptomes. PLoS One 2013; 8:e54732. [PMID: 23382950 PMCID: PMC3559784 DOI: 10.1371/journal.pone.0054732] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/14/2012] [Indexed: 01/20/2023] Open
Abstract
Clonorchis sinensis (C. sinensis), an important food-borne parasite that inhabits the intrahepatic bile duct and causes clonorchiasis, is of interest to both the public health field and the scientific research community. To learn more about the migration, parasitism and pathogenesis of C. sinensis at the molecular level, the present study developed an upgraded genomic assembly and annotation by sequencing paired-end and mate-paired libraries. We also performed transcriptome sequence analyses on multiple C. sinensis tissues (sucker, muscle, ovary and testis). Genes encoding molecules involved in responses to stimuli and muscle-related development were abundantly expressed in the oral sucker. Compared with other species, genes encoding molecules that facilitate the recognition and transport of cholesterol were observed in high copy numbers in the genome and were highly expressed in the oral sucker. Genes encoding transporters for fatty acids, glucose, amino acids and oxygen were also highly expressed, along with other molecules involved in metabolizing these substrates. All genes involved in energy metabolism pathways, including the β-oxidation of fatty acids, the citrate cycle, oxidative phosphorylation, and fumarate reduction, were expressed in the adults. Finally, we also provide valuable insights into the mechanism underlying the process of pathogenesis by characterizing the secretome of C. sinensis. The characterization and elaborate analysis of the upgraded genome and the tissue transcriptomes not only form a detailed and fundamental C. sinensis resource but also provide novel insights into the physiology and pathogenesis of C. sinensis. We anticipate that this work will aid the development of innovative strategies for the prevention and control of clonorchiasis.
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Affiliation(s)
- Yan Huang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Wenjun Chen
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Xiaoyun Wang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Hailiang Liu
- Guangzhou iGenomics Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Yangyi Chen
- Guangzhou iGenomics Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Lei Guo
- Guangzhou iGenomics Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Fang Luo
- Guangzhou iGenomics Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Jiufeng Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Qiang Mao
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Pei Liang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Zhizhi Xie
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Chenhui Zhou
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Yanli Tian
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Xiaoli Lv
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Lisi Huang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Juanjuan Zhou
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Yue Hu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Ran Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Fan Zhang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Huali Lei
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Wenfang Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Xuchu Hu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Chi Liang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Jin Xu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- * E-mail: (XBY); (XRL); (JX)
| | - Xuerong Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- * E-mail: (XBY); (XRL); (JX)
| | - Xinbing Yu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
- * E-mail: (XBY); (XRL); (JX)
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18
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Wang D, Xia Y, Li X, Hou L, Yu J. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Res 2012. [PMID: 23193278 PMCID: PMC3531066 DOI: 10.1093/nar/gks1225] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases—sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions–deletions.
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Affiliation(s)
- Dapeng Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
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19
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Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, Berkman PJ, Lai K, Batley J, Edwards D. Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP. BIOLOGY 2012; 1:370-82. [PMID: 24832230 PMCID: PMC4009776 DOI: 10.3390/biology1020370] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/09/2012] [Accepted: 08/10/2012] [Indexed: 01/01/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are becoming the dominant form of molecular marker for genetic and genomic analysis. The advances in second generation DNA sequencing provide opportunities to identify very large numbers of SNPs in a range of species. However, SNP identification remains a challenge for large and polyploid genomes due to their size and complexity. We have developed a pipeline for the robust identification of SNPs in large and complex genomes using Illumina second generation DNA sequence data and demonstrated this by the discovery of SNPs in the hexaploid wheat genome. We have developed a SNP discovery pipeline called SGSautoSNP (Second-Generation Sequencing AutoSNP) and applied this to discover more than 800,000 SNPs between four hexaploid wheat cultivars across chromosomes 7A, 7B and 7D. All SNPs are presented for download and viewing within a public GBrowse database. Validation suggests an accuracy of greater than 93% of SNPs represent polymorphisms between wheat cultivars and hence are valuable for detailed diversity analysis, marker assisted selection and genotyping by sequencing. The pipeline produces output in GFF3, VCF, Flapjack or Illumina Infinium design format for further genotyping diverse populations. As well as providing an unprecedented resource for wheat diversity analysis, the method establishes a foundation for high resolution SNP discovery in other large and complex genomes.
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Affiliation(s)
- Michał T Lorenc
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Satomi Hayashi
- Centre for Integrative Legume Research, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Jiri Stiller
- CSIRO Plant Industry, Brisbane, QLD 4072, Australia.
| | - Hong Lee
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Pradeep Ruperao
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Paul Visendi
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | | | - Kaitao Lai
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Jacqueline Batley
- Centre for Integrative Legume Research, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
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20
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Zuccaro A, Lahrmann U, Güldener U, Langen G, Pfiffi S, Biedenkopf D, Wong P, Samans B, Grimm C, Basiewicz M, Murat C, Martin F, Kogel KH. Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Pathog 2011; 7:e1002290. [PMID: 22022265 PMCID: PMC3192844 DOI: 10.1371/journal.ppat.1002290] [Citation(s) in RCA: 238] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/14/2011] [Indexed: 11/18/2022] Open
Abstract
Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead barley roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyle strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarray analysis, argues for a biphasic root colonization strategy of P. indica. This is supported by a cytological study that shows an early biotrophic growth followed by a cell death-associated phase. About 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP), including several lectin-like proteins and members of a P. indica-specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. Similar to effectors found in other filamentous organisms, the occurrence of the DELDs correlated with the presence of transposable elements in gene-poor repeat-rich regions of the genome. This is the first in depth genomic study describing a mutualistic symbiont with a biphasic lifestyle. Our findings provide a significant advance in understanding development of biotrophic plant symbionts and suggest a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi.
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Affiliation(s)
- Alga Zuccaro
- Department of Organismic Interactions, Max-Planck Institute (MPI) for Terrestrial Microbiology, Marburg, Germany.
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21
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Ficklin SP, Sanderson LA, Cheng CH, Staton ME, Lee T, Cho IH, Jung S, Bett KE, Main D. Tripal: a construction toolkit for online genome databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2011; 2011:bar044. [PMID: 21959868 PMCID: PMC3263599 DOI: 10.1093/database/bar044] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net
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Affiliation(s)
- Stephen P Ficklin
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
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22
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Web-based metabolic network visualization with a zooming user interface. BMC Bioinformatics 2011; 12:176. [PMID: 21595965 PMCID: PMC3113945 DOI: 10.1186/1471-2105-12-176] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 05/19/2011] [Indexed: 12/26/2022] Open
Abstract
Background Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging. Description We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams. Conclusions This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.
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23
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Mungall CJ, Batchelor C, Eilbeck K. Evolution of the Sequence Ontology terms and relationships. J Biomed Inform 2010; 44:87-93. [PMID: 20226267 DOI: 10.1016/j.jbi.2010.03.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 02/11/2010] [Accepted: 03/05/2010] [Indexed: 10/19/2022]
Abstract
The Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both genomic and derived sequence. The SO is working within the guidelines of the OBO Foundry to provide interoperability between SO and the other related OBO ontologies. Here, we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence.
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Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 2009; 11:40-79. [PMID: 19955237 DOI: 10.1093/bib/bbp043] [Citation(s) in RCA: 325] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry.
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Affiliation(s)
- Peter D Karp
- Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA.
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25
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Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean. DNA Res 2009; 16:353-69. [PMID: 19884168 PMCID: PMC2780956 DOI: 10.1093/dnares/dsp023] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 10/05/2009] [Indexed: 12/29/2022] Open
Abstract
Sequence-specific DNA-binding transcription factors (TFs) are often termed as 'master regulators' which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families. We constructed a database named SoybeanTFDB (http://soybeantfdb.psc.riken.jp) containing the full compilation of soybean TFs and significant information such as: functional motifs, full-length cDNAs, domain alignments, promoter regions, genomic organization and putative regulatory functions based on annotations of gene ontology (GO) inferred by comparative analysis with Arabidopsis. With particular interest in abiotic stress signalling, we analysed the promoter regions for all of the TF encoding genes as a means to identify abiotic stress responsive cis-elements as well as all types of cis-motifs provided by the PLACE database. SoybeanTFDB enables scientists to easily access cis-element and GO annotations to aid in the prediction of TF function and selection of TFs with functions of interest. This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takuhiro Yoshida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Kazuo Shinozaki
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Lam-Son Phan Tran
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Wilming L, Harrow J. Gene Annotation Methods. Bioinformatics 2009. [DOI: 10.1007/978-0-387-92738-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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