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      Data access for the 1,000 Plants (1KP) project

      review-article
      1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 8 , 8 , 9 , 2 , 10 , 10 , 11 , 11 , 11 , 12 , 12 , 13 , 10 , 14 , 15 , 16 , 17 , 18 , 18 , 10 , 15 , 19 , 10 , 15 , 19 , 20 , 21 , 20 , 22 , 20 , 23 , 23 , 24 , 25 , 26 , 26 , 27 , 5 , 3 , 4 , 4 , 4 , 4 , 4 , 9 , , 4 , 5 , 28 ,
      GigaScience
      BioMed Central
      Viridiplantae, Biodiversity, Transcriptomes, Phylogenomics, Interactions, Pathways

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          Abstract

          The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

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          Most cited references5

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          The iPlant Collaborative: Cyberinfrastructure for Plant Biology

          The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.
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            Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

            Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.
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              A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity.

              Transcription factors (TFs) are key players in evolution. Changes affecting their function can yield novel life forms but may also have deleterious effects. Consequently, gene duplication events that release one gene copy from selective pressure are thought to be the common mechanism by which TFs acquire new activities. Here, we show that LEAFY, a major regulator of flower development and cell division in land plants, underwent changes to its DNA binding specificity, even though plant genomes generally contain a single copy of the LEAFY gene. We examined how these changes occurred at the structural level and identify an intermediate LEAFY form in hornworts that appears to adopt all different specificities. This promiscuous intermediate could have smoothed the evolutionary transitions, thereby allowing LEAFY to evolve new binding specificities while remaining a single-copy gene.

                Author and article information

                Contributors
                Journal
                Gigascience
                Gigascience
                GigaScience
                BioMed Central
                2047-217X
                2014
                27 October 2014
                : 3
                : 17
                Affiliations
                [1 ]iPlant Collaborative, Tucson 85721, AZ, USA
                [2 ]Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA
                [3 ]Department of Microbiology, University of Washington, Seattle 98109, WA, USA
                [4 ]BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China
                [5 ]Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
                [6 ]Chicago Botanic Garden, Glencoe 60022, IL, USA
                [7 ]Program in Biological Sciences, Northwestern University, Evanston 60208, IL, USA
                [8 ]Department of Computer Science, University of Texas, Austin, TX, 78712, USA
                [9 ]Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
                [10 ]Department of Biology, University of Florida, Gainesville, FL 32611, USA
                [11 ]Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA
                [12 ]Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada
                [13 ]CNRS, USR 2936, Station d’ Ecologie Expérimentale du CNRS, Moulis 09200, France
                [14 ]Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA
                [15 ]Florida Museum of Natural History, Gainesville, FL, 32611, USA
                [16 ]Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
                [17 ]Arnold Arboretum of Harvard University, Cambridge, MA, 02138, USA
                [18 ]Botanical Institute, Universität zu Köln, Köln D-50674, Germany
                [19 ]Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
                [20 ]Department of Biology, Duke University, Durham, NC 27708, USA
                [21 ]Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
                [22 ]Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
                [23 ]New York Botanical Garden, Bronx, NY, 10458, USA
                [24 ]Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
                [25 ]Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China
                [26 ]Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
                [27 ]Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
                [28 ]Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
                Article
                2047-217X-3-17
                10.1186/2047-217X-3-17
                4306014
                25625010
                abbc8795-5c74-41cd-a49c-fb04a2cdd0e1
                Copyright © 2014 Matasci et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 22 May 2014
                : 2 October 2014
                Categories
                Review

                viridiplantae,biodiversity,transcriptomes,phylogenomics,interactions,pathways

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