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

GigaScience

Gane Ka-Shu Wong^1,19  Jim Leebens-Mack⁵  Jun Wang^1,12  Yong Zhang^1,12  Xiao Sun^1,12  Xiaolei Wu^1,12  Zhijian Tian^1,12  Ram Samudrala⁷  Michael K Deyholos^1,19  Regina S Baucom^1,14  Megan Rolf³  Toni M Kutchan³  Tao Chen^1,13  Juan Carlos Villarreal^1,16  Dennis W Stevenson^2,21  Lisa DeGironimo^2,21  Jonathan A Shaw⁶  Lisa Pokorny^1,15  Carl Rothfels²  Pamela S Soltis¹  Douglas E Soltis¹  Michael Melkonian^1,17  Barbara Surek^1,17  Sarah Mathews^1,18  Sean W Graham⁴  Nicholas W Miles⁸  Brad R Ruhfel^1,10  Hervé Philippe^2,24  Béatrice Roure^2,25  Claude W dePamphilis^1,11  Joshua P Der^1,11  Eric Wafula^1,11  Matthew A Gitzendanner^2,23  J Gordon Burleigh^2,23  Michael Barker^2,20  Saravanaraj Ayyampalayam⁵  Tandy Warnow⁹  Nam Nguyen⁹  Siavash Mirarab⁹  Norman J Wickett^2,22  Eric J Carpenter^1,19  Zhixiang Yan^1,12  Ling-Hong Hung⁷  Naim Matasci^2,20 

[1] Genetics Institute, University of Florida, Gainesville, FL, 32611, USA;Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada;Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA;Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA;Department of Biology, Duke University, Durham, NC 27708, USA;Department of Microbiology, University of Washington, Seattle 98109, WA, USA;Florida Museum of Natural History, Gainesville, FL, 32611, USA;Department of Computer Science, University of Texas, Austin, TX, 78712, USA;Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA;Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA;BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China;Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China;Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA;Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain;Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany;Botanical Institute, Universität zu Köln, Köln D-50674, Germany;Arnold Arboretum of Harvard University, Cambridge, MA, 02138, USA;Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada;Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA;New York Botanical Garden, Bronx, NY, 10458, USA;Program in Biological Sciences, Northwestern University, Evanston 60208, IL, USA;Department of Biology, University of Florida, Gainesville, FL 32611, USA;CNRS, USR 2936, Station d’ Ecologie Expérimentale du CNRS, Moulis 09200, France;Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada

关键词: Pathways;    Interactions;    Phylogenomics;    Transcriptomes;    Biodiversity;    Viridiplantae;   

Others  :  1118581
DOI  :  10.1186/2047-217X-3-17

 received in 2014-05-22, accepted in 2014-10-02,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Matasci et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

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