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

Naim Matasci (1, 2) , Ling-Hong Hung (3) , Zhixiang Yan (4) , Eric Carpenter (5) , Norman Wickett (6) , Siavash Mirarab (7, 8) , Nam Nguyen (8) , Tandy Warnow (8) , Saravanaraj Ayyampalayam (9) , Michael Barker (2) , J Gordon Burleigh (10) , Matthew Gitzendanner (10) , Eric Wafula (11) , Joshua Der (11) , Claude Depamphilis (11) , Béatrice Roure (12) , Herve Philippe (13, 12) , Brad Ruhfel (10, 14) , Nicholas Miles (15) , Sean Graham (16) , Sarah Mathews (17) , Barbara Surek (18) , Michael Melkonian (18) , Douglas Soltis (10, 15) , Pamela Soltis (19, 16) , Carl Rothfels (19, 20) , Lisa Pokorny (20, 19) , Jonathan Shaw (19) , Lisa Degironimo (21) , Dennis Stevenson (21) , Juan Carlos Villarreal (22) , Tao Chen (23) , Toni Kutchan (24) , Megan Rolf (24) , Regina Baucom (25) , Michael Deyholos (5) , Ram Samudrala (3) , Zhijian Tian (4) , Xiaolei Wu (4) , Xiao Sun (4) , Yong Zhang (4) , Jun Wang (4) , Jim Leebens-Mack (9) , Gane Ka-Shu Wong (4, 5)

1 School of Plant Sciences, iPlant Collaborative
2 University of Arizona
3 University of Washington [Seattle]
4 BGI - Beijing Genomics Institute [Shenzhen]
5 University of Alberta
6 Chicago Botanic Garden
7 Northwestern University [Evanston]
8 University of Texas at Austin [Austin]
9 University of Georgia [USA]
10 UF - University of Florida [Gainesville]
11 Penn State - Pennsylvania State University
12 UdeM - Université de Montréal
13 SEEM - Station d’Ecologie Expérimentale du CNRS à Moulis
14 Eastern Kentucky University
15 Florida Museum of Natural History [Gainesville]
16 UBC - University of British Columbia
17 Harvard University
18 Universität zu Köln = University of Cologne
19 Duke University [Durham]
20 RJB - Real Jardín Botánico de Madrid
21 NYBG - New York Botanical Garden
22 LMU - Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München
23 CAS - Chinese Academy of Sciences [Beijing]
24 Donald Danforth Plant Science Center
25 University of Michigan [Ann Arbor]

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.

Mots clés: Biodiversity; Transcriptomes; Phylogenomics; Interactions; Pathways; Viridiplantae

Domaines: Biologie végétale

Naim Matasci, Ling-Hong Hung, Zhixiang Yan, Eric Carpenter, Norman Wickett, et al.. Data access for the 1,000 Plants (1KP) project. GigaScience, 2014, 3, ⟨10.1186/2047-217X-3-17⟩. ⟨hal-02958660⟩