title: Data access for the 1,000 Plants (1KP) project.
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.
authors.affiliation: iPlant Collaborative, Tucson 85721, AZ, USA ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
authors.forename: Naim
authors.initials: N
authors.lastname: Matasci
authors.affiliation: Department of Microbiology, University of Washington, Seattle 98109, WA, USA.
authors.forename: Ling-Hong
authors.initials: LH
authors.lastname: Hung
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Zhixiang
authors.initials: Z
authors.lastname: Yan
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Carpenter
authors.affiliation: Chicago Botanic Garden, Glencoe 60022, IL, USA ; Program in Biological Sciences, Northwestern University, Evanston 60208, IL, USA.
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Wickett
authors.affiliation: Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
authors.forename: Siavash
authors.initials: S
authors.lastname: Mirarab
authors.affiliation: Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
authors.forename: Nam
authors.initials: N
authors.lastname: Nguyen
authors.affiliation: Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Saravanaraj
authors.initials: S
authors.lastname: Ayyampalayam
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Barker
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.
authors.forename: J Gordon
authors.initials: JG
authors.lastname: Burleigh
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Gitzendanner
authors.affiliation: Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Wafula
authors.affiliation: Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
authors.forename: Joshua P
authors.initials: JP
authors.lastname: Der
authors.affiliation: Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
authors.forename: Claude W
authors.initials: CW
authors.lastname: dePamphilis
authors.affiliation: Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada.
authors.forename: Béatrice
authors.initials: B
authors.lastname: Roure
authors.affiliation: Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada ; CNRS, USR 2936, Station d' Ecologie Expérimentale du CNRS, Moulis 09200, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Philippe
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA.
authors.forename: Brad R
authors.initials: BR
authors.lastname: Ruhfel
authors.affiliation: Florida Museum of Natural History, Gainesville, FL, 32611, USA.
authors.forename: Nicholas W
authors.initials: NW
authors.lastname: Miles
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Sean W
authors.initials: SW
authors.lastname: Graham
authors.affiliation: Arnold Arboretum of Harvard University, Cambridge, MA, 02138, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mathews
authors.affiliation: Botanical Institute, Universität zu Köln, Köln D-50674, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Surek
authors.affiliation: Botanical Institute, Universität zu Köln, Köln D-50674, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Melkonian
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Gainesville, FL, 32611, USA ; Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Gainesville, FL, 32611, USA ; Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Carl
authors.initials: C
authors.lastname: Rothfels
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain.
authors.forename: Lisa
authors.initials: L
authors.lastname: Pokorny
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Shaw
authors.affiliation: New York Botanical Garden, Bronx, NY, 10458, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: DeGironimo
authors.affiliation: New York Botanical Garden, Bronx, NY, 10458, USA.
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
authors.affiliation: Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Villarreal
authors.affiliation: Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
authors.forename: Toni M
authors.initials: TM
authors.lastname: Kutchan
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
authors.forename: Megan
authors.initials: M
authors.lastname: Rolf
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Regina S
authors.initials: RS
authors.lastname: Baucom
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Deyholos
authors.affiliation: Department of Microbiology, University of Washington, Seattle 98109, WA, USA.
authors.forename: Ram
authors.initials: R
authors.lastname: Samudrala
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Tian
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Sun
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Jim
authors.initials: J
authors.lastname: Leebens-Mack
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China ; Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada ; Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
keywords: Biodiversity; Interactions; Pathways; Phylogenomics; Transcriptomes; Viridiplantae