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Review
. 2014 Oct 27:3:17.
doi: 10.1186/2047-217X-3-17. eCollection 2014.

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

Naim Matasci  1 , Ling-Hong Hung  2 , Zhixiang Yan  3 , Eric J Carpenter  4 , Norman J Wickett  5 , Siavash Mirarab  6 , Nam Nguyen  6 , Tandy Warnow  6 , Saravanaraj Ayyampalayam  7 , Michael Barker  8 , J Gordon Burleigh  9 , Matthew A Gitzendanner  9 , Eric Wafula  10 , Joshua P Der  10 , Claude W dePamphilis  10 , Béatrice Roure  11 , Hervé Philippe  12 , Brad R Ruhfel  13 , Nicholas W Miles  14 , Sean W Graham  15 , Sarah Mathews  16 , Barbara Surek  17 , Michael Melkonian  17 , Douglas E Soltis  18 , Pamela S Soltis  18 , Carl Rothfels  19 , Lisa Pokorny  20 , Jonathan A Shaw  21 , Lisa DeGironimo  22 , Dennis W Stevenson  22 , Juan Carlos Villarreal  23 , Tao Chen  24 , Toni M Kutchan  25 , Megan Rolf  25 , Regina S Baucom  26 , Michael K Deyholos  4 , Ram Samudrala  2 , Zhijian Tian  3 , Xiaolei Wu  3 , Xiao Sun  3 , Yong Zhang  3 , Jun Wang  3 , Jim Leebens-Mack  7 , Gane Ka-Shu Wong  27
Affiliations
Review

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

Naim Matasci et al. Gigascience. .

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.

Keywords: Biodiversity; Interactions; Pathways; Phylogenomics; Transcriptomes; Viridiplantae.

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Figures

Figure 1
Figure 1
iPlant DE data window.
Figure 2
Figure 2
Bulk download window if Java is disabled. Click on the circled link to access the instructions to install and configure an iDrop desktop.
Figure 3
Figure 3
Realigning a group of sequences using Muscle.
Figure 4
Figure 4
Phylozoom display of 1KP species phylogeny.
Figure 5
Figure 5
Phenylpropanoid synthesis pathway for Colchicum autumnale. Labelled rectangles are proteins. Small circles are metabolites. Black lines show the KEGG pathway. Red lines show the BioGRID interactions emanating from protein (K12355), which was interactively selected. A right-click on the protein will display the inferred function and a link to the sequence(s).
See this image and copyright information in PMC

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