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

doi:10.1186/2047-217X-3-17

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 Matasci¹, Ling-Hong Hung², Zhixiang Yan³, Eric J Carpenter⁴, Norman J Wickett⁵, Siavash Mirarab⁶, Nam Nguyen⁶, Tandy Warnow⁶, Saravanaraj Ayyampalayam⁷, Michael Barker⁸, J Gordon Burleigh⁹, Matthew A Gitzendanner⁹, Eric Wafula¹⁰, Joshua P Der¹⁰, Claude W dePamphilis¹⁰, Béatrice Roure¹¹, Hervé Philippe¹², Brad R Ruhfel¹³, Nicholas W Miles¹⁴, Sean W Graham¹⁵, Sarah Mathews¹⁶, Barbara Surek¹⁷, Michael Melkonian¹⁷, Douglas E Soltis¹⁸, Pamela S Soltis¹⁸, Carl Rothfels¹⁹, Lisa Pokorny²⁰, Jonathan A Shaw²¹, Lisa DeGironimo²², Dennis W Stevenson²², Juan Carlos Villarreal²³, Tao Chen²⁴, Toni M Kutchan²⁵, Megan Rolf²⁵, Regina S Baucom²⁶, Michael K Deyholos⁴, Ram Samudrala², Zhijian Tian³, Xiaolei Wu³, Xiao Sun³, Yong Zhang³, Jun Wang³, Jim Leebens-Mack⁷, Gane Ka-Shu Wong²⁷

Affiliations

¹ iPlant Collaborative, Tucson 85721, AZ, USA ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
² Department of Microbiology, University of Washington, Seattle 98109, WA, USA.
³ BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
⁴ Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada.
⁵ Chicago Botanic Garden, Glencoe 60022, IL, USA ; Program in Biological Sciences, Northwestern University, Evanston 60208, IL, USA.
⁶ Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
⁷ Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
⁸ Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
⁹ Department of Biology, University of Florida, Gainesville, FL 32611, USA.
¹⁰ Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
¹¹ Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada.
¹² 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.
¹³ Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA.
¹⁴ Florida Museum of Natural History, Gainesville, FL, 32611, USA.
¹⁵ Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
¹⁶ Arnold Arboretum of Harvard University, Cambridge, MA, 02138, USA.
¹⁷ Botanical Institute, Universität zu Köln, Köln D-50674, Germany.
¹⁸ 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.
¹⁹ Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
²⁰ Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain.
²¹ Department of Biology, Duke University, Durham, NC 27708, USA.
²² New York Botanical Garden, Bronx, NY, 10458, USA.
²³ Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
²⁴ Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China.
²⁵ Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
²⁶ Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
²⁷ 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.

PMID: 25625010
PMCID: PMC4306014
DOI: 10.1186/2047-217X-3-17

Review

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

Naim Matasci et al. Gigascience. 2014.

. 2014 Oct 27:3:17.

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

Authors

Affiliations

¹ iPlant Collaborative, Tucson 85721, AZ, USA ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
² Department of Microbiology, University of Washington, Seattle 98109, WA, USA.
³ BGI-Shenzhen, Bei Shan Industrial Zone, Shenzhen, China.
⁴ Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada.
⁵ Chicago Botanic Garden, Glencoe 60022, IL, USA ; Program in Biological Sciences, Northwestern University, Evanston 60208, IL, USA.
⁶ Department of Computer Science, University of Texas, Austin, TX, 78712, USA.
⁷ Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
⁸ Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.
⁹ Department of Biology, University of Florida, Gainesville, FL 32611, USA.
¹⁰ Department of Biology, Penn State University, University Park, Pennsylvania, PA, 16801, USA.
¹¹ Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada.
¹² 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.
¹³ Department of Biology, University of Florida, Gainesville, FL 32611, USA ; Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, 40475, USA.
¹⁴ Florida Museum of Natural History, Gainesville, FL, 32611, USA.
¹⁵ Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
¹⁶ Arnold Arboretum of Harvard University, Cambridge, MA, 02138, USA.
¹⁷ Botanical Institute, Universität zu Köln, Köln D-50674, Germany.
¹⁸ 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.
¹⁹ Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
²⁰ Department of Biology, Duke University, Durham, NC 27708, USA ; Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain.
²¹ Department of Biology, Duke University, Durham, NC 27708, USA.
²² New York Botanical Garden, Bronx, NY, 10458, USA.
²³ Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
²⁴ Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China.
²⁵ Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
²⁶ Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
²⁷ 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.

PMID: 25625010
PMCID: PMC4306014
DOI: 10.1186/2047-217X-3-17

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 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**
**Realigning a group of sequences using** ***Muscle.***

**Figure 4**
***Phylozoom*** **display of 1KP species phylogeny.**

**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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References

1. Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH. et al.The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci. 2011;2:34. - PMC - PubMed
1. 1KP BLAST Search Portal. [ http://www.bioinfodata.org/app/Blast4OneKP/home]
1. Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, dePamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr. et al.Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One. 2012;7:e50226. doi: 10.1371/journal.pone.0050226. - DOI - PMC - PubMed
1. Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J. SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30:1660–1666. doi: 10.1093/bioinformatics/btu077. - DOI - PubMed
1. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Ruhfel B, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels C, Pokorny L, Shaw AJ, deGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, A phylotranscriptomics analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A. IN PRESS. - PMC - PubMed

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[1] Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH. et al.The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci. 2011;2:34. - PMC - PubMed

[2] Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH. et al.The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci. 2011;2:34. - PMC - PubMed

[3] 1KP BLAST Search Portal. [ http://www.bioinfodata.org/app/Blast4OneKP/home]

[4] 1KP BLAST Search Portal. [ http://www.bioinfodata.org/app/Blast4OneKP/home]

[5] Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, dePamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr. et al.Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One. 2012;7:e50226. doi: 10.1371/journal.pone.0050226. - DOI - PMC - PubMed

[6] Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, dePamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr. et al.Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One. 2012;7:e50226. doi: 10.1371/journal.pone.0050226. - DOI - PMC - PubMed

[7] Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J. SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30:1660–1666. doi: 10.1093/bioinformatics/btu077. - DOI - PubMed

[8] Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J. SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30:1660–1666. doi: 10.1093/bioinformatics/btu077. - DOI - PubMed

[9] Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Ruhfel B, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels C, Pokorny L, Shaw AJ, deGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, A phylotranscriptomics analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A. IN PRESS. - PMC - PubMed

[10] Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Ruhfel B, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels C, Pokorny L, Shaw AJ, deGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, A phylotranscriptomics analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A. IN PRESS. - PMC - PubMed

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

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

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