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.

Introduction

The 1,000 plants (1KP) project is an international multidisciplinary consortium that has now generated transcriptome data from over 1,000 plant species. One of the goals of our species selection process was to provide exemplars for all of the major lineages across the Viridip l antae (green plants), representing approximately one billion years of evolution, including flowering plants, conifers, ferns, mosses and streptophyte green algae. Whereas genomics has long strived for completeness within species (e.g., every gene in the species), we were focused on completeness across an evolutionary clade — obviously not every species, but one representative species for everything at some phylogenetic level (e.g., one species per family, and perhaps more than one species when the family is especially large). Because many of our species had never been subjected to large-scale sequencing, 2 gigabases (Gb) of data per sample was sufficient to increase the number of plant genes by approximately 100-fold in comparison to the totality of the public databases.

The 1KP project began as a public-private partnership, with 75% of the funding provided by the Government of Alberta and 25% by Musea Ventures. Significant in-kind contributions were provided by BGI-Shenzhen in the form of reduced sequencing costs and by the NSF-funded iPlant collaborative [1] in the form of computational informatics support. Many plant scientists from around the world were involved in the collection of live tissue samples and in the extraction of RNA. Additional computing resources were provided by Compute Canada and by the China National GeneBank. Despite the constraints of this funding model, we released our data (on a collaborative basis) to scientists who approached us with goals that did not compete with ours. For the general community, access was provided through a BLAST portal [2].

We believed that there would be intrinsic value in data of this nature that is beyond our imagination. But for the initial publication, we agreed on two objectives. Firstly, by adopting a phylogenomics approach we hoped to resolve many of the lingering uncertainties in species relationships, especially in the early lineages of streptophyte green algae and land plants, where previous analyses were based on comparatively sparse taxonomic densities. And secondly, despite the limitations of these data, we hoped to identify some of the gene changes associated with the major innovations in Viridiplantae evolution, such as multicellularity, transitions from marine to freshwater or terrestrial environments, maternal retention of zygotes and embryos, complex life history involving haploid and diploid phases, vascular systems, seeds and flowers.

Our RNA extraction protocols [3] and our RNA-Seq transcriptome assembly algorithms [4] have already been published. Here, we are publishing the second of two linked papers. The first is a review of the state-of-knowledge for Viridiplantae species relationships and our initial foray into the phylogenomics on a subset of 1KP [5]. The other is a description of the websites that we created in order to provide access to the data (from raw reads to computed results), visualize the results, and perform custom analyses in conjunction with external data that the users can upload. An initial gene annotation is also provided, which focuses on the functional relationships between proteins and their associated metabolites.

Review

Access to raw and processed data

Our initial phylogenomics effort used sequences from multiple sources. They include transcriptomes from 1KP representing 85 species, transcriptomes from other sources representing 7 species, and genomes representing an additional 11 species. A summary of these data sources is given in Table 1. We submitted all of the unassembled reads from the 1KP transcriptomes to the Short Reads Archive (SRA) under project accession PRJEB4921 “1000 Plant (1KP) Transcriptome: The Pilot Study.” Note that, with the exception of Eschscholzia californica, we sequenced only one sample per species.

To make it easier for others to reproduce our phylogenomics analyses, we are releasing our intermediate computations, not just the final results. Everything is hosted at the iPlant Data Store, a high performance, large capacity, distributed storage system. The contents include transcriptome assemblies, putative coding sequences, orthogroups (i.e., from the 11 reference genomes), as well as gene and species trees with related sequence alignments. There are quite a lot of files and their total sizes are not negligible; so before users begin to download these files, we suggest that they consult Table 2 for a description of what to expect.

At the simplest level, anonymous downloads are permitted from a designated area of the iPlant Data Store [6]. However, much greater functionality is available through the iPlant resources that we describe in the following sections.

Visualization and custom analyses

To take full advantage of the iPlant computational infrastructure, it is necessary to first register at [7]. Accounts are free, and in addition to 1KP data, users will find high performance computing and cloud-based services. Multiple access modalities are supported: anonymous and secure web interfaces, desktop clients and high-speed command lines. However, we feel that for most users the best option is the iPlant discovery environment (DE), a web-based interface that provides users with high-performance computing resources and data storage. Most contemporary web browsers are supported, including Safari v. 6.1, Firefox v. 24, and Chrome v. 34. The caveat is that some of these functionalities (see below) require Java 1.6.

To guide users through its resources, iPlant is constantly producing new tutorials and teaching materials, including live and recorded webinars. The full catalog can be found at [8]. Here, we describe the new resources specifically created for 1KP.

Discovery environment (DE)

For access to the 1KP files, users should visit [9] and search for a folder called Community Data/onekp_pilotFigure 1.

From the data window it is possible to download individual files or perform bulk downloads of multiple files and directories through a Java plugin. Note that for security reasons, some operating systems will not allow users to run Java applets. In this instance, a window will pop up to tell the user that there is a problem, and the user should follow the instructions that are given to configure an iDrop desktop [10] Figure 2.

It is possible to perform analyses directly in the DE using any of the 1KP files as input; for example, users can re-compute the sequence alignments and gene trees using different algorithms and parameters [11] Figure 3. More generally, users can select from a variety of applications in the Apps catalogue, which is constantly growing, and includes many popular bioinformatics tools for large-scale phylogenetics, genome-wide associations and next generation sequence analyses.

Species and gene trees can be explored with the iPlant tree viewer, Phylozoom, a newly developed web-based phylogenetic tree viewer that supports trees with hundreds of thousand leaves and allows for semantic zooming Figure 4. To access the tree viewer, users need only click on a tree file. This will open a preview window with two tabs: one for the tree's newick string (a format for graph-theoretical trees as defined at [12]) and another for the web link that opens a window to the tree display. Notice that pop-ups must be enabled on the user's browser.

To zoom in and expand the collapsed clades, click on the node of interest. To zoom out, click and drag the tree figure to the left. To zoom out completely, click the space bar. The web address is a unique identifier that can be shared with others to let them to visualize the tree.

Table 1

Data sources for phylogenomics analyses

Species Type Accession iPlant ID 
Arabidopsis thaliana genome n/a n/a 
Brachypodium distachyon genome n/a n/a 
Carica papaya genome n/a n/a 
Medicago truncatula genome n/a n/a 
Oryza sativa genome n/a n/a 
Physcomitrella patens genome n/a n/a 
Populus trichocarpa genome n/a n/a 
Selaginella moellendorffii genome n/a n/a 
Sorghum bicolor genome n/a n/a 
Vitis vinifera genome n/a n/a 
Zea mays genome n/a n/a 
Aquilegia formosa meta-assembly PlantGDB AQUI 
Cycas rumphii meta-assembly SRX022306, SRX022215 CYCA 
Liriodendron tulipifera meta-assembly PRJNA46857 LIRI 
Persea americana meta-assembly PRJNA46857 PERS 
Pinus taeda meta-assembly PRJNA79733 PINU 
Pteridium aquilinum meta-assembly PRJNA48473 PTER 
Zamia vazquezii meta-assembly PRJNA46857 ZAMI 
Acorus americanus OneKP meta-assembly ERR364395, PRJNA46857 ACOR 
Amborella trichopoda OneKP meta-assembly ERR364329, PRJNA46857 AMBO 
Catharanthus roseus OneKP meta-assembly ERR364390, PRJNA79951, PRJNA236160 CATH 
Eschscholzia californica OneKP meta-assembly ERR364338, ERR364335, ERR364336, ERR364337, ERR364334, SRX002988, SRX002987, PlantGDB ESCH 
Ginkgo biloba OneKP meta-assembly ERR364401, PlantGDB GINK 
Nuphar advena OneKP meta-assembly ERR364330, PRJNA46857 NUPH 
Ophioglossum petiolatum OneKP meta-assembly ERR364410, SRX666586 OPHI 
Saruma henryi OneKP meta-assembly ERR364383, PRJNA46857 SARU 
Welwitschia mirabilis OneKP meta-assembly ERR364404, PRJNA46857 WELW 
Allamanda cathartica OneKP ERR364389 MGVU 
Angiopteris evecta OneKP ERR364409 NHCM 
Anomodon attenuatus OneKP ERR364349 QMWB 
Bazzania trilobata OneKP ERR364415 WZYK 
Boehmeria nivea OneKP ERR364387 ACFP 
Bryum argenteum OneKP ERR364348 JMXW 
Cedrus libani OneKP ERR364342 GGEA 
Ceratodon purpureus OneKP ERR364350 FFPD 
Chaetosphaeridium globosum OneKP ERR364369 DRGY 
Chara vulgaris OneKP ERR364366 CHAR 
Chlorokybus atmophyticus OneKP ERR364371 AZZW 
Colchicum autumnale OneKP ERR364397 NHIX 
Coleochaete irregularis OneKP ERR364367 QPDY 
Coleochaete scutata OneKP ERR364368 VQBJ 
Cosmarium ochthodes OneKP ERR364376 STKJ 
Cunninghamia lanceolata OneKP ERR364340 OUOI 
Cyathea (Alsophila) spinulosa OneKP ERR364412 GANB 
Cycas micholitzii OneKP ERR364405 XZUY 
Cylindrocystis brebissonii OneKP ERR364378 YOXI 
Cylindrocystis cushleckae OneKP ERR364373 JOJQ 
Dendrolycopodium obscurum OneKP ERR364346 XNXF 
Dioscorea villosa OneKP ERR364396 OCWZ 
Diospyros malabarica OneKP ERR364339 KVFU 
Entransia fimbriata OneKP ERR364372 BFIK 
Ephedra sinica OneKP ERR364402 VDAO 
Equisetum diffusum OneKP ERR364408 CAPN 
Gnetum montanum OneKP ERR364403 GTHK 
Hedwigia ciliata OneKP ERR364352 YWNF 
Hibiscus cannabinus OneKP ERR364388 OLXF 
Houttuynia cordata OneKP ERR364332 CSSK 
Huperzia squarrosa OneKP ERR364407 GAON 
Inula helenium OneKP ERR364393 AFQQ 
Ipomoea purpurea OneKP ERR364392 VXKB 
Juniperus scopulorum OneKP ERR364341 XMGP 
Kadsura heteroclita OneKP ERR364331 NWMY 
Klebsormidium subtile OneKP ERR364370 FQLP 
Kochia scoparia OneKP ERR364385 WGET 
Larrea tridentata OneKP ERR364386 UDUT 
Leucodon brachypus OneKP ERR364353 ZACW 
Marchantia emarginata OneKP ERR364417 TFYI 
Marchantia polymorpha OneKP ERR364416 JPYU 
Mesostigma viride OneKP ERR364365 KYIO 
Mesotaenium endlicherianum OneKP ERR364377 WDCW 
Metzgeria crassipilis OneKP ERR364359 NRWZ 
Monomastix opisthostigma OneKP ERR364362 BTFM 
Mougeotia sp. OneKP ERR364374 ZRMT 
Nephroselmis pyriformis OneKP ERR364363 ISIM 
Netrium digitus OneKP ERR364379 FFGR 
Nothoceros aenigmaticus OneKP ERR364356 DXOU 
Nothoceros vincentianus OneKP ERR364357 TCBC 
Penium margaritaceum OneKP ERR364382 AEKF 
Podophyllum peltatum OneKP ERR364384 WFBF 
Polytrichum commune OneKP ERR364413 SZYG 
Prumnopitys andina OneKP ERR364343 EGLZ 
Pseudolycopodiella caroliniana OneKP ERR364345 UPMJ 
Psilotum nudum OneKP ERR364411 QVMR 
Pyramimonas parkeae OneKP ERR364361 TNAW 
Rhynchostegium serrulatum OneKP ERR364355 JADL 
Ricciocarpos natans OneKP ERR364358 WJLO 
Rosmarinus officinalis OneKP ERR364391 FDMM 
Rosulabryum cf. capillare OneKP ERR364351 XWHK 
Roya obtusa OneKP ERR364380 XRTZ 
Sabal bermudana OneKP ERR364400 HWUP 
Sarcandra glabra OneKP ERR364333 OSHQ 
Sciadopitys verticillata OneKP ERR364344 YFZK 
Selaginella stauntoniana OneKP ERR364347 ZZOL 
Smilax bona-nox OneKP ERR364398 MWYQ 
Sphaerocarpos texanus OneKP ERR364360 HERT 
Sphagnum lescurii OneKP ERR364414 GOWD 
Spirogyra sp. OneKP ERR364375 HAOX 
Spirotaenia minuta OneKP ERR364381 NNHQ 
Tanacetum parthenium OneKP ERR364394 DUQG 
Taxus baccata OneKP ERR364406 WWSS 
Thuidium delicatulum OneKP ERR364354 EEMJ 
Uronema sp. OneKP ERR364364 ISGT 
Yucca filamentosa OneKP ERR364399 ICNN 
Species Type Accession iPlant ID 
Arabidopsis thaliana genome n/a n/a 
Brachypodium distachyon genome n/a n/a 
Carica papaya genome n/a n/a 
Medicago truncatula genome n/a n/a 
Oryza sativa genome n/a n/a 
Physcomitrella patens genome n/a n/a 
Populus trichocarpa genome n/a n/a 
Selaginella moellendorffii genome n/a n/a 
Sorghum bicolor genome n/a n/a 
Vitis vinifera genome n/a n/a 
Zea mays genome n/a n/a 
Aquilegia formosa meta-assembly PlantGDB AQUI 
Cycas rumphii meta-assembly SRX022306, SRX022215 CYCA 
Liriodendron tulipifera meta-assembly PRJNA46857 LIRI 
Persea americana meta-assembly PRJNA46857 PERS 
Pinus taeda meta-assembly PRJNA79733 PINU 
Pteridium aquilinum meta-assembly PRJNA48473 PTER 
Zamia vazquezii meta-assembly PRJNA46857 ZAMI 
Acorus americanus OneKP meta-assembly ERR364395, PRJNA46857 ACOR 
Amborella trichopoda OneKP meta-assembly ERR364329, PRJNA46857 AMBO 
Catharanthus roseus OneKP meta-assembly ERR364390, PRJNA79951, PRJNA236160 CATH 
Eschscholzia californica OneKP meta-assembly ERR364338, ERR364335, ERR364336, ERR364337, ERR364334, SRX002988, SRX002987, PlantGDB ESCH 
Ginkgo biloba OneKP meta-assembly ERR364401, PlantGDB GINK 
Nuphar advena OneKP meta-assembly ERR364330, PRJNA46857 NUPH 
Ophioglossum petiolatum OneKP meta-assembly ERR364410, SRX666586 OPHI 
Saruma henryi OneKP meta-assembly ERR364383, PRJNA46857 SARU 
Welwitschia mirabilis OneKP meta-assembly ERR364404, PRJNA46857 WELW 
Allamanda cathartica OneKP ERR364389 MGVU 
Angiopteris evecta OneKP ERR364409 NHCM 
Anomodon attenuatus OneKP ERR364349 QMWB 
Bazzania trilobata OneKP ERR364415 WZYK 
Boehmeria nivea OneKP ERR364387 ACFP 
Bryum argenteum OneKP ERR364348 JMXW 
Cedrus libani OneKP ERR364342 GGEA 
Ceratodon purpureus OneKP ERR364350 FFPD 
Chaetosphaeridium globosum OneKP ERR364369 DRGY 
Chara vulgaris OneKP ERR364366 CHAR 
Chlorokybus atmophyticus OneKP ERR364371 AZZW 
Colchicum autumnale OneKP ERR364397 NHIX 
Coleochaete irregularis OneKP ERR364367 QPDY 
Coleochaete scutata OneKP ERR364368 VQBJ 
Cosmarium ochthodes OneKP ERR364376 STKJ 
Cunninghamia lanceolata OneKP ERR364340 OUOI 
Cyathea (Alsophila) spinulosa OneKP ERR364412 GANB 
Cycas micholitzii OneKP ERR364405 XZUY 
Cylindrocystis brebissonii OneKP ERR364378 YOXI 
Cylindrocystis cushleckae OneKP ERR364373 JOJQ 
Dendrolycopodium obscurum OneKP ERR364346 XNXF 
Dioscorea villosa OneKP ERR364396 OCWZ 
Diospyros malabarica OneKP ERR364339 KVFU 
Entransia fimbriata OneKP ERR364372 BFIK 
Ephedra sinica OneKP ERR364402 VDAO 
Equisetum diffusum OneKP ERR364408 CAPN 
Gnetum montanum OneKP ERR364403 GTHK 
Hedwigia ciliata OneKP ERR364352 YWNF 
Hibiscus cannabinus OneKP ERR364388 OLXF 
Houttuynia cordata OneKP ERR364332 CSSK 
Huperzia squarrosa OneKP ERR364407 GAON 
Inula helenium OneKP ERR364393 AFQQ 
Ipomoea purpurea OneKP ERR364392 VXKB 
Juniperus scopulorum OneKP ERR364341 XMGP 
Kadsura heteroclita OneKP ERR364331 NWMY 
Klebsormidium subtile OneKP ERR364370 FQLP 
Kochia scoparia OneKP ERR364385 WGET 
Larrea tridentata OneKP ERR364386 UDUT 
Leucodon brachypus OneKP ERR364353 ZACW 
Marchantia emarginata OneKP ERR364417 TFYI 
Marchantia polymorpha OneKP ERR364416 JPYU 
Mesostigma viride OneKP ERR364365 KYIO 
Mesotaenium endlicherianum OneKP ERR364377 WDCW 
Metzgeria crassipilis OneKP ERR364359 NRWZ 
Monomastix opisthostigma OneKP ERR364362 BTFM 
Mougeotia sp. OneKP ERR364374 ZRMT 
Nephroselmis pyriformis OneKP ERR364363 ISIM 
Netrium digitus OneKP ERR364379 FFGR 
Nothoceros aenigmaticus OneKP ERR364356 DXOU 
Nothoceros vincentianus OneKP ERR364357 TCBC 
Penium margaritaceum OneKP ERR364382 AEKF 
Podophyllum peltatum OneKP ERR364384 WFBF 
Polytrichum commune OneKP ERR364413 SZYG 
Prumnopitys andina OneKP ERR364343 EGLZ 
Pseudolycopodiella caroliniana OneKP ERR364345 UPMJ 
Psilotum nudum OneKP ERR364411 QVMR 
Pyramimonas parkeae OneKP ERR364361 TNAW 
Rhynchostegium serrulatum OneKP ERR364355 JADL 
Ricciocarpos natans OneKP ERR364358 WJLO 
Rosmarinus officinalis OneKP ERR364391 FDMM 
Rosulabryum cf. capillare OneKP ERR364351 XWHK 
Roya obtusa OneKP ERR364380 XRTZ 
Sabal bermudana OneKP ERR364400 HWUP 
Sarcandra glabra OneKP ERR364333 OSHQ 
Sciadopitys verticillata OneKP ERR364344 YFZK 
Selaginella stauntoniana OneKP ERR364347 ZZOL 
Smilax bona-nox OneKP ERR364398 MWYQ 
Sphaerocarpos texanus OneKP ERR364360 HERT 
Sphagnum lescurii OneKP ERR364414 GOWD 
Spirogyra sp. OneKP ERR364375 HAOX 
Spirotaenia minuta OneKP ERR364381 NNHQ 
Tanacetum parthenium OneKP ERR364394 DUQG 
Taxus baccata OneKP ERR364406 WWSS 
Thuidium delicatulum OneKP ERR364354 EEMJ 
Uronema sp. OneKP ERR364364 ISGT 
Yucca filamentosa OneKP ERR364399 ICNN 

Meta-assembly refers to a transcriptome assembled from more than one sequenced sample. Some of these were a combination of 1KP and other data; some were entirely non-1KP. Accession numbers (SRA or otherwise) are given for all of the transcriptomes that we used.

For more advanced users wanting to perform more complicated procedures, iPlant capabilities are available from a command line. It is based on the integrated ruleoriented data system (iRODS) [13]. All the user has to do is install a command line utility, icommands, which mimics UNIX and enables high-speed parallel data transfers. Instructions are available at [14].

Interactions and pathways

In addition to the tree-based species and gene relationships at the iPlant site, functional relationships between proteins and their associated metabolites are available from the Computational Biology Group at the University of Washington, developers of CANDO [15]. Sequence similarity-based methods are used to map 1KP proteins to curated repositories of proteinprotein interactions (i.e., BioGRID [16]) and biochemical pathways (i.e., Kyoto Encylopedia of Genes and Genomes [KEGG] [17]). The user can select any metabolic pathway defined by KEGG and, within this context, see all the 1KP proteins from their chosen species, with functional annotations inferred from KEGG. This website is at [18] Figure 5.

Note that, over the course of this project, there have been many improvements in the transcriptome assemblies. The phylogenomics work (now being published) was done with the SOAPdenovo algorithm. A second assembly was subsequently done with the newer SOAPdenovo-trans algorithm, which we incorporated into the newer interactions and pathways work. However, both sets of assemblies are available through the iPlant data store.

Conclusions

The rest of the 1KP data will be released, on much the same platform, along with our analyses of all one thousand species. Our scientific objectives are given at [19]. We have always been open about our intentions, because we wanted to avoid conflict among the scientists who were already working with 1KP and offer early pre-publication access to other non-competing scientists. As soon as we see a draft of a paper, we track its progress through the review process at [20]. Some of these papers have already been published, and more than a few required years of follow-up experiments, resulting for example in fundamental discoveries for molecular evolution [21] and (surprisingly) new tools for mammalian neurosciences [22].

Many of these studies were not anticipated when 1KP was conceived. We only knew that, just as there was value in sequencing every gene in a genome, despite not knowing a priori what many of the genes might do, there would be value in sequencing across an ancient and ecologically dominant clade, even when many of the species have no obvious economic or scientific value that would justify a genome sequencing effort. Transcriptomes were a less expensive way to explore plant diversity, and demonstrate value beyond the obvious species.

Table 2

Number and size of data files on websites

File count Median size (Mb) Average size (Mb) Largest size (Mb) Total size (Mb) Similar directories iPlant directory name 
68,253 0.0 0.3 481.1 23,116.6  onekp_pilot 
48,053 0.0 0.3 481.1 14,956.7  onekp_pilot/orthogroups 
19,220 0.1 0.7 243.8 13,276.5  onekp_pilot/orthogroups/alignments 
9,610 0.1 0.3 79.8 3,289.6  onekp_pilot/orthogroups/alignments/FAA 
9,610 0.2 1.0 243.8 9,986.9  onekp_pilot/orthogroups/alignments/FNA 
28,833 0.0 0.1 481.1 1,680.2  onekp_pilot/orthogroups/gene_trees 
9,611 0.0 0.1 481.1 583.3  onekp_pilot/orthogroups/gene_trees/FAA 
9,610 0.0 0.0 0.5 102.2  onekp_pilot/orthogroups/gene_trees/FAA/trees 
19,222 0.0 0.1 458.0 1,096.8  onekp_pilot/orthogroups/gene_trees/FNA 
9,611 0.0 0.1 458.0 556.6  onekp_pilot/orthogroups/gene_trees/FNA/12_codon 
9,610 0.0 0.0 0.5 98.5  onekp_pilot/orthogroups/gene_trees/FNA/12_codon/trees 
9,611 0.0 0.1 439.1 540.3  onekp_pilot/orthogroups/gene_trees/FNA/all_codon 
9,610 0.0 0.0 0.5 101.2  onekp_pilot/orthogroups/gene_trees/FNA/all_codon/dna_tree 
19,919 0.0 0.2 175.2 3,468.8  onekp_pilot/phylogenetic_analysis 
2,556 0.1 0.1 1.0 292.7  onekp_pilot/phylogenetic_analysis/alignments 
852 0.0 0.0 0.3 41.8  onekp_pilot/phylogenetic_analysis/alignments/FAA 
852 0.1 0.1 1.0 125.5  onekp_pilot/phylogenetic_analysis/alignments/FNA 
852 0.1 0.1 0.9 125.4  onekp_pilot/phylogenetic_analysis/alignments/FNA2AA 
17,197 0.0 0.1 0.4 1,827.3  onekp_pilot/phylogenetic_analysis/gene_trees 
1,704 0.0 0.1 0.4 238.3  onekp_pilot/phylogenetic_analysis/gene_trees/FAA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FAA/raxmlboot.#### 
1,704 0.0 0.1 0.4 238.3  onekp_pilot/phylogenetic_analysis/gene_trees/FNA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FNA/raxmlboot.#### 
3,408 0.0 0.1 0.4 476.7  onekp_pilot/phylogenetic_analysis/gene_trees/FNA2AA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FNA2AA/raxmlboot.#### 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FNA2AA/raxmlboot.####.c1c2 
10,381 0.0 0.1 0.4 874.0  onekp_pilot/phylogenetic_analysis/gene_trees/filtered 
2,548 0.0 0.1 0.4 169.3  onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FAA 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FAA/raxmlboot.####.f25 
0.2 0.1 0.4 0.2 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FAA/raxmlboot.####.filterlen33 
852 0.0 0.0 0.0 3.8  onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA/raxmlboot.####.f25 
6,980 0.0 0.1 0.4 700.9  onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.GAMMA.2 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.c1c2.GAMMA.2 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.c1c2.f25 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.f25 
0.2 0.1 0.4 0.2 844 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.filterlen33 
0.3 0.3 0.4 0.3 180 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.filtered25.GAMMA.2 
166 0.0 8.1 175.2 1,348.8  onekp_pilot/phylogenetic_analysis/species_level 
50 15.0 27.0 175.2 1,348.1  onekp_pilot/phylogenetic_analysis/species_level/alignments 
15 14.7 14.3 58.3 214.2  onekp_pilot/phylogenetic_analysis/species_level/alignments/FAA 
35 29.4 32.4 175.2 1,133.9  onekp_pilot/phylogenetic_analysis/species_level/alignments/FNA 
116 0.0 0.0 0.0 0.6  onekp_pilot/phylogenetic_analysis/species_level/trees 
276 10.0 17.0 157.4 4,691.1  onekp_pilot/taxa 
9.7 17.0 157.4 51.0 92 onekp_pilot/taxa/####-############ 
30.8 17.0 157.4 36.0 92 onekp_pilot/taxa/####-############/assemblies 
9.7 7.5 45.2 15.0 92 onekp_pilot/taxa/####-############/translations 
0.0 0.0 0.0 0.1  onekp_pilot/tools 
File count Median size (Mb) Average size (Mb) Largest size (Mb) Total size (Mb) Similar directories iPlant directory name 
68,253 0.0 0.3 481.1 23,116.6  onekp_pilot 
48,053 0.0 0.3 481.1 14,956.7  onekp_pilot/orthogroups 
19,220 0.1 0.7 243.8 13,276.5  onekp_pilot/orthogroups/alignments 
9,610 0.1 0.3 79.8 3,289.6  onekp_pilot/orthogroups/alignments/FAA 
9,610 0.2 1.0 243.8 9,986.9  onekp_pilot/orthogroups/alignments/FNA 
28,833 0.0 0.1 481.1 1,680.2  onekp_pilot/orthogroups/gene_trees 
9,611 0.0 0.1 481.1 583.3  onekp_pilot/orthogroups/gene_trees/FAA 
9,610 0.0 0.0 0.5 102.2  onekp_pilot/orthogroups/gene_trees/FAA/trees 
19,222 0.0 0.1 458.0 1,096.8  onekp_pilot/orthogroups/gene_trees/FNA 
9,611 0.0 0.1 458.0 556.6  onekp_pilot/orthogroups/gene_trees/FNA/12_codon 
9,610 0.0 0.0 0.5 98.5  onekp_pilot/orthogroups/gene_trees/FNA/12_codon/trees 
9,611 0.0 0.1 439.1 540.3  onekp_pilot/orthogroups/gene_trees/FNA/all_codon 
9,610 0.0 0.0 0.5 101.2  onekp_pilot/orthogroups/gene_trees/FNA/all_codon/dna_tree 
19,919 0.0 0.2 175.2 3,468.8  onekp_pilot/phylogenetic_analysis 
2,556 0.1 0.1 1.0 292.7  onekp_pilot/phylogenetic_analysis/alignments 
852 0.0 0.0 0.3 41.8  onekp_pilot/phylogenetic_analysis/alignments/FAA 
852 0.1 0.1 1.0 125.5  onekp_pilot/phylogenetic_analysis/alignments/FNA 
852 0.1 0.1 0.9 125.4  onekp_pilot/phylogenetic_analysis/alignments/FNA2AA 
17,197 0.0 0.1 0.4 1,827.3  onekp_pilot/phylogenetic_analysis/gene_trees 
1,704 0.0 0.1 0.4 238.3  onekp_pilot/phylogenetic_analysis/gene_trees/FAA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FAA/raxmlboot.#### 
1,704 0.0 0.1 0.4 238.3  onekp_pilot/phylogenetic_analysis/gene_trees/FNA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FNA/raxmlboot.#### 
3,408 0.0 0.1 0.4 476.7  onekp_pilot/phylogenetic_analysis/gene_trees/FNA2AA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FNA2AA/raxmlboot.#### 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/FNA2AA/raxmlboot.####.c1c2 
10,381 0.0 0.1 0.4 874.0  onekp_pilot/phylogenetic_analysis/gene_trees/filtered 
2,548 0.0 0.1 0.4 169.3  onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FAA 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FAA/raxmlboot.####.f25 
0.2 0.1 0.4 0.2 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FAA/raxmlboot.####.filterlen33 
852 0.0 0.0 0.0 3.8  onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA/raxmlboot.####.f25 
6,980 0.0 0.1 0.4 700.9  onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.GAMMA.2 
0.3 0.1 0.4 0.3 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.c1c2.GAMMA.2 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.c1c2.f25 
0.0 0.0 0.0 0.0 852 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.f25 
0.2 0.1 0.4 0.2 844 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.filterlen33 
0.3 0.3 0.4 0.3 180 onekp_pilot/phylogenetic_analysis/gene_trees/filtered/FNA2AA/raxmlboot.####.filtered25.GAMMA.2 
166 0.0 8.1 175.2 1,348.8  onekp_pilot/phylogenetic_analysis/species_level 
50 15.0 27.0 175.2 1,348.1  onekp_pilot/phylogenetic_analysis/species_level/alignments 
15 14.7 14.3 58.3 214.2  onekp_pilot/phylogenetic_analysis/species_level/alignments/FAA 
35 29.4 32.4 175.2 1,133.9  onekp_pilot/phylogenetic_analysis/species_level/alignments/FNA 
116 0.0 0.0 0.0 0.6  onekp_pilot/phylogenetic_analysis/species_level/trees 
276 10.0 17.0 157.4 4,691.1  onekp_pilot/taxa 
9.7 17.0 157.4 51.0 92 onekp_pilot/taxa/####-############ 
30.8 17.0 157.4 36.0 92 onekp_pilot/taxa/####-############/assemblies 
9.7 7.5 45.2 15.0 92 onekp_pilot/taxa/####-############/translations 
0.0 0.0 0.0 0.1  onekp_pilot/tools 
File count Median size (Mb) Average size(Mb) Largest size (Mb) Total size (Mb) Similar directories Contents at SRA (PRJEB4921) 
178 1,915.0 2,045.5 3,371.0 364,100.0  total of all short reads — uncompressed, but downloads are compressed to a quarter of these sizes 
1,915.0 2,045.5 3,371.0 4,091.0 89 expecting per sample — uncompressed, but downloads are compressed to a quarter of these sizes 
File count Median size (Mb) Average size(Mb) Largest size (Mb) Total size (Mb) Similar directories Contents at SRA (PRJEB4921) 
178 1,915.0 2,045.5 3,371.0 364,100.0  total of all short reads — uncompressed, but downloads are compressed to a quarter of these sizes 
1,915.0 2,045.5 3,371.0 4,091.0 89 expecting per sample — uncompressed, but downloads are compressed to a quarter of these sizes 

In some instances, users will find many directories with similar names, as indicated in this table by hash (#) marks. The total number of directories is given in the preceding column.

Figure 1

iPlant DE data window.

Figure 1

iPlant DE data window.

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 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 3

Realigning a group of sequences using Muscle.

Figure 4

Phylozoom display of 1KP species phylogeny.

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).

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).

Abbreviations

  • 1KP

    1,000 Plants project

  • DE

    Discovery Environment

  • KEEG

    Kyoto Encyclopedia of Genes and Genomes

  • NSF

    National Science Foundation

  • SRA

    Short Reads Archive

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

CWD, BRR, NWM, SWG, S Ma, BS, MM, DES, PSS, CR, LP, JAS, LD, DWS, JCV, TC, TMK, MR, RSB, MKD, and JLM collected the plant samples. NM, NJW, S Mi, NN, TW, SA, MB, JGB, MAG, EW, JPD, CWD, BR, HP, BRR, and JLM performed the phylogenomic analyses. NM, LHH, ZY, and EJC setup and maintained web-resources used to communicate data. LHH and RS performed the protein and KEGG pathway analyses. EJC, ZT, XW, XS, YZ, JW, and GKW generated the sequence data. GKW and JLM designed and oversaw the research. All authors read and approved the final manuscript.

Acknowledgments

The 1000 Plants (1KP) initiative, led by GKW, is funded by the Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centre of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National GeneBank (CNGB). We thank the many people responsible for sample collection on 1KP and the staff at BGI-Shenzhen for doing our sequencing. Phylogenomic analyses were supported by the US National Science Foundation through the iPlant collaborative. CANDO was funded by an NIH Director's Pioneer Award 1DP1OD006779-01.

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.  . 
2011
The iPlant Collaborative: Cyberinfrastructure for Plant Biology
Front Plant Sci
 , vol. 
2
 pg. 
34
 
2.
3.
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.  . 
2012
Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes
PLoS One
 , vol. 
7
 pg. 
e50226
  
10.1371/journal.pone.0050226
4.
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
2014
SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
Bioinformatics
 , vol. 
30
 (pg. 
1660
-
1666
10.1093/bioinformatics/btu077
5.
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
7.
iPlant User Registration
  
9.
iPlant Discovery Environment
  
11.
Matasci
N
McKay
SJ
2013
Phylogenetic analysis with the iPlant discovery environment
Curr Protoc Bioinformatics
 , vol. 
6
 pg. 
Unit 6.13
 
13.
iRODS Data Management Software
  
15.
Minie
M
Chopra
G
Sethi
G
Horst
J
White
G
Roy
A
Hatti
K
Samudrala
R
2014
CANDO and the infinite drug discovery frontier
Drug Discov Today
 , vol. 
19
 (pg. 
1353
-
1363
10.1016/j.drudis.2014.06.018
16.
BioGRID Interactions
  
17.
Kyoto Encylopedia of Genes and Genomes (KEGG)
  
18.
1KP Protein-Protein Interactions Mapped to Metabolic Pathways
  
21.
Sayou
C
Monniaux
M
Nanao
MH
Moyroud
E
Brockington
SF
Thévenon
E
Chahtane
H
Warthmann
N
Melkonian
M
Zhang
Y
Wong
GK
Weigel
D
Parcy
F
Dumas
R
2014
A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity
Science
 , vol. 
343
 (pg. 
645
-
648
10.1126/science.1248229
22.
Klapoetke
NC
Murata
Y
Kim
SS
Pulver
SR
Birdsey-Benson
A
Cho
YK
Morimoto
TK
Chuong
AS
Carpenter
EJ
Tian
Z
Wang
J
Xie
Y
Yan
Z
Zhang
Y
Chow
BY
Surek
B
Melkonian
M
Jayaraman
V
Constantine-Paton
M
Wong
GK
Boyden
ES
2014
Independent optical excitation of distinct neural populations
Nat Methods
 , vol. 
11
 (pg. 
338
-
346
10.1038/nmeth.2836
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