Open Tools and Resources for Arabidopsis Researchers
The Bio-Analytic Resource is a collection of user-friendly web-based tools for working with functional genomics and other data for hypothesis generation and confirmation. Most are designed with the plant (mainly Arabidopsis) researcher in mind. Data sets include:
* 150 million gene expression measurements (75 million from A.th.), plus “expressologs” (homologs showing similar patterns of expression in equivalent tissues) for many genes across 12 species. View expression patterns with our popular eFP Browser or newer ePlant tool.
* 70,944 predicted protein-protein interactions plus 62,626 experimentally determined PPIs (rice interologs also available!) and ~2.8 million protein-DNA interactions, which can be explored with our new Arabidopsis Interactions Viewer 2 tool.
* 29,180 predicted protein tertiary structures and experimentally determined structures for 402 Arabidopsis proteins.
* Millions of non-synonymous SNPs from the 1001 Arabidopsis Genomes project, now delivered via the 1001 Genomes API.
* Documented subcellular localizations for 11.7k proteins, predicted localization for most of Arabidopsis proteome, from the SUBA database at the University of Western Australia.
The news from December 2018 that Araport would not continue to be funded by the National Science Foundation in the U.S. precipitated a meeting in March, 2019 at which it was agreed that the BAR and TAIR would resuscitate the existing Thalemine and JBrowse instances, respectively, and that Araport’s previous functionality would be expanded by adding a Genome Context Viewer from the National Center for Genome Resources to enable the viewing of multiple fully assembled Arabidopsis thaliana genomes. The Bio-Analytic Resource rolled out a revived and updated version of Araport’s Thalemine at https://bar.utoronto.ca/thalemine/ in December 2019.
The BAR also published its eFP-Seq Browser at https://bar.utoronto.ca/eFP-Seq_Browser/ for exploring RNA-seq data as both read map profiles and summarized gene expression levels across two large compendia, in order to be able to quickly identify samples with the highest level of expression or where alternative splicing might be occurring (Sullivan et al., 2019).
The BAR was also happy to announce its first single cell RNA-seq eFP Browser view at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Single_Cell, based on root single cell data RNA-seq from John Schiefelbein’s lab at the University of Michigan (Ryu et al., 2019). We also added a DNA damage RNA-seq data set by Bourbousse et al. (2018) to the eFP Browser at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=DNA_Damage, which is one of seven RNA-seq-based eFP Browser views, coming soon to ePlant.
We enabled links for 2.8 M Ecker Lab DAP-seq PDIs in our AIV2 tool (http://bar.utoronto.ca/interactions2/) to corresponding peak data in the Ecker Lab’s AnnoJ Browser. The Gazzarrini and Lumba Labs at the University of Toronto (Carianopol et al., 2020) identified 125 SnRK1 complex interacting proteins using a meso-scale Y2H screening approach against ABA-regulated gene products and we’ve added these, along with hundreds of other PPIs published in the past year, into the AIV2 tool and database.
For non-Arabidopsis plant researchers, May the 4th 2019 was with you! ePlants for 15 agronomically important species became available on the BAR homepage at http://bar.utoronto.ca. We will be growing these in the future by adding more data, and we welcome comments and ideas for new data sets for them.
For maize researchers, new BAR eFP images and links to an updated gene atlas were enabled in MaizeGDB based on data from the Buell Lab (Hoopes et al., 2019).
We collaborated to create a new eFP view for Thomas Widiez and colleagues microdissection work to generate RNA-seq data from an early timepoint in maize seed development (Doll et al., 2020): http://bar.utoronto.ca/efp_maize/cgi-bin/efpWeb.cgi?dataSource=Maize_Kernel.
The Mutwil Lab in Singapore published a Selaginella moellendorffii expression atlas (Ferrari et al., 2020). We collaborated to create an eFP Browser for it: http://bar.utoronto.ca/efp_selaginella/cgi-bin/efpWeb.cgi. Jin Zhang, Xiaohan Yang and colleagues published a nice paper on how light quality and intensity modulates the transcriptome in Kalanchoe (Zhang et al., 2020). We collaborated to create our first CAM plant eFP Browser, see http://bar.utoronto.ca/efp_kalanchoe/cgi-bin/efpWeb.cgi.
BAR Publications (plus 2 citations* mentioned above, not in collaboration with the BAR)
Bourbousse, C., Vegesna, N., and Law, J.A. (2018). SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 115: E12453–E12462*.
Carianopol, C.S., Chan, A.L., Dong, S., Provart, N.J., Lumba, S., and Gazzarrini, S. (2020). An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response. Commun. Biol. 3: 145.
Doll, N.M., Just, J., Brunaud, V., Caïus, J., Grimault, A., Depège-Fargeix, N., Esteban, E., Pasha, A., Provart, N.J., Ingram, G.C., Rogowsky, P.M., and Widiez, T. (2020). Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. Plant Cell 32: 833.
Ferrari, C., Shivhare, D., Hansen, B.O., Pasha, A., Esteban, E., Provart, N.J., Kragler, F., Fernie, A., Tohge, T., and Mutwil, M. (2020). Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. Plant Cell 32: 853.
Hoopes, G.M., Hamilton, J.P., Wood, J.C., Esteban, E., Pasha, A., Vaillancourt, B., Provart, N.J., and Buell, C.R. (2019). An updated gene atlas for maize reveals organ-specific and stress-induced genes. Plant J. 97: 1154–1167.
Ryu, K.H., Huang, L., Kang, H.M., and Schiefelbein, J. (2019). Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells. Plant Physiol. 179: 1444*.
Sullivan, A. et al. (2019). An ‘eFP-Seq Browser’ for visualizing and exploring RNA sequencing data. Plant J. 100: 641–654.
Zhang, J. et al. (2020). Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism. GigaScience 9.
Planned future activities
A custom eFP view in ePlant for a researcher’s own RNA-seq data is in the works, along with “Gaia” (kind of like Siri or Alexa, but for Arabidopsis information) as part of a new award from Genome Canada. Several new ePlants are also planned as part of this project, and an ecosystem viewer will also be developed.
Conferences, Workshops and Training events
The BAR participated in the 2019 American Society of Plant Biology (ASPB) Plant Biology conference in San Jose, as part of the Plant AgData Outreach booth and in the Plant Bioinformatics workshop; and Plant and Animal Genomes (PAG) XXVIII at the start of 2020 in San Diego, California.
The BAR principal investigator Nicholas Provart released a “Plant Bioinformatic Methods” specialization in plant bioinformatics, encompassing 4 courses on Coursera.org, see https://www.coursera.org/specializations/plant-bioinformatic-methods. These may be audited for free, or you can get a certificate for a small fee.